101
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Membrane Activity of LL-37 Derived Antimicrobial Peptides against Enterococcus hirae: Superiority of SAAP-148 over OP-145. Biomolecules 2022; 12:biom12040523. [PMID: 35454112 PMCID: PMC9028586 DOI: 10.3390/biom12040523] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 03/25/2022] [Accepted: 03/27/2022] [Indexed: 12/07/2022] Open
Abstract
The development of antimicrobial agents against multidrug-resistant bacteria is an important medical challenge. Antimicrobial peptides (AMPs), human cathelicidin LL-37 and its derivative OP-145, possess a potent antimicrobial activity and were under consideration for clinical trials. In order to overcome some of the challenges to their therapeutic potential, a very promising AMP, SAAP-148 was designed. Here, we studied the mode of action of highly cationic SAAP-148 in comparison with OP-145 on membranes of Enterococcus hirae at both cellular and molecular levels using model membranes composed of major constituents of enterococcal membranes, that is, anionic phosphatidylglycerol (PG) and cardiolipin (CL). In all assays used, SAAP-148 was consistently more efficient than OP-145, but both peptides displayed pronounced time and concentration dependences in killing bacteria and performing at the membrane. At cellular level, Nile Red-staining of enterococcal membranes showed abnormalities and cell shrinkage, which is also reflected in depolarization and permeabilization of E. hirae membranes. At the molecular level, both peptides abolished the thermotropic phase transition and induced disruption of PG/CL. Interestingly, the membrane was disrupted before the peptides neutralized the negative surface charge of PG/CL. Our results demonstrate that SAAP-148, which kills bacteria at a significantly lower concentration than OP-145, shows stronger effects on membranes at the cellular and molecular levels.
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102
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Equilibrium Between Dimeric and Monomeric Forms of Human Epidermal Growth Factor is Shifted Towards Dimers in a Solution. Protein J 2022; 41:245-259. [PMID: 35348971 DOI: 10.1007/s10930-022-10051-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/22/2022] [Indexed: 10/18/2022]
Abstract
An interplay between monomeric and dimeric forms of human epidermal growth factor (EGF) affecting its interaction with EGF receptor (EGFR) is poorly understood. While EGF dimeric structure was resolved at pH 8.1, the possibility of EGF dimerization under physiological conditions is still unclear. This study aimed to describe the oligomeric state of EGF in a solution at physiological pH value. With centrifugal ultrafiltration followed by blue native gel electrophoresis, we showed that synthetic human EGF in a solution at a concentration of 0.1 mg/ml exists mainly in the dimeric form at pH 7.4 and temperature of 37 °C, although a small fraction of its monomers was also observed. Based on bioinformatics predictions, we introduced the D46G substitution to examine if EGF C-terminal part is directly involved in the intermolecular interface formation of the observed dimers. We found a reduced ability of the resulting EGF D46G dimers to dissociate at temperatures up to 50 °C. The D46G substitution also increased the intermolecular antiparallel β-structure content within the EGF peptide in a solution according to the CD spectra analysis that was confirmed by HATR-FTIR results. Additionally, the energy transfer between Tyr and Trp residues was detected by fluorescence spectroscopy for the EGF D46G mutant, but not for the native EGF. This allowed us to suggest the elongation and rearrangement of the intermolecular β-structure that leads to the observed stabilization of EGF D46G dimers. The results imply EGF dimerization under physiological pH value and temperature and the involvement of EGF C-terminal part in this process.
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103
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Segawa K, Igarashi K, Murayama K. The Cys-Pro motifs in the intrinsically disordered regions of the transcription factor BACH1 mediate distinct and overlapping functions upon heme binding. FEBS Lett 2022; 596:1576-1585. [PMID: 35302665 DOI: 10.1002/1873-3468.14338] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 03/08/2022] [Accepted: 03/11/2022] [Indexed: 11/09/2022]
Abstract
The function of the transcription factor BACH1 is regulated by heme binding to multiple Cys-Pro (CP) motifs within its intrinsically disordered regions. Here, biochemical analyses were conducted to reveal the individual functional roles of the CP motifs. Our findings revealed that four CP motifs in BACH1 individually contributed to the regulation of BACH1 activity by accepting heme in five- and six-coordination manner. The model structure around the bZip domain indicated that the CP motifs are in the N- and C-terminal heme-binding regions, which are approximately 9 nm apart, suggesting that spatial location is important for the individual function of the CP motifs. The presence of multiple CP motifs with distinct roles may ensure the multifaceted, strict regulation of BACH1 by heme.
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Affiliation(s)
- Kei Segawa
- Division of Biomedical Measurements and Diagnostics, Graduate School of Biomedical Engineering, Tohoku University, Seiryo 2-1, Aoba, Sendai, 980-8575, Japan.,Pharmaceutical Discovery Research Laboratories, Teijin Pharma Limited, Asahigaoka 4-3-2, Hino, 191-8512, Tokyo, Japan
| | - Kazuhiko Igarashi
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Seiryo 2-1, Aoba, Sendai, 980-8575, Japan
| | - Kazutaka Murayama
- Division of Biomedical Measurements and Diagnostics, Graduate School of Biomedical Engineering, Tohoku University, Seiryo 2-1, Aoba, Sendai, 980-8575, Japan
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104
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Binette V, Mousseau N, Tuffery P. A Generalized Attraction-Repulsion Potential and Revisited Fragment Library Improves PEP-FOLD Peptide Structure Prediction. J Chem Theory Comput 2022; 18:2720-2736. [PMID: 35298162 DOI: 10.1021/acs.jctc.1c01293] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Fast and accurate structure prediction is essential to the study of peptide function, molecular targets, and interactions and has been the subject of considerable efforts in the past decade. In this work, we present improvements to the popular simplified PEP-FOLD technique for small peptide structure prediction. PEP-FOLD originality is threefold: (i) it uses a predetermined structural alphabet, (ii) it uses a sequential algorithm to reconstruct the tridimensional structures of these peptides in a discrete space using a fragment library, and (iii) it assesses the energy of these structures using a coarse-grained representation in which all of the backbone atoms but the α-hydrogen are present, and the side chain corresponds to a unique bead. In former versions of PEP-FOLD, a van der Waals formulation was used for non-bonded interactions, with each side chain being associated with a fixed radius. Here, we explore the relevance of using instead a generalized formulation in which not only the optimal distance of interaction and the energy at this distance are parameters but also the distance at which the potential is zero. This allows each side chain to be associated with a different radius and potential energy shape, depending on its interaction partner, and in principle to make more effective the coarse-grained representation. In addition, the new PEP-FOLD version is associated with an updated library of fragments. We show that these modifications lead to important improvements for many of the problematic targets identified with the former PEP-FOLD version while maintaining already correct predictions. The improvement is in terms of both model ranking and model accuracy. We also compare the PEP-FOLD enhanced version to state-of-the-art techniques for both peptide and structure predictions: APPTest, RaptorX, and AlphaFold2. We find that the new predictions are superior, in particular with respect to the prediction of small β-targets, to those of APPTest and RaptorX and bring, with its original approach, additional understanding on folded structures, even when less precise than AlphaFold2. With their strong physical influence, the revised structural library and coarse-grained potential offer, however, the means for a deeper understanding of the nature of folding and open a solid basis for studying flexibility and other dynamical properties not accessible to IA structure prediction approaches.
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Affiliation(s)
- Vincent Binette
- Départment de Physique, Université de Montréal, Case postale 6128, succursale Centre-ville, Montréal, QC H3C 3J7, Canada
| | - Normand Mousseau
- Départment de Physique, Université de Montréal, Case postale 6128, succursale Centre-ville, Montréal, QC H3C 3J7, Canada
| | - Pierre Tuffery
- Université de Paris, INSERM U1133, CNRS UMR 8251, F-75205 Paris, France
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105
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Soltan MA, Behairy MY, Abdelkader MS, Albogami S, Fayad E, Eid RA, Darwish KM, Elhady SS, Lotfy AM, Alaa Eldeen M. In silico Designing of an Epitope-Based Vaccine Against Common E. coli Pathotypes. Front Med (Lausanne) 2022; 9:829467. [PMID: 35308494 PMCID: PMC8931290 DOI: 10.3389/fmed.2022.829467] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 01/21/2022] [Indexed: 12/20/2022] Open
Abstract
Escherichia coli (E. coli) is a Gram-negative bacterium that belongs to the family Enterobacteriaceae. While E. coli can stay as an innocuous resident in the digestive tract, it can cause a group of symptoms ranging from diarrhea to live threatening complications. Due to the increased rate of antibiotic resistance worldwide, the development of an effective vaccine against E. coli pathotypes is a major health priority. In this study, a reverse vaccinology approach along with immunoinformatics has been applied for the detection of potential antigens to develop an effective vaccine. Based on our screening of 5,155 proteins, we identified lipopolysaccharide assembly protein (LptD) and outer membrane protein assembly factor (BamA) as vaccine candidates for the current study. The conservancy of these proteins in the main E. coli pathotypes was assessed through BLASTp to make sure that the designed vaccine will be protective against major E. coli pathotypes. The multitope vaccine was constructed using cytotoxic T lymphocyte (CTL), helper T lymphocyte (HTL), and B cell lymphocyte (BCL) epitopes with suitable linkers and adjuvant. Following that, it was analyzed computationally where it was found to be antigenic, soluble, stable, and non-allergen. Additionally, the adopted docking study, as well as all-atom molecular dynamics simulation, illustrated the promising predicted affinity and free binding energy of this constructed vaccine against the human Toll-like receptor-4 (hTLR-4) dimeric state. In this regard, wet lab studies are required to prove the efficacy of the potential vaccine construct that demonstrated promising results through computational validation.
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Affiliation(s)
- Mohamed A. Soltan
- Department of Microbiology and Immunology, Faculty of Pharmacy, Sinai University, Ismailia, Egypt
| | - Mohammed Y. Behairy
- Department of Microbiology and Immunology, Faculty of Pharmacy, University of Sadat City, Sadat City, Egypt
| | - Mennatallah S. Abdelkader
- Department of Microbiology and Immunology, Faculty of Pharmacy, Suez Canal University, Ismailia, Egypt
| | - Sarah Albogami
- Department of Biotechnology, College of Science, Taif University, Taif, Saudi Arabia
| | - Eman Fayad
- Department of Biotechnology, College of Science, Taif University, Taif, Saudi Arabia
| | - Refaat A. Eid
- Department of Pathology, College of Medicine, King Khalid University, Abha, Saudi Arabia
| | - Khaled M. Darwish
- Department of Medicinal Chemistry, Faculty of Pharmacy, Suez Canal University, Ismailia, Egypt
| | - Sameh S. Elhady
- Department of Natural Products, Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ahmed M. Lotfy
- Department of Pharmacology, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Muhammad Alaa Eldeen
- Division of Cell Biology, Histology and Genetics, Department of Zoology, Faculty of Science, Zagazig University, Zagazig, Egypt
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106
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Nagarajan SK, Babu S, Devaraju P, Sohn H, Madhavan T. Structure and dynamics of the somatostatin receptor 3-ligand binding in the presence of lipids examined using computational structural biology methods. Proteins 2022; 90:704-719. [PMID: 34661304 DOI: 10.1002/prot.26267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 09/29/2021] [Accepted: 10/12/2021] [Indexed: 11/08/2022]
Abstract
In the past two decades, the structural biology studies on G-protein coupled receptors (GPCRs) are on the rise. Understanding the relation between the structure and function of GPCRs is important as they play a huge role in various signaling mechanisms in a eukaryotic cell. Somatostatin receptor 3 (SSTR3), one of the GPCRs, is one such important receptor which oversees different cellular processes including cell-to-cell signaling. However, the information available regarding the structural features of SSTR3 responsible for their bioactivity is scarce. In this study, we report a structural understanding of SSTR3-ligand binding that could be helpful in demystifying the structural complexities related to functioning of the receptor. An integrated protocol consisting of different computational structural biology tools including protein structure prediction via comparative modeling, binding site characterization, three-dimensional quantitative structure-activity relationship based on comparative molecular field analysis and comparative molecular similarity indices analysis, density functional theory, and molecular dynamics simulations were performed. Different understandings from the simulation of SSTR3-ligand complexes, mainly the conditions that are favorable for the formation of lowest bioactive state of SSTR3 ligands are reported. In addition to that, we report the important physicochemical descriptors of SSTR3 ligands that could significantly influence their bioactivity. The results of the study could be helpful in developing novel SSTR3 ligands (both agonists and antagonists) with high potency and receptor selectivity.
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Affiliation(s)
- Santhosh Kumar Nagarajan
- Computational Biology Lab, Department of Genetic Engineering, School of Bioengineering, SRM Institute of Science and Technology, Chennai, India
| | - Sathya Babu
- Computational Biology Lab, Department of Genetic Engineering, School of Bioengineering, SRM Institute of Science and Technology, Chennai, India
| | - Panneer Devaraju
- Division of Microbiology and Molecular Biology, Vector Control Research Centre, Indian Council of Medical Research, Pondicherry, India
| | - Honglae Sohn
- Department of Chemistry, Chosun University, Gwangju, South Korea
- Department of Carbon Materials, Chosun University, Gwangju, South Korea
| | - Thirumurthy Madhavan
- Computational Biology Lab, Department of Genetic Engineering, School of Bioengineering, SRM Institute of Science and Technology, Chennai, India
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107
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Lin B, Hung A, Li R, Barlow A, Singleton W, Matthyssen T, Sani MA, Hossain MA, Wade JD, O'Brien-Simpson NM, Li W. Systematic comparison of activity and mechanism of antimicrobial peptides against nosocomial pathogens. Eur J Med Chem 2022; 231:114135. [DOI: 10.1016/j.ejmech.2022.114135] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/10/2022] [Accepted: 01/14/2022] [Indexed: 12/20/2022]
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108
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Spitz O, Erenburg IN, Kanonenberg K, Peherstorfer S, Lenders MHH, Reiners J, Ma M, Luisi BF, Smits SHJ, Schmitt L. Identity Determinants of the Translocation Signal for a Type 1 Secretion System. Front Physiol 2022; 12:804646. [PMID: 35222063 PMCID: PMC8870123 DOI: 10.3389/fphys.2021.804646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 12/31/2021] [Indexed: 11/28/2022] Open
Abstract
The toxin hemolysin A was first identified in uropathogenic E. coli strains and shown to be secreted in a one-step mechanism by a dedicated secretion machinery. This machinery, which belongs to the Type I secretion system family of the Gram-negative bacteria, is composed of the outer membrane protein TolC, the membrane fusion protein HlyD and the ABC transporter HlyB. The N-terminal domain of HlyA represents the toxin which is followed by a RTX (Repeats in Toxins) domain harboring nonapeptide repeat sequences and the secretion signal at the extreme C-terminus. This secretion signal, which is necessary and sufficient for secretion, does not appear to require a defined sequence, and the nature of the encoded signal remains unknown. Here, we have combined structure prediction based on the AlphaFold algorithm together with functional and in silico data to examine the role of secondary structure in secretion. Based on the presented data, a C-terminal, amphipathic helix is proposed between residues 975 and 987 that plays an essential role in the early steps of the secretion process.
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Affiliation(s)
- Olivia Spitz
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Isabelle N. Erenburg
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Kerstin Kanonenberg
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Sandra Peherstorfer
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Michael H. H. Lenders
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Jens Reiners
- Center for Structural Studies, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Miao Ma
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Ben F. Luisi
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Sander H. J. Smits
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Center for Structural Studies, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Lutz Schmitt
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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109
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Theta-Defensins to Counter COVID-19 as Furin Inhibitors: In Silico Efficiency Prediction and Novel Compound Design. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:9735626. [PMID: 35154362 PMCID: PMC8829439 DOI: 10.1155/2022/9735626] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 12/28/2021] [Accepted: 01/21/2022] [Indexed: 12/13/2022]
Abstract
Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was characterized as a pandemic by the World Health Organization (WHO) in Dec. 2019. SARS-CoV-2 binds to the cell membrane through spike proteins on its surface and infects the cell. Furin, a host-cell enzyme, possesses a binding site for the spike protein. Thus, molecules that block furin could potentially be a therapeutic solution. Defensins are antimicrobial peptides that can hypothetically inhibit furin because of their arginine-rich structure. Theta-defensins, a subclass of defensins, have attracted attention as drug candidates due to their small size, unique structure, and involvement in several defense mechanisms. Theta-defensins could be a potential treatment for COVID-19 through furin inhibition and an anti-inflammatory mechanism. Note that inflammatory events are a significant and deadly condition that could happen at the later stages of COVID-19 infection. Here, the potential of theta-defensins against SARS-CoV-2 infection was investigated through in silico approaches. Based on docking analysis results, theta-defensins can function as furin inhibitors. Additionally, a novel candidate peptide against COVID-19 with optimal properties regarding antigenicity, stability, electrostatic potential, and binding strength was proposed. Further in vitro/in vivo investigations could verify the efficiency of the designed novel peptide.
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110
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He J, Guo H, Zhang M, Wang M, Sun L, Zhuang Y. Purification and Characterization of a Novel Calcium-Binding Heptapeptide from the Hydrolysate of Tilapia Bone with Its Osteogenic Activity. Foods 2022; 11:foods11030468. [PMID: 35159617 PMCID: PMC8834476 DOI: 10.3390/foods11030468] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 01/28/2022] [Accepted: 02/02/2022] [Indexed: 02/01/2023] Open
Abstract
In this study, a calcium-binding peptide was obtained by hydrolyzing tilapia bone and its osteogenic activity was evaluated. Animal protease was selected from nine enzymes, and its hydrolysate was purified through preparative and semi-preparative reverse phase high-performance liquid chromatography. The purified peptide was identified as DGPSGPK (656.32 Da) and its calcium-binding capacity reached 111.98 µg/mg. The peptide calcium chelate (DGPSGPK-Ca) was obtained, and its structure was characterized through Fourier transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), scanning electron microscopy (SEM), and mass spectrometry (MS). The results of XRD and SEM showed that DGPSGPK-Ca was formed as a new compound. The carboxyl and amino groups of Lys and Asp residues may be the chelating sites of DGPSGPK according to the FTIR and MS results. The molecular simulation showed the carbonyl groups of Asp, Pro, Ser, and Lys residues involved in the binding of calcium. The interaction of DGPSGPK and different integrins was evaluated by molecular docking simulation, and the main forces involved were electrostatic interaction forces, hydrogen bonding and hydrophobic interactions. Furthermore, DGPSGPK could inhibit the differentiation of osteoclast and promote the proliferation, differentiation and mineralization of osteoblasts.
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111
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Immunoinformatics-based characterization of immunogenic CD8 T-cell epitopes for a broad-spectrum cell-mediated immunity against high-risk human papillomavirus infection. Microb Pathog 2022; 165:105462. [DOI: 10.1016/j.micpath.2022.105462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/23/2022] [Accepted: 02/24/2022] [Indexed: 12/24/2022]
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112
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Loustau T, Abou-Faycal C, Erne W, zur Wiesch PA, Ksouri A, Imhof T, Mörgelin M, Li C, Mathieu M, Salomé N, Crémel G, Dhaouadi S, Bouhaouala-Zahar B, Koch M, Orend G. Modulating tenascin-C functions by targeting the MAtrix REgulating MOtif, “MAREMO”. Matrix Biol 2022; 108:20-38. [DOI: 10.1016/j.matbio.2022.02.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 01/31/2022] [Accepted: 02/23/2022] [Indexed: 12/11/2022]
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113
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Folberth A, Bharadwaj S, van der Vegt NFA. Small-to-large length scale transition of TMAO interaction with hydrophobic solutes. Phys Chem Chem Phys 2022; 24:2080-2087. [PMID: 35018925 DOI: 10.1039/d1cp05167a] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We report the effect of trimethylamine N-oxide (TMAO) on the solvation of nonpolar solutes in water studied with molecular dynamics (MD) simulations and free-energy calculations. The simulation data indicate the occurrence of a length scale crossover in the TMAO interaction with repulsive Weeks-Chandler-Andersen (WCA) solutes: while TMAO is depleted from the hydration shell of a small WCA solute (methane) and increases the free-energy cost of solute-cavity formation, it preferentially binds to a large WCA solute (α-helical polyalanine), reducing the free-energy cost of solute-cavity formation via a surfactant-like mechanism. Significantly, we show that this surfactant-like behaviour of TMAO reinforces the solvent-mediated attraction between large WCA solutes by means of an entropic force linked to the interfacial accumulation of TMAO. Specifically, this entropic force arises from the natural tendency of adsorbed TMAO molecules to mix back into the bulk. It therefore favours solute-solute contact states that minimise the surface area exposed to the solvent and have a small overall number of TMAO molecules adsorbed. In contrast to the well-known depletion force, its effect is compensated by enthalpic solute-solvent interactions. Correspondingly, the hydrophobic association free energy of the large α-helical solutes passes through a minimum at low TMAO concentration when cohesive solute-solvent van der Waals interactions are considered. The observations reported herein are reminiscent to cosolvent effects on hydrophobic polymer coil-globule collapse free energies (Bharadwaj et al., Commun. Chem. 2020, 3, 165) and may be of general significance in systems whose properties are determined by hydrophobic self-assembly.
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Affiliation(s)
- Angelina Folberth
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Strasse 10, 64287 Darmstadt, Germany.
| | - Swaminath Bharadwaj
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Strasse 10, 64287 Darmstadt, Germany.
| | - Nico F A van der Vegt
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Strasse 10, 64287 Darmstadt, Germany.
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114
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Bagga T, Su Ning L, Sivaraman J, Shankar S. Sequence Preference and Scaffolding Requirement for the Inhibition of Human Neutrophil Elastase by Ecotin Peptide. Protein Sci 2022; 31:933-941. [PMID: 35014748 PMCID: PMC8927871 DOI: 10.1002/pro.4274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 01/04/2022] [Accepted: 01/06/2022] [Indexed: 11/07/2022]
Abstract
Human neutrophil elastase (hNE) is an abundant serine protease that is a major constituent of lung elastolytic activity. However, when secreted in excess, if not properly attenuated by selective inhibitor proteins, it can have detrimental effects on host tissues, leading to chronic lung inflammation and non-small cell lung cancer. To improve upon the design of inhibitors against hNE for therapeutic applications, here, we report the crystal structure of hNE in complex with an ecotin-derived peptide inhibitor. We show that the peptide binds in the non-prime substrate binding site. Unexpectedly, compared with full-length ecotin, we find that our short linear peptides and circular amide-backbone-linked peptides of ecotin are incapable of efficient hNE inhibition. Our structural insights point to a preferred amino acid sequence and the potential benefit of a scaffold for optimal binding and function of the peptide inhibitor, both of which are retained in the full-length ecotin protein. These findings will aid in the development of effective peptide-based inhibitors against hNE for targeted therapy. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Tanaya Bagga
- Department of Biological Sciences, 14 Science Drive 4, National University of Singapore, Singapore
| | - Loh Su Ning
- Department of Biological Sciences, 14 Science Drive 4, National University of Singapore, Singapore
| | - J Sivaraman
- Department of Biological Sciences, 14 Science Drive 4, National University of Singapore, Singapore
| | - Srihari Shankar
- Department of Biological Sciences, 14 Science Drive 4, National University of Singapore, Singapore
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115
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Kumar P, Bhardwaj T, Garg N, Giri R. Microsecond simulations and CD spectroscopy reveals the intrinsically disordered nature of SARS-CoV-2 spike-C-terminal cytoplasmic tail (residues 1242-1273) in isolation. Virology 2022; 566:42-55. [PMID: 34864296 PMCID: PMC8626822 DOI: 10.1016/j.virol.2021.11.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 11/01/2021] [Accepted: 11/17/2021] [Indexed: 01/04/2023]
Abstract
All available SARS-CoV-2 spike protein crystal and cryo-EM structures have shown missing electron densities for cytosolic C-terminal regions (CTR). Generally, the missing electron densities point towards the intrinsically disordered nature of the protein region (IDPR). This curiosity has led us to investigate the cytosolic CTR of the spike glycoprotein of SARS-CoV-2 in isolation. The spike CTR is supposed to be from 1235 to 1273 residues or 1242-1273 residues based on our used prediction. Therefore, we have demonstrated the structural conformation of cytosolic region and its dynamics through computer simulations up to microsecond timescale using OPLS and CHARMM forcefields. The simulations have revealed the unstructured conformation of cytosolic region. Further, we have validated our computational observations with circular dichroism (CD) spectroscopy-based experiments and found its signature spectra at 198 nm. We believe that our findings will surely help in understanding the structure-function relationship of the spike protein's cytosolic region.
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Affiliation(s)
- Prateek Kumar
- School of Basic Sciences, Indian Institute of Technology Mandi, VPO Kamand, Himachal Pradesh, 175005, India
| | - Taniya Bhardwaj
- School of Basic Sciences, Indian Institute of Technology Mandi, VPO Kamand, Himachal Pradesh, 175005, India
| | - Neha Garg
- Department of Medicinal Chemistry, Faculty of Ayurveda, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India
| | - Rajanish Giri
- School of Basic Sciences, Indian Institute of Technology Mandi, VPO Kamand, Himachal Pradesh, 175005, India,Corresponding author
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Nguyen PH, Derreumaux P. Computer Simulations Aimed at Exploring Protein Aggregation and Dissociation. Methods Mol Biol 2022; 2340:175-196. [PMID: 35167075 DOI: 10.1007/978-1-0716-1546-1_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Protein aggregation can lead to well-defined structures that are functional, but is also the cause of the death of neuron cells in many neurodegenerative diseases. The complexity of the molecular events involved in the aggregation kinetics of amyloid proteins and the transient and heterogeneous characters of all oligomers prevent high-resolution structural experiments. As a result, computer simulations have been used to determine the atomic structures of amyloid proteins at different association stages as well as to understand fibril dissociation. In this chapter, we first review the current computer simulation methods used for aggregation with some atomistic and coarse-grained results aimed at better characterizing the early formed oligomers and amyloid fibril formation. Then we present the applications of non-equilibrium molecular dynamics simulations to comprehend the dissociation of protein assemblies.
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Affiliation(s)
- Phuong H Nguyen
- Laboratoire de Biochimie Théorique, UPR 9080, CNRS, Université de Paris, Paris, France
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, PSL Research University, Paris, France
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique, UPR 9080, CNRS, Université de Paris, Paris, France.
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, PSL Research University, Paris, France.
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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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Mollazadeh S, Bakhshesh M, Keyvanfar H, Nikbakht Brujeni G. Identification of Cytotoxic T lymphocyte (CTL) Epitope and design of an immunogenic multi-epitope of Bovine Ephemeral Fever Virus (BEFV) Glycoprotein G for Vaccine Development. Res Vet Sci 2022; 144:18-26. [PMID: 35033847 DOI: 10.1016/j.rvsc.2021.12.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 12/08/2021] [Accepted: 12/28/2021] [Indexed: 11/24/2022]
Abstract
Bovine ephemeral fever (BEF), a vector-borne disease of cattle and water buffalo, is enzootic in tropical and subtropical zones of Asia, Australia, and Africa. Since cytotoxic T lymphocytes (CTL) responses may play a key role in the control of bovine ephemeral fever virus (BEFV) infection, it is important to identify and characterize the CTL target epitopes of BEFV antigens. The current study has been designed to identify and characterize the potential CTL epitopes using the Immuno-informatics tools, and it helped find the potent vaccine candidates against BEF. Antigenicity, toxicity, allergenicity, and immunogenicity testing of predicted CTL epitopes was done. Total four CTL epitopes for BEFV G protein, have been identified as potential epitopes. Prediction of the 3D structure of multi-epitope (final structure) was performed using I-TASSER server. Model 1 was selected as the best model with C-Score: -3.71. The modeled G protein structure and multi-epitope structure were validated by the Ramachandran plots Prosa and Verify 3D server. Epitopic regions of 3D protein structure were identified by Chimera UCSF software. Physicochemical properties of the Multi epitope were evaluated using ProtParam server. This is the first report of CTL epitope in the G protein of BEFV. In this manner, they would play an important role in evoking the immune response as well as vaccine development. However, in vitro and in vivo experimental studies are required for suggested epitopes verification. The multi-epitope was designed from regions of the G protein sequence that lacked mutation and genomic diversity. Therefore, it can be introduced as a protein vaccine from all strains of BEFV as a vaccine candidate for design.
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Affiliation(s)
- Shima Mollazadeh
- Department of Pathobiology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Mehran Bakhshesh
- Department of Animal Virology, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Organization (AREEO), Karaj, Iran.
| | - Hadi Keyvanfar
- Department of Pathobiology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Gholamreza Nikbakht Brujeni
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
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Zhang Y, Wang Y, Zeng L, Liu Y, Sun H, Li S, Wang S, Shu L, Liu N, Yin S, Wang J, Ni D, Wu Y, Yang Y, He L, Meng B, Yang X. Amphibian-derived peptide homodimer OA-GL17d promotes skin wound regeneration through the miR-663a/TGF-β1/Smad axis. BURNS & TRAUMA 2022; 10:tkac032. [PMID: 35832307 PMCID: PMC9273405 DOI: 10.1093/burnst/tkac032] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/08/2022] [Indexed: 11/29/2022]
Abstract
Background Amphibian-derived peptides exhibit considerable potential in the discovery and development of new therapeutic interventions for clinically challenging chronic skin wounds. MicroRNAs (miRNAs) are also considered promising targets for the development of effective therapies against skin wounds. However, further research in this field is anticipated. This study aims to identify and provide a new peptide drug candidate, as well as to explore the underlying miRNA mechanisms and possible miRNA drug target for skin wound healing. Methods A combination of Edman degradation, mass spectrometry and cDNA cloning were adopted to determine the amino acid sequence of a peptide that was fractionated from the secretion of Odorrana andersonii frog skin using gel-filtration and reversed-phase high-performance liquid chromatography. The toxicity of the peptide was evaluated by Calcein-AM/propidium iodide (PI) double staining against human keratinocytes (HaCaT cells), hemolytic activity against mice blood cells and acute toxicity against mice. The stability of the peptide in plasma was also evaluated. The prohealing potency of the peptide was determined by MTS, scratch healing and a Transwell experiment against HaCaT cells, full-thickness injury wounds and scald wounds in the dorsal skin of mice. miRNA transcriptome sequencing analysis, enzyme-linked immunosorbent assay, real-time polymerase chain reaction and western blotting were performed to explore the molecular mechanisms. Results A novel peptide homodimer (named OA-GL17d) that contains a disulfide bond between the 16th cysteine residue of the peptide monomer and the sequence ‘GLFKWHPRCGEEQSMWT’ was identified. Analysis showed that OA-GL17d exhibited no hemolytic activity or acute toxicity, but effectively promoted keratinocyte proliferation and migration and strongly stimulated the repair of full-thickness injury wounds and scald wounds in the dorsal skin of mice. Mechanistically, OA-GL17d decreased the level of miR-663a to increase the level of transforming growth factor-β1 (TGF-β1) and activate the subsequent TGF-β1/Smad signaling pathway, thereby resulting in accelerated skin wound re-epithelialization and granular tissue formation. Conclusions Our results suggest that OA-GL17d is a new peptide drug candidate for skin wound repair. This study emphasizes the importance of exogenous peptides as molecular probes for exploring competing endogenous RNA mechanisms and indicates that miR-663a may be an effective target for promoting skin repair.
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Affiliation(s)
- Yue Zhang
- Department of Anatomy and Histology & Embryology , Faculty of Basic Medical Science, , Kunming 650500, Yunnan, China
- Kunming Medical University , Faculty of Basic Medical Science, , Kunming 650500, Yunnan, China
| | - Ying Wang
- Key Laboratory of Chemistry in Ethnic Medicinal Resources & Key Laboratory of Natural Products Synthetic Biology of Ethnic Medicinal Endophytes , State Ethnic Affairs Commission & Ministry of Education, School of Ethnomedicine and Ethnopharmacy, , Kunming 650504, Yunnan, China
- Yunnan MinZu University , State Ethnic Affairs Commission & Ministry of Education, School of Ethnomedicine and Ethnopharmacy, , Kunming 650504, Yunnan, China
| | - Lin Zeng
- Institutional Center for Shared Technologies and Facilities of Kunming Institute of Zoology, Chinese Academy of Sciences , Kunming 650223, Yunnan, China
| | - Yixiang Liu
- Key Laboratory of Chemistry in Ethnic Medicinal Resources & Key Laboratory of Natural Products Synthetic Biology of Ethnic Medicinal Endophytes , State Ethnic Affairs Commission & Ministry of Education, School of Ethnomedicine and Ethnopharmacy, , Kunming 650504, Yunnan, China
- Yunnan MinZu University , State Ethnic Affairs Commission & Ministry of Education, School of Ethnomedicine and Ethnopharmacy, , Kunming 650504, Yunnan, China
| | - Huiling Sun
- Department of Anatomy and Histology & Embryology , Faculty of Basic Medical Science, , Kunming 650500, Yunnan, China
- Kunming Medical University , Faculty of Basic Medical Science, , Kunming 650500, Yunnan, China
| | - Shanshan Li
- Department of Anatomy and Histology & Embryology , Faculty of Basic Medical Science, , Kunming 650500, Yunnan, China
- Kunming Medical University , Faculty of Basic Medical Science, , Kunming 650500, Yunnan, China
| | - Siyu Wang
- Department of Anatomy and Histology & Embryology , Faculty of Basic Medical Science, , Kunming 650500, Yunnan, China
- Kunming Medical University , Faculty of Basic Medical Science, , Kunming 650500, Yunnan, China
| | - Longjun Shu
- Key Laboratory of Chemistry in Ethnic Medicinal Resources & Key Laboratory of Natural Products Synthetic Biology of Ethnic Medicinal Endophytes , State Ethnic Affairs Commission & Ministry of Education, School of Ethnomedicine and Ethnopharmacy, , Kunming 650504, Yunnan, China
- Yunnan MinZu University , State Ethnic Affairs Commission & Ministry of Education, School of Ethnomedicine and Ethnopharmacy, , Kunming 650504, Yunnan, China
| | - Naixin Liu
- Department of Anatomy and Histology & Embryology , Faculty of Basic Medical Science, , Kunming 650500, Yunnan, China
- Kunming Medical University , Faculty of Basic Medical Science, , Kunming 650500, Yunnan, China
| | - Saige Yin
- Department of Anatomy and Histology & Embryology , Faculty of Basic Medical Science, , Kunming 650500, Yunnan, China
- Kunming Medical University , Faculty of Basic Medical Science, , Kunming 650500, Yunnan, China
| | - Junsong Wang
- Department of Anatomy and Histology & Embryology , Faculty of Basic Medical Science, , Kunming 650500, Yunnan, China
- Kunming Medical University , Faculty of Basic Medical Science, , Kunming 650500, Yunnan, China
| | - Dan Ni
- Department of Anatomy and Histology & Embryology , Faculty of Basic Medical Science, , Kunming 650500, Yunnan, China
- Kunming Medical University , Faculty of Basic Medical Science, , Kunming 650500, Yunnan, China
| | - Yutong Wu
- Department of Anatomy and Histology & Embryology , Faculty of Basic Medical Science, , Kunming 650500, Yunnan, China
- Kunming Medical University , Faculty of Basic Medical Science, , Kunming 650500, Yunnan, China
| | - Ying Yang
- Endocrinology Department of Affiliated Hospital of Yunnan University , Kunming 650021, Yunnan, China
| | - Li He
- Department of Dermatology, First Affiliated Hospital of Kunming Medical University , Kunming, 650500, Yunnan, China
| | - Buliang Meng
- Department of Anatomy and Histology & Embryology , Faculty of Basic Medical Science, , Kunming 650500, Yunnan, China
- Kunming Medical University , Faculty of Basic Medical Science, , Kunming 650500, Yunnan, China
| | - Xinwang Yang
- Department of Anatomy and Histology & Embryology , Faculty of Basic Medical Science, , Kunming 650500, Yunnan, China
- Kunming Medical University , Faculty of Basic Medical Science, , Kunming 650500, Yunnan, China
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Cruz J, Suárez-Barrera M, Rondón-Villarreal P, Olarte-Diaz A, Guzmán F, Visser L, Rueda-Forero N. Computational study, synthesis and evaluation of active peptides derived from Parasporin-2 and spike protein from Alphacoronavirus against colorectal cancer cells. Biosci Rep 2021; 41:BSR20211964. [PMID: 34796903 PMCID: PMC8661510 DOI: 10.1042/bsr20211964] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 11/03/2021] [Accepted: 11/15/2021] [Indexed: 11/21/2022] Open
Abstract
Parasporin-2Aa1 (PS2Aa1) is a toxic protein of 37 KDa (30 kDa, activated form produced by proteolysis) that was shown to be cytotoxic against specific human cancer cells, although its mechanism of action has not been elucidated yet. In order to study the role of some native peptide fragments of proteins on anticancer activity, here we investigated the cytotoxic effect of peptide fragments from domain-1 of PS2Aa1 and one of the loops present in the binding region of the virus spike protein from Alphacoronavirus (HCoV-229E), the latter according to scientific reports, who showed interaction with the human APN (h-APN) receptor, evidence corroborated through computational simulations, and thus being possible active against colon cancer cells. Peptides namely P264-G274, Loop1-PS2Aa, and Loop2-PS2Aa were synthesized using the Fmoc solid-phase synthesis and characterized by mass spectrometry (MS). Additionally, one region from loop 1 of HCoV-229E, Loop1-HCoV-229E, was also synthesized and characterized. The A4W-GGN5 anticancer peptide and 5-fluorouracil (5-FU) were taken as a control in all experiments. Circular dichroism revealed an α-helix structure for the peptides derived from PS2Aa1 (P264-G274, Loop1-PS2Aa, and Loop2-PS2Aa) and β-laminar structure for the peptide derived from Alphacoronavirus spike protein Loop1-HCoV-229E. Peptides showed a hemolysis percentage of less than 20% at 100 µM concentration. Besides, peptides exhibited stronger anticancer activity against SW480 and SW620 cells after exposure for 48 h. Likewise, these compounds showed significantly lower toxicity against normal cells CHO-K1. The results suggest that native peptide fragments from Ps2Aa1 may be optimized as a novel potential cancer-therapeutic agents.
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Affiliation(s)
- Jenniffer Cruz
- Universidad de Santander, Facultad de Ciencias Médicas y de la Salud, Instituto de Investigación Masira, Bucaramanga, Colombia
| | - Miguel Orlando Suárez-Barrera
- Universidad de Santander, Facultad de Ciencias Médicas y de la Salud, Instituto de Investigación Masira, Bucaramanga, Colombia
- Department of Pathology and Medical Biology, University of Groningen, University medical Center Groningen, Groningen, Netherlands
- Corporación Académica Ciencias Básicas Biomédicas Universidad de Antioquia, Medellín, Colombia
| | - Paola Rondón-Villarreal
- Universidad de Santander, Facultad de Ciencias Médicas y de la Salud, Instituto de Investigación Masira, Bucaramanga, Colombia
| | - Andrés Olarte-Diaz
- Universidad de Santander, Facultad de Ciencias Médicas y de la Salud, Instituto de Investigación Masira, Bucaramanga, Colombia
| | - Fanny Guzmán
- NBC Núcleo de Biotecnología Curauma, Pontificia Universidad Católica de Valparaíso, Campus Curauma, Av. Universidad 330, Valparaíso, Chile
| | - Lydia Visser
- Department of Pathology and Medical Biology, University of Groningen, University medical Center Groningen, Groningen, Netherlands
| | - Nohora Juliana Rueda-Forero
- Universidad de Santander, Facultad de Ciencias Médicas y de la Salud, Instituto de Investigación Masira, Bucaramanga, Colombia
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Characterization of the AGR2 interactome uncovers new players of Protein Disulfide Isomerase network in cancer cells. Mol Cell Proteomics 2021; 21:100188. [PMID: 34929376 PMCID: PMC8816719 DOI: 10.1016/j.mcpro.2021.100188] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 12/03/2021] [Accepted: 12/14/2021] [Indexed: 12/03/2022] Open
Abstract
Anterior gradient 2 (AGR2) is an endoplasmic reticulum (ER)-resident protein disulfide isomerase (PDI) known to be overexpressed in many human epithelial cancers and is involved in cell migration, cellular transformation, angiogenesis, and metastasis. This protein inhibits the activity of the tumor suppressor p53, and its expression levels can be used to predict cancer patient outcome. However, the precise network of AGR2-interacting partners and clients remains to be fully characterized. Herein, we used label-free quantification and also stable isotope labeling with amino acids in cell culture–based LC–MS/MS analyses to identify proteins interacting with AGR2. Functional annotation confirmed that AGR2 and its interaction partners are associated with processes in the ER that maintain intracellular metabolic homeostasis and participate in the unfolded protein response, including those associated with changes in cellular metabolism, energy, and redox states in response to ER stress. As a proof of concept, the interaction between AGR2 and PDIA3, another ER-resident PDI, was studied in more detail. Pathway analysis revealed that AGR2 and PDIA3 play roles in protein folding in ER, including post-translational modification and in cellular response to stress. We confirmed the AGR2–PDIA3 complex formation in cancer cells, which was enhanced in response to ER stress. Accordingly, molecular docking characterized potential quaternary structure of this complex; however, it remains to be elucidated whether AGR2 rather contributes to PDIA3 maturation in ER, the complex directly acts in cellular signaling, or mediates AGR2 secretion. Our study provides a comprehensive insight into the protein–protein interaction network of AGR2 by identifying functionally relevant proteins and related cellular and biochemical pathways associated with the role of AGR2 in cancer cells. LC–MS/MS analysis of AGR2-interacting proteins in T47D and H1299 cells. About 15 overlapping AGR2 interactors, including PDIA3 and PDIA6, were identified in both cell lines. PDI family members represent the key part of the network. AGR2–PDIA3 interaction is even stronger under ER stress. AGR2–PDIA3 complex formation supports extracellular secretion of AGR2.
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Zahid S, Basharat S, Fakhar M, Rashid S. Molecular dynamics and structural analysis of the binding of COP1 E3 ubiquitin ligase to β-catenin and TRIB pseudokinases. Proteins 2021; 90:993-1004. [PMID: 34881468 DOI: 10.1002/prot.26292] [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: 03/17/2021] [Revised: 11/14/2021] [Accepted: 12/02/2021] [Indexed: 12/30/2022]
Abstract
Tribbles pseudokinases, Tribbles homolog 1 (TRIB1), Tribbles homolog 2 (TRIB2), and Tribbles homolog 3 (TRIB3), bind to constitutive photomorphogenesis protein 1 (COP1) E3 ligase to mediate the regulation of β-catenin expression. The interaction mechanism between COP1 E3 ligase and β-catenin has not been addressed to date. Based on the functional presence of TRIBs in wingless-related integration site (WNT) signaling, we analyzed their interaction patterns with β-catenin and COP1. Here, through in silico approaches, we ascribe the COP1 binding pattern against TRIBs and β-catenin. TRIB1 (355-DQIVPEY-361), TRIB2 (326-DQLVPDV-332), and TRIB3 (333-AQVVPDG-339) peptides revealed a shallow binding pocket at the COP1 interface to accommodate the V-P sequence motif. Reinvigoration of the comparative binding pattern and subtle structural analysis via docking, molecular dynamics simulations, molecular mechanics Poisson-Boltzmann surface area, topological, and tunnel analysis revealed that both β-catenin phosphodegron (DSGXXS) and TRIB (D/E/AQXVPD/E) motifs occupied a common COP1 binding site. Current study suggests a structural paradigm of TRIB homologs bearing a conserved motif that may compete with β-catenin phosphodegron signature for binding to WD40 domain of COP1. Thorough understanding of the structural basis for TRIB-mediated regulation of WNT/β-catenin signaling may help in devising more promising therapeutic strategy for liver and colorectal cancers.
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Affiliation(s)
- Sana Zahid
- National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Saba Basharat
- National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Muhammad Fakhar
- National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Sajid Rashid
- National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
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Computational Screening for the Anticancer Potential of Seed-Derived Antioxidant Peptides: A Cheminformatic Approach. Molecules 2021; 26:molecules26237396. [PMID: 34885982 PMCID: PMC8659047 DOI: 10.3390/molecules26237396] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/01/2021] [Accepted: 12/02/2021] [Indexed: 11/17/2022] Open
Abstract
Some seed-derived antioxidant peptides are known to regulate cellular modulators of ROS production, including those proposed to be promising targets of anticancer therapy. Nevertheless, research in this direction is relatively slow owing to the inevitable time-consuming nature of wet-lab experimentations. To help expedite such explorations, we performed structure-based virtual screening on seed-derived antioxidant peptides in the literature for anticancer potential. The ability of the peptides to interact with myeloperoxidase, xanthine oxidase, Keap1, and p47phox was examined. We generated a virtual library of 677 peptides based on a database and literature search. Screening for anticancer potential, non-toxicity, non-allergenicity, non-hemolyticity narrowed down the collection to five candidates. Molecular docking found LYSPH as the most promising in targeting myeloperoxidase, xanthine oxidase, and Keap1, whereas PSYLNTPLL was the best candidate to bind stably to key residues in p47phox. Stability of the four peptide-target complexes was supported by molecular dynamics simulation. LYSPH and PSYLNTPLL were predicted to have cell- and blood-brain barrier penetrating potential, although intolerant to gastrointestinal digestion. Computational alanine scanning found tyrosine residues in both peptides as crucial to stable binding to the targets. Overall, LYSPH and PSYLNTPLL are two potential anticancer peptides that deserve deeper exploration in future.
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Gopalakrishnan S, Uma SK, Mohan G, Mohan A, Shanmugam G, Kumar VTV, J S, Chandrika SK, Vasudevan D, Nori SRC, Sathi SN, George S, Maliekal TT. SSTP1, a Host Defense Peptide, Exploits the Immunomodulatory IL6 Pathway to Induce Apoptosis in Cancer Cells. Front Immunol 2021; 12:740620. [PMID: 34867962 PMCID: PMC8639500 DOI: 10.3389/fimmu.2021.740620] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 10/27/2021] [Indexed: 12/30/2022] Open
Abstract
While the immunomodulatory pathways initiated in immune cells contribute to therapeutic response, their activation in cancer cells play a role in cancer progression. Also, many of the aberrantly expressed immunomodulators on cancer cells are considered as therapeutic targets. Here, we introduce host defense peptide (HDP), a known immuomodulator, as a therapeutic agent to target them. The cationic host defense peptides (HDPs), an integral part of the innate immune system, possess membranolytic activity, which imparts antimicrobial and antitumor efficacy to it. They act as immunomodulators by activating the immune cells. Though their antimicrobial function has been recently reassigned to immunoregulation, their antitumor activity is still attributed to its membranolytic activity. This membrane pore formation ability, which is proportional to the concentration of the peptide, also leads to side effects like hemolysis, limiting their therapeutic application. So, despite the identification of a variety of anticancer HDPs, their clinical utility is limited. Though HDPs are shown to exert the immunomodulatory activity through specific membrane targets on immune cells, their targets on cancer cells are unknown. We show that SSTP1, a novel HDP identified by shotgun cloning, binds to the active IL6/IL6Rα/gp130 complex on cancer cells, rearranging the active site residues. In contrast to the IL6 blockers inhibiting JAK/STAT activity, SSTP1 shifts the proliferative IL6/JAK/STAT signaling to the apoptotic IL6/JNK/AP1 pathway. In IL6Rα-overexpressing cancer cells, SSTP1 induces apoptosis at low concentration through JNK pathway, without causing significant membrane disruption. We highlight the importance of immunomodulatory pathways in cancer apoptosis, apart from its established role in immune cell regulation and cancer cell proliferation. Our study suggests that identification of the membrane targets for the promising anticancer HDPs might lead to the identification of new drugs for targeted therapy.
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Affiliation(s)
- Shyla Gopalakrishnan
- Cancer Research, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
- Interdisciplinary Biology, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
| | - Soumya Krishnan Uma
- Cancer Research, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
| | - Gayathri Mohan
- Cancer Research, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
- Regional Centre for Biotechnology, Faridabad, India
| | - Amrutha Mohan
- Cancer Research, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
- Manipal Academy of Higher Education, Manipal, India
| | - Geetha Shanmugam
- Cancer Research, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
| | - Vineeth T. V. Kumar
- Interdisciplinary Biology, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
| | - Sreekumar J
- Statistics, Section of Extension and Social Science, The Indian Council of Agricultural Research (ICAR) Central Tuber Crops Research Institute, Thiruvananthapuram, India
| | - Sivakumar K. Chandrika
- Genomics Core Facility, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
| | | | - Sai Ravi Chandra Nori
- Interdisciplinary Biology, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
| | - Shijulal Nelson Sathi
- Interdisciplinary Biology, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
| | - Sanil George
- Interdisciplinary Biology, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
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Purification, Identification and Characterization of Antioxidant Peptides from Corn Silk Tryptic Hydrolysate: An Integrated In Vitro-In Silico Approach. Antioxidants (Basel) 2021; 10:antiox10111822. [PMID: 34829693 PMCID: PMC8615004 DOI: 10.3390/antiox10111822] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 11/08/2021] [Accepted: 11/12/2021] [Indexed: 11/23/2022] Open
Abstract
Corn silk (CS) is an agro-by-product from corn cultivation. It is used in folk medicines in some countries, besides being commercialized as health-promoting supplements and beverages. Unlike CS-derived natural products, their bioactive peptides, particularly antioxidant peptides, are understudied. This study aimed to purify, identify and characterize antioxidant peptides from trypsin-hydrolyzed CS proteins. Purification was accomplished by membrane ultrafiltration, gel filtration chromatography, and strong-cation-exchange solid-phase extraction, guided by 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) diammonium salt radical cation (ABTS•+) scavenging, hydrogen peroxide scavenging, and lipid peroxidation inhibition assays. De novo sequencing identified 29 peptides (6–14 residues; 633–1518 Da). The peptides consisted of 33–86% hydrophobic and 10–67% basic residues. Molecular docking found MCFHHHFHK, VHFNKGKKR, and PVVWAAKR having the strongest affinity (−4.7 to −4.8 kcal/mol) to ABTS•+, via hydrogen bonds and hydrophobic interactions. Potential cellular mechanisms of the peptides were supported by their interactions with modulators of intracellular oxidant status: Kelch-like ECH-associated protein 1, myeloperoxidase, and xanthine oxidase. NDGPSR (Asn-Asp-Gly-Pro-Ser-Arg), the most promising peptide, showed stable binding to all three cellular targets, besides exhibiting low toxicity, low allergenicity, and cell-penetrating potential. Overall, CS peptides have potential application as natural antioxidant additives and functional food ingredients.
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Villa A, Brunialti E, Dellavedova J, Meda C, Rebecchi M, Conti M, Donnici L, De Francesco R, Reggiani A, Lionetti V, Ciana P. DNA aptamers masking angiotensin converting enzyme 2 as an innovative way to treat SARS-CoV-2 pandemic. Pharmacol Res 2021; 175:105982. [PMID: 34798263 PMCID: PMC8594078 DOI: 10.1016/j.phrs.2021.105982] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 11/09/2021] [Accepted: 11/09/2021] [Indexed: 12/15/2022]
Abstract
All the different coronavirus SARS-CoV-2 variants isolated so far share the same mechanism of infection mediated by the interaction of their spike (S) glycoprotein with specific residues on their cellular receptor: the angiotensin converting enzyme 2 (ACE2). Therefore, the steric hindrance on this cellular receptor created by a bulk macromolecule may represent an effective strategy for the prevention of the viral spreading and the onset of severe forms of Corona Virus disease 19 (COVID-19). Here, we applied a systematic evolution of ligands by exponential enrichment (SELEX) procedure to identify two single strand DNA molecules (aptamers) binding specifically to the region surrounding the K353, the key residue in human ACE2 interacting with the N501 amino acid of the SARS-CoV-2 S. 3D docking in silico experiments and biochemical assays demonstrated that these aptamers bind to this region, efficiently prevent the SARS-CoV-2 S/human ACE2 interaction and the viral infection in the nanomolar range, regardless of the viral variant, thus suggesting the possible clinical development of these aptamers as SARS-CoV-2 infection inhibitors. Our approach brings a significant innovation to the therapeutic paradigm of the SARS-CoV-2 pandemic by protecting the target cell instead of focusing on the virus; this is particularly attractive in light of the increasing number of viral mutants that may potentially escape the currently developed immune-mediated neutralization strategies.
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Affiliation(s)
- Alessandro Villa
- Department of Health Sciences, University of Milan, Milan 20146, Italy
| | - Electra Brunialti
- Department of Health Sciences, University of Milan, Milan 20146, Italy
| | | | - Clara Meda
- Department of Health Sciences, University of Milan, Milan 20146, Italy
| | - Monica Rebecchi
- Department of Health Sciences, University of Milan, Milan 20146, Italy
| | - Matteo Conti
- INGM - Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan 20122, Italy
| | - Lorena Donnici
- INGM - Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan 20122, Italy
| | - Raffaele De Francesco
- INGM - Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan 20122, Italy; Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan 20133, Italy
| | - Angelo Reggiani
- D3 Validation Research Line, Italian Institute of Technology, Genoa 16163, Italy
| | - Vincenzo Lionetti
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa 56127, Italy
| | - Paolo Ciana
- D3 Validation Research Line, Italian Institute of Technology, Genoa 16163, Italy.
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127
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Chng CP, Cho NJ, Hsia KJ, Huang C. Role of Membrane Stretch in Adsorption of Antiviral Peptides onto Lipid Membranes and Membrane Pore Formation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:13390-13398. [PMID: 34724382 DOI: 10.1021/acs.langmuir.1c02067] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Many medically important viruses are enveloped viruses, which are surrounded by a structurally conserved, host-derived lipid membrane coating. Agents that target and disrupt this membrane coating could potentially function as broad-spectrum antiviral drugs. The amphipathic α-helical (AH) peptide derived from the N-terminus of the hepatitis C virus NS5A protein is one such candidate and has been demonstrated to be able to selectively rupture lipid vesicles in the size range of viruses (<160 nm diameter). However, the mechanism underlying this membrane curvature selectivity remains elusive. In this study, we have performed molecular dynamics simulations to study the binding of the AH peptide to model membranes that are stretched to resemble the looser lipid headgroup packing present on highly curved outer membranes of nanoscale vesicles. We found that the AH peptide binds more favorably to membranes that are stretched. In addition, a tetrameric placement of peptides across the membrane induced stable pore formation in the stretched membrane. Thus, our results suggest that the AH peptide senses the high curvature of nanoscale vesicles via the enhanced exposure of lipid packing defects induced by membrane area strain.
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Affiliation(s)
- Choon-Peng Chng
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore 639798, Republic of Singapore
| | - Nam-Joon Cho
- School of Materials Science and Engineering, Nanyang Technological University, Singapore 637553, Republic of Singapore
- China-Singapore International Joint Research Institute (CSIJRI), Guangzhou 510000, P. R. China
| | - K Jimmy Hsia
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore 639798, Republic of Singapore
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore 637459, Republic of Singapore
| | - Changjin Huang
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore 639798, Republic of Singapore
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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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129
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Rational design and synthesis of modified natural peptides from Boana pulchella (anura) as acetylcholinesterase inhibitors and antioxidants. Amino Acids 2021; 54:181-192. [PMID: 34738177 DOI: 10.1007/s00726-021-03096-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 10/26/2021] [Indexed: 10/19/2022]
Abstract
The use of acetylcholinesterase (AChE) inhibitors, antioxidants or multitarget compounds are among the main strategies against Alzheimer's disease (AD). Between AChE inhibitors, those targeting the peripheral anionic site (PAS) are of special interest. Here, we describe the rational design and synthesis of peptide analogs of a natural PAS-targeting sequence that we recently discovered, aiming at increasing its activity against AChE. We also tested their radical scavenging and metal chelating properties. Our design strategy was based on the position-specific, computer-aided insertion of aromatic residues. The analog named as W3 showed a 30-fold higher inhibitory activity than the original sequence and an improved antioxidant activity. W3 is the most potent modified natural peptide against Electrophorus electricus AChE ever reported with an IC50 of 10.42 μM (± 1.02). In addition, it showed a radical scavenging activity of 47.00% ± 3.11 at 50 μM and 93.47% ± 1.53 at 400 μM. Since peptides are receiving increasing interest as drugs, we propose the W3 analog as an attractive sequence for the development of new peptide-based multitarget drugs for AD. Besides, this work sheds light on the importance of the aromatic residues in the modulation of AChE activity and their effect on the radical scavenging activity of a peptide.
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Soltan MA, Eldeen MA, Elbassiouny N, Kamel HL, Abdelraheem KM, El-Gayyed HA, Gouda AM, Sheha MF, Fayad E, Ali OAA, Ghany KAE, El-damasy DA, Darwish KM, Elhady SS, Sileem AE. In Silico Designing of a Multitope Vaccine against Rhizopus microsporus with Potential Activity against Other Mucormycosis Causing Fungi. Cells 2021; 10:3014. [PMID: 34831237 PMCID: PMC8616407 DOI: 10.3390/cells10113014] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 10/27/2021] [Accepted: 10/27/2021] [Indexed: 12/27/2022] Open
Abstract
During the current era of the COVID-19 pandemic, the dissemination of Mucorales has been reported globally, with elevated rates of infection in India, and because of the high rate of mortality and morbidity, designing an effective vaccine against mucormycosis is a major health priority, especially for immunocompromised patients. In the current study, we studied shared Mucorales proteins, which have been reported as virulence factors, and after analysis of several virulent proteins for their antigenicity and subcellular localization, we selected spore coat (CotH) and serine protease (SP) proteins as the targets of epitope mapping. The current study proposes a vaccine constructed based on top-ranking cytotoxic T lymphocyte (CTL), helper T lymphocyte (HTL), and B cell lymphocyte (BCL) epitopes from filtered proteins. In addition to the selected epitopes, β-defensins adjuvant and PADRE peptide were included in the constructed vaccine to improve the stimulated immune response. Computational tools were used to estimate the physicochemical and immunological features of the proposed vaccine and validate its binding with TLR-2, where the output data of these assessments potentiate the probability of the constructed vaccine to stimulate a specific immune response against mucormycosis. Here, we demonstrate the approach of potential vaccine construction and assessment through computational tools, and to the best of our knowledge, this is the first study of a proposed vaccine against mucormycosis based on the immunoinformatics approach.
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Affiliation(s)
- Mohamed A. Soltan
- Department of Microbiology and Immunology, Faculty of Pharmacy, Sinai University, Ismailia 41611, Egypt;
| | - Muhammad Alaa Eldeen
- Cell Biology, Histology & Genetics Division, Zoology Department, Faculty of Science, Zagazig University, Zagazig 44519, Egypt;
| | - Nada Elbassiouny
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Sinai University, Ismailia 41611, Egypt;
| | - Hasnaa L. Kamel
- Department of Microbiology and Immunology, Faculty of Pharmacy, Sinai University, Ismailia 41611, Egypt;
| | - Kareem M. Abdelraheem
- Department of Biochemistry, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt; (K.M.A.); (H.A.E.-G.)
| | - Hanaa Abd El-Gayyed
- Department of Biochemistry, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt; (K.M.A.); (H.A.E.-G.)
| | - Ahmed M. Gouda
- Department of Pharmacy Practice, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt;
| | - Mohammed F. Sheha
- Department of Biochemistry, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt;
| | - Eman Fayad
- Department of Biotechnology, Faculty of Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia;
| | - Ola A. Abu Ali
- Department of Chemistry, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia;
| | | | - Dalia A. El-damasy
- Department of Microbiology and Immunology, Faculty of Pharmacy, Egyptian Russian University, Cairo 11829, Egypt;
| | - Khaled M. Darwish
- Department of Medicinal Chemistry, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt;
| | - Sameh S. Elhady
- Department of Natural Products, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
| | - Ashraf E. Sileem
- Department of Chest Diseases, Faculty of Medicine, Zagazig University, Zagazig 44519, Egypt;
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131
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Bhattacharjee S, Bhattacharyya R. PRFF Peptide Mimic Interferes with Toxic Fibrin-Aβ 42 Interaction by Emulating the Aβ Binding Interface on Fibrinogen. ACS Chem Neurosci 2021; 12:4144-4152. [PMID: 34669381 DOI: 10.1021/acschemneuro.1c00519] [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: 01/22/2023] Open
Abstract
Cerebrovascular dysfunction is a common phenomenon in Alzheimer's patients, where fibrinogen is a major player. With the blood-brain barrier compromised, fibrinogen gains access to the brain, where its interaction with Aβ42 results in plasmin-resistant abnormal blood clots that are deposited in the cerebral blood vessels, a condition commonly encountered in Alzheimer's disease (AD) patients called cerebral amyloid angiopathy (CAA). So far, there have been no effective therapeutics available to combat AD-associated CAA. This study reports a 13-amino acid peptide (Pα-NPGRPEPGSAGTW) as a potential inhibitor of the fibrin-Aβ42 interaction along with the property to dissolve pre-existing plasmin-resistant abnormal clots. Strikingly, the identified sequence was found to be partially similar to a fragment of the fibrinogen α-chain reported to bind Aβ42, the plasmin-resistant fibrinogen fragment (PRFF). Mechanistically, Pα interacts with Aβ42 in place of fibrinogen, thus inhibiting the toxic fibrin-Aβ42 interaction. However, it does not interfere with normal fibrin polymerization.
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Affiliation(s)
- Sayan Bhattacharjee
- Structural Biology & Bio-Informatics Division, CSIR − Indian Institute of Chemical Biology, Kolkata 700032, India
| | - Rajanya Bhattacharyya
- Structural Biology & Bio-Informatics Division, CSIR − Indian Institute of Chemical Biology, Kolkata 700032, India
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132
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Fritz ZR, Schloss RS, Yarmush ML, Williams LJ. HSymM-guided engineering of the immunodominant p53 transactivation domain putative peptide antigen for improved binding to its anti-p53 monoclonal antibody. Bioorg Med Chem Lett 2021; 51:128341. [PMID: 34454062 PMCID: PMC8526406 DOI: 10.1016/j.bmcl.2021.128341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 08/17/2021] [Accepted: 08/22/2021] [Indexed: 02/07/2023]
Abstract
A novel engineering strategy to improve autoantibody detection with peptide fragments derived from the parent antigen is presented. The model system studied was the binding of the putative p53 TAD peptide antigen (residues 46-55) to its cognate anti-p53 antibody, ab28. Each engineered peptide contained the full decapeptide epitope and differed only in the flanking regions. Since minimal structural information was available to guide the design, a simple epitope:paratope binding model was applied. The Hidden Symmetry Model, which we recently reported, was used to guide peptide design and estimate per-residue contributions to interaction free energy as a function of added C- and N-terminal flanking peptides. Twenty-four peptide constructs were designed, synthesized, and assessed for binding affinity to ab28 by surface plasmon resonance, and a subset of these peptides were evaluated in a simulated immunoassay for limit of detection. Many peptides exhibited over 200-fold enhancements in binding affinity and improved limits of detection. The epitope was reevaluated and is proposed to be the undecapeptide corresponding to residues 45-55. HSymM calculated binding free energy and experimental data were found to be in good agreement (R2 > 0.75).
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Affiliation(s)
- Zachary R Fritz
- Department of Biomedical Engineering, Rutgers University, Piscataway, NJ 08854, United States
| | - Rene S Schloss
- Department of Biomedical Engineering, Rutgers University, Piscataway, NJ 08854, United States
| | - Martin L Yarmush
- Department of Biomedical Engineering, Rutgers University, Piscataway, NJ 08854, United States
| | - Lawrence J Williams
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, United States.
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Tariq MH, Bhatti R, Ali NF, Ashfaq UA, Shahid F, Almatroudi A, Khurshid M. Rational design of chimeric Multiepitope Based Vaccine (MEBV) against human T-cell lymphotropic virus type 1: An integrated vaccine informatics and molecular docking based approach. PLoS One 2021; 16:e0258443. [PMID: 34705829 PMCID: PMC8550388 DOI: 10.1371/journal.pone.0258443] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 09/27/2021] [Indexed: 01/03/2023] Open
Abstract
Human T-cell lymphotropic virus type 1 (HTLV-1) is an infectious virus that has been linked to adult T cell leukemia /lymphoma, aggressive CD4-T cell malignancy and many other immune-related medical illnesses. So far, no effective vaccine is known to combat HTLV-1, hence, the current research work was performed to design a potential multi-epitope-based subunit vaccine (MEBV) by adopting the latest methodology of reverse vaccinology. Briefly, three highly antigenic proteins (Glycoprotein, Accessory protein, and Tax protein) with no or minimal (<37%) similarity with human proteome were sorted out and potential B- and T-cell epitopes were forecasted from them. Highly antigenic, immunogenic, non-toxic, non-allergenic and overlapping epitopes were short-listed for vaccine development. The chosen T-cell epitopes displayed a strong binding affinity with their corresponding Human Leukocyte Antigen alleles and demonstrated 95.8% coverage of the world's population. Finally, nine Cytotoxic T Lymphocytes, six Helper T Lymphocytes and five Linear B Lymphocytes epitopes, joint through linkers and adjuvant, were exploited to design the final MEBV construct, comprising of 382 amino acids. The developed MEBV structure showed highly antigenic properties while being non-toxic, soluble, non-allergenic, and stable in nature. Moreover, disulphide engineering further enhanced the stability of the final vaccine protein. Additionally, Molecular docking analysis and Molecular Dynamics (MD) simulations confirmed the strong association between MEBV construct and human pathogenic immune receptor TLR-3. Repeated-exposure simulations and Immune simulations ensured the rapid antigen clearance and higher levels of cell-mediated immunity, respectively. Furthermore, MEBV codon optimization and in-silico cloning was carried out to confirm its augmented expression. Results of our experiments suggested that the proposed MEBV could be a potential immunogenic against HTLV-1; nevertheless, additional wet lab experiments are needed to elucidate our conclusion.
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Affiliation(s)
- Muhammad Hamza Tariq
- Atta ur Rehman School of Applied Bioscience, National University of Science and Technology, Islamabad, Pakistan
| | - Rashid Bhatti
- Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Nida Fatima Ali
- Atta ur Rehman School of Applied Bioscience, National University of Science and Technology, Islamabad, Pakistan
| | - Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Farah Shahid
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Ahmad Almatroudi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Mohsin Khurshid
- Department of Microbiology, Government College University Faisalabad, Faisalabad, Pakistan
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A Re-evaluation of the Free Energy Profiles for Cell-Penetrating Peptides Across DOPC Membranes. Int J Pept Res Ther 2021. [DOI: 10.1007/s10989-021-10301-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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135
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NPF activates a specific NPF receptor and regulates food intake in Pacific abalone Haliotis discus hannai. Sci Rep 2021; 11:20912. [PMID: 34686694 PMCID: PMC8536682 DOI: 10.1038/s41598-021-00238-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 10/07/2021] [Indexed: 01/13/2023] Open
Abstract
Neuropeptides function through G protein-coupled receptors (GPCRs) with high specificity, implying a significant degree of neuropeptide-GPCR coevolution. However, potential neuropeptide signaling systems in non-chordates are relatively elusive. We determined the specificity of the neuropeptide F (Hdh-NPF) signaling system with a cognate receptor (Hdh-NPFR) in the Pacific abalone, Haliotis discus hannai. Phylogenetic and exon–intron arrangement analyses of bilaterian NPF and the chordate ortholog NPY with their receptor sequences revealed a likely common ancestor, and Hdh-NPFR was similar to the NPYR2 subtype among the NPYR1, NPYR2, and NPYR5 subtypes. Among four Hdh-NPFR-related receptors, Hdh-NPFR specifically responded to Hdh-NPF peptide, supported by the dose–response luciferase reporter curve, intracellular Ca2+ mobilization, and phosphorylation of ERK1/2 and its inhibition with a protein kinase C inhibitor. Peptide fragmentations and shuffling of Hdh-NPF with human NPY could not activate the cellular response of Hdh-NPFR. Three-dimensional in silico modeling suggested that interaction of Hdh-NPF C-terminal amino acids with the extracellular loops of Hdh-NPFR is critical for Hdh-NPFR activation. In vivo injection of Hdh-NPF peptide increased food consumption, and knockdown of Hdh-NPF expression decreased food consumption in Pacific abalone. These findings provide evidence for co-evolution of the NPF/Y ligand-receptor system, enabling further research on mollusk orexigenic neuropeptides.
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Kumar A, Kumar P, Saumya KU, Giri R. Investigating the conformational dynamics of SARS-CoV-2 NSP6 protein with emphasis on non-transmembrane 91-112 & 231-290 regions. Microb Pathog 2021; 161:105236. [PMID: 34648928 PMCID: PMC8505028 DOI: 10.1016/j.micpath.2021.105236] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 12/05/2022]
Abstract
The NSP6 protein of SARS-CoV-2 is a transmembrane protein, with some regions lying outside the membrane. Besides a brief role of NSP6 in autophagosome formation, this is not studied significantly. Also, there is no structural information available to date. Based on the prediction by TMHMM server for transmembrane prediction, it is found that the N-terminal residues (1-11), middle region residues (91–112), and C-terminal residues (231–290) lies outside the membrane. Molecular Dynamics (MD) simulations showed that NSP6 consists of helical structures. In contrast, the membrane outside lying region (91–112) showed partial helicity, which was further used as a model and obtained disordered type conformation during 1.5 μs. Additionally, a 200ns simulation study of residues 231–290 have shown significant conformational changes. As compared to helical and beta-sheet conformations in its structure model, the 200ns simulation resulted in the loss of beta-sheet structures while helical regions remained intact. Further, we have experimentally characterized the residue 91–112 by using reductionist approaches. CD spectroscopy suggests that the NSP6 (91–112) is disordered-like region in isolation, which gains helical conformation in different biological mimic environmental conditions. These studies can be helpful to study NSP6 (91–112) interactions with host proteins, where different protein conformations might play a significant role. The present study adds up more information about the NSP6 protein aspect, which could be exploited for its host protein interaction and pathogenesis.
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Affiliation(s)
- Amit Kumar
- School of Basic Sciences, Indian Institute of Technology Mandi, VPO Kamand, Himachal Pradesh, 175005, India
| | - Prateek Kumar
- School of Basic Sciences, Indian Institute of Technology Mandi, VPO Kamand, Himachal Pradesh, 175005, India
| | - Kumar Udit Saumya
- School of Basic Sciences, Indian Institute of Technology Mandi, VPO Kamand, Himachal Pradesh, 175005, India
| | - Rajanish Giri
- School of Basic Sciences, Indian Institute of Technology Mandi, VPO Kamand, Himachal Pradesh, 175005, India.
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137
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Ong JH, Wong WL, Wong FC, Chai TT. Targeting PirA vp and PirB vp Toxins of Vibrio parahaemolyticus with Oilseed Peptides: An In Silico Approach. Antibiotics (Basel) 2021; 10:1211. [PMID: 34680792 PMCID: PMC8532646 DOI: 10.3390/antibiotics10101211] [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: 09/05/2021] [Revised: 09/28/2021] [Accepted: 09/28/2021] [Indexed: 01/18/2023] Open
Abstract
Acute hepatopancreatic necrosis disease (AHPND), caused by PirAvp- and PirBvp-releasing Vibrio parahaemolyticus strains, has resulted in massive mortality in shrimp aquaculture. Excessive use of antibiotics for AHPND management has led to antibiotic resistance, highlighting the urgency to search for alternatives. Using an in silico approach, we aimed to discover PirAvp/PirBvp-binding peptides from oilseed meals as alternatives to antibiotics. To search for peptides that remain intact in the shrimp digestive tract, and therefore would be available for toxin binding, we focused on peptides released from tryptic hydrolysis of 37 major proteins from seeds of hemp, pumpkin, rape, sesame, and sunflower. This yielded 809 peptides. Further screening led to 24 peptides predicted as being non-toxic to shrimp, fish, and humans, with thermal stability and low water solubility. Molecular docking on the 24 peptides revealed six dual-target peptides capable of binding to key regions responsible for complex formation on both PirAvp and PirBvp. The peptides (ISYVVQGMGISGR, LTFVVHGHALMGK, QSLGVPPQLGNACNLDNLDVLQPTETIK, ISTINSQTLPILSQLR, PQFLVGASSILR, and VQVVNHMGQK) are 1139-2977 Da in mass and 10-28 residues in length. Such peptides are potential candidates for the future development of peptide-based anti-AHPND agents which potentially mitigate V. parahaemolyticus pathogenesis by intercepting PirAvp/PirBvp complex formation.
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Affiliation(s)
- Joe-Hui Ong
- Department of Chemical Science, Faculty of Science, Universiti Tunku Abdul Rahman, Jalan Universiti, Bandar Barat, Kampar 31900, Perak, Malaysia; (J.-H.O.); (F.-C.W.)
| | - Wey-Lim Wong
- Department of Biological Science, Faculty of Science, Universiti Tunku Abdul Rahman, Jalan Universiti, Bandar Barat, Kampar 31900, Perak, Malaysia;
- Center for Agriculture and Food Research, Universiti Tunku Abdul Rahman, Jalan Universiti, Bandar Barat, Kampar 31900, Perak, Malaysia
| | - Fai-Chu Wong
- Department of Chemical Science, Faculty of Science, Universiti Tunku Abdul Rahman, Jalan Universiti, Bandar Barat, Kampar 31900, Perak, Malaysia; (J.-H.O.); (F.-C.W.)
- Center for Agriculture and Food Research, Universiti Tunku Abdul Rahman, Jalan Universiti, Bandar Barat, Kampar 31900, Perak, Malaysia
| | - Tsun-Thai Chai
- Department of Chemical Science, Faculty of Science, Universiti Tunku Abdul Rahman, Jalan Universiti, Bandar Barat, Kampar 31900, Perak, Malaysia; (J.-H.O.); (F.-C.W.)
- Center for Agriculture and Food Research, Universiti Tunku Abdul Rahman, Jalan Universiti, Bandar Barat, Kampar 31900, Perak, Malaysia
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Bukhari SNH, Jain A, Haq E, Khder MA, Neware R, Bhola J, Lari Najafi M. Machine Learning-Based Ensemble Model for Zika Virus T-Cell Epitope Prediction. JOURNAL OF HEALTHCARE ENGINEERING 2021; 2021:9591670. [PMID: 34631001 PMCID: PMC8500748 DOI: 10.1155/2021/9591670] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 08/23/2021] [Accepted: 08/29/2021] [Indexed: 12/12/2022]
Abstract
Zika virus (ZIKV), the causative agent of Zika fever in humans, is an RNA virus that belongs to the genus Flavivirus. Currently, there is no approved vaccine for clinical use to combat the ZIKV infection and contain the epidemic. Epitope-based peptide vaccines have a large untapped potential for boosting vaccination safety, cross-reactivity, and immunogenicity. Though many attempts have been made to develop vaccines for ZIKV, none of these have proved to be successful. Epitope-based peptide vaccines can act as powerful alternatives to conventional vaccines due to their low production cost, less reactogenic, and allergenic responses. For designing an effective and viable epitope-based peptide vaccine against this deadly virus, it is essential to select the antigenic T-cell epitopes since epitope-based vaccines are considered safe. The in silico machine-learning-based approach for ZIKV T-cell epitope prediction would save a lot of physical experimental time and efforts for speedy vaccine development compared to in vivo approaches. We hereby have trained a machine-learning-based computational model to predict novel ZIKV T-cell epitopes by employing physicochemical properties of amino acids. The proposed ensemble model based on a voting mechanism works by blending the predictions for each class (epitope or nonepitope) from each base classifier. Predictions obtained for each class by the individual classifier are summed up, and the class with the majority vote is predicted upon. An odd number of classifiers have been used to avoid the occurrence of ties in the voting. Experimentally determined ZIKV peptide sequences data set was collected from Immune Epitope Database and Analysis Resource (IEDB) repository. The data set consists of 3,519 sequences, of which 1,762 are epitopes and 1,757 are nonepitopes. The length of sequences ranges from 6 to 30 meter. For each sequence, we extracted 13 physicochemical features. The proposed ensemble model achieved sensitivity, specificity, Gini coefficient, AUC, precision, F-score, and accuracy of 0.976, 0.959, 0.993, 0.994, 0.989, 0.985, and 97.13%, respectively. To check the consistency of the model, we carried out five-fold cross-validation and an average accuracy of 96.072% is reported. Finally, a comparative analysis of the proposed model with existing methods has been carried out using a separate validation data set, suggesting the proposed ensemble model as a better model. The proposed ensemble model will help predict novel ZIKV vaccine candidates to save lives globally and prevent future epidemic-scale outbreaks.
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Affiliation(s)
| | - Amit Jain
- University Institute of Computing, Chandigarh University, Mohali, Punjab, India
| | - Ehtishamul Haq
- Department of Biotechnology, University of Kashmir, Srinagar, J & K, India
| | | | - Rahul Neware
- Department of Computing, Mathematics and Physics, Western Norway University of Applied Sciences, Bergen, Norway
| | - Jyoti Bhola
- Electronics & Communication Engineering Department, National Institute of Technology, Hamirpur, India
| | - Moslem Lari Najafi
- Pharmaceutical Science and Cosmetic Products Research Center, Kerman University of Medical Sciences, Kerman, Iran
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139
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Ascencio-Ibáñez JT, Bobay BG. Conserved Structural Motif Identified in Peptides That Bind to Geminivirus Replication Protein Rep. Biochemistry 2021; 60:2795-2809. [PMID: 34464102 DOI: 10.1021/acs.biochem.1c00408] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The geminivirus replication protein, Rep, has long been recognized as a high-value target for control of geminivirus infections as this protein is highly conserved and essential for viral replication and proliferation. In addition, inhibition of viral replication has been pursued through various antiviral strategies with varying degrees of success, including inhibitory peptides that target Rep. While much effort has centered around sequence characterization of the Rep protein and inhibitory peptides, detailed structural analysis has been missing. This study computationally investigated the presence of common structural features within these inhibitory peptides and if these features could inform if a particular peptide will bind Rep and/or interfere with viral replication. Molecular dynamics simulations of the inhibitory peptide library showed that simply possessing stable structural features does not inform interference of viral replication regardless of the binding of Rep. Additionally, nearly all known Rep inhibitory peptides sample a conserved β-sheet structural motif, possibly informing structure-function relationships in binding Rep. In particular, two peptides (A22 and A64) characterized by this structural motif were computationally docked against a wide variety of geminivirus Rep proteins to determine a mechanism of action. Computational docking revealed these peptides utilize a common Rep protein sequence motif for binding, HHN-x1/2-Q. The results identified residues in both Rep and the inhibitory peptides that play a significant role in the interaction, establishing the foundation for a rational structure-based design approach for the construction of both broadly reactive and geminivirus species-specific inhibitors.
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Affiliation(s)
- J Trinidad Ascencio-Ibáñez
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Benjamin G Bobay
- Department of Biochemistry, Duke University, Durham, North Carolina 27710, United States.,Department of Radiology, Duke University, Durham, North Carolina 27710, United States.,Duke University NMR Center, Duke University Medical Center, Durham, North Carolina 27710, United States
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140
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Devaux CA, Pinault L, Delerce J, Raoult D, Levasseur A, Frutos R. Spread of Mink SARS-CoV-2 Variants in Humans: A Model of Sarbecovirus Interspecies Evolution. Front Microbiol 2021; 12:675528. [PMID: 34616371 PMCID: PMC8488371 DOI: 10.3389/fmicb.2021.675528] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 09/03/2021] [Indexed: 01/08/2023] Open
Abstract
The rapid spread of SARS-CoV-2 variants has quickly spanned doubts and the fear about their ability escape vaccine protection. Some of these variants initially identified in caged were also found in humans. The claim that these variants exhibited lower susceptibility to antibody neutralization led to the slaughter of 17 million minks in Denmark. SARS-CoV-2 prevalence tests led to the discovery of infected farmed minks worldwide. In this study, we revisit the issue of the circulation of SARS-CoV-2 variants in minks as a model of sarbecovirus interspecies evolution by: (1) comparing human and mink angiotensin I converting enzyme 2 (ACE2) and neuropilin 1 (NRP-1) receptors; (2) comparing SARS-CoV-2 sequences from humans and minks; (3) analyzing the impact of mutations on the 3D structure of the spike protein; and (4) predicting linear epitope targets for immune response. Mink-selected SARS-CoV-2 variants carrying the Y453F/D614G mutations display an increased affinity for human ACE2 and can escape neutralization by one monoclonal antibody. However, they are unlikely to lose most of the major epitopes predicted to be targets for neutralizing antibodies. We discuss the consequences of these results for the rational use of SARS-CoV-2 vaccines.
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Affiliation(s)
- Christian A. Devaux
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU–Méditerranée Infection, Marseille, France
- CNRS, Marseille, France
- Fondation IHU–Méditerranée Infection, Marseille, France
| | - Lucile Pinault
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU–Méditerranée Infection, Marseille, France
| | - Jérémy Delerce
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU–Méditerranée Infection, Marseille, France
| | - Didier Raoult
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU–Méditerranée Infection, Marseille, France
| | - Anthony Levasseur
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU–Méditerranée Infection, Marseille, France
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Orlando M, Fortuna S, Oloketuyi S, Bajc G, Goldenzweig A, de Marco A. CDR1 Composition Can Affect Nanobody Recombinant Expression Yields. Biomolecules 2021; 11:biom11091362. [PMID: 34572576 PMCID: PMC8465892 DOI: 10.3390/biom11091362] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/10/2021] [Accepted: 09/13/2021] [Indexed: 01/03/2023] Open
Abstract
The isolation of nanobodies from pre-immune libraries by means of biopanning is a straightforward process. Nevertheless, the recovered candidates often require optimization to improve some of their biophysical characteristics. In principle, CDRs are not mutated because they are likely to be part of the antibody paratope, but in this work, we describe a mutagenesis strategy that specifically addresses CDR1. Its sequence was identified as an instability hot spot by the PROSS program, and the available structural information indicated that four CDR1 residues bound directly to the antigen. We therefore modified the loop flexibility with the addition of an extra glycine rather than by mutating single amino acids. This approach significantly increased the nanobody yields but traded-off with moderate affinity loss. Accurate modeling coupled with atomistic molecular dynamics simulations enabled the modifications induced by the glycine insertion and the rationale behind the engineering design to be described in detail.
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Affiliation(s)
- Marco Orlando
- Department of Biotechnology and Life Sciences, University of Insubria, Via J. H. Dunant 3, 21100 Varese, Italy;
| | - Sara Fortuna
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri 1, 34127 Trieste, Italy;
| | - Sandra Oloketuyi
- Lab of Environmental and Life Sciences, University of Nova Gorica, Vipavska cesta 13, Rožna Dolina, 5000 Nova Gorica, Slovenia;
| | - Gregor Bajc
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, 1000 Ljubljana, Slovenia;
| | - Adi Goldenzweig
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel;
| | - Ario de Marco
- Lab of Environmental and Life Sciences, University of Nova Gorica, Vipavska cesta 13, Rožna Dolina, 5000 Nova Gorica, Slovenia;
- Correspondence: ; Tel.: +386-(05)-3315295
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Liwo A, Czaplewski C, Sieradzan AK, Lipska AG, Samsonov SA, Murarka RK. Theory and Practice of Coarse-Grained Molecular Dynamics of Biologically Important Systems. Biomolecules 2021; 11:1347. [PMID: 34572559 PMCID: PMC8465211 DOI: 10.3390/biom11091347] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/03/2021] [Accepted: 09/09/2021] [Indexed: 12/16/2022] Open
Abstract
Molecular dynamics with coarse-grained models is nowadays extensively used to simulate biomolecular systems at large time and size scales, compared to those accessible to all-atom molecular dynamics. In this review article, we describe the physical basis of coarse-grained molecular dynamics, the coarse-grained force fields, the equations of motion and the respective numerical integration algorithms, and selected practical applications of coarse-grained molecular dynamics. We demonstrate that the motion of coarse-grained sites is governed by the potential of mean force and the friction and stochastic forces, resulting from integrating out the secondary degrees of freedom. Consequently, Langevin dynamics is a natural means of describing the motion of a system at the coarse-grained level and the potential of mean force is the physical basis of the coarse-grained force fields. Moreover, the choice of coarse-grained variables and the fact that coarse-grained sites often do not have spherical symmetry implies a non-diagonal inertia tensor. We describe selected coarse-grained models used in molecular dynamics simulations, including the most popular MARTINI model developed by Marrink's group and the UNICORN model of biological macromolecules developed in our laboratory. We conclude by discussing examples of the application of coarse-grained molecular dynamics to study biologically important processes.
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Affiliation(s)
- Adam Liwo
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland; (C.C.); (A.K.S.); (A.G.L.); (S.A.S.)
| | - Cezary Czaplewski
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland; (C.C.); (A.K.S.); (A.G.L.); (S.A.S.)
| | - Adam K. Sieradzan
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland; (C.C.); (A.K.S.); (A.G.L.); (S.A.S.)
| | - Agnieszka G. Lipska
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland; (C.C.); (A.K.S.); (A.G.L.); (S.A.S.)
| | - Sergey A. Samsonov
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland; (C.C.); (A.K.S.); (A.G.L.); (S.A.S.)
| | - Rajesh K. Murarka
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal 462066, MP, India;
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143
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Epitope-Based Immunoinformatic Approach on Heat Shock 70 kDa Protein Complex of Cryptococcus neoformans var. grubii. J Immunol Res 2021; 2021:9921620. [PMID: 34471644 PMCID: PMC8405342 DOI: 10.1155/2021/9921620] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 07/06/2021] [Accepted: 08/06/2021] [Indexed: 12/18/2022] Open
Abstract
Introduction Cryptococcosis is a ubiquitous opportunistic fungal disease caused by Cryptococcus neoformans var. grubii. It has high global morbidity and mortality among HIV patients and non-HIV carriers with 99% and 95%, respectively. Furthermore, the increasing prevalence of undesired toxicity profile of antifungal, multidrug-resistant organisms and the scarcity of FDA-authorized vaccines were the hallmark in the present days. This study was undertaken to design a reliable epitope-based peptide vaccine through targeting highly conserved immunodominant heat shock 70 kDa protein of Cryptococcus neoformans var. grubii that covers a considerable digit of the world population through implementing a computational vaccinology approach. Materials and Methods A total of 38 sequences of Cryptococcus neoformans var. grubii's heat shock 70 kDa protein were retrieved from the NCBI protein database. Different prediction tools were used to analyze the aforementioned protein at the Immune Epitope Database (IEDB) to discriminate the most promising T-cell and B-cell epitopes. The proposed T-cell epitopes were subjected to the population coverage analysis tool to compute the global population's coverage. Finally, the T-cell projected epitopes were ranked based on their binding scores and modes using AutoDock Vina software. Results and Discussion. The epitopes (ANYVQASEK, QSEKPKNVNPVI, SEKPKNVNPVI, and EKPKNVNPVI) had shown very strong binding affinity and immunogenic properties to B-cell. (FTQLVAAYL, YVYDTRGKL) and (FFGGKVLNF, FINAQLVDV, and FDYALVQHF) exhibited a very strong binding affinity to MHC-I and MHC-II, respectively, with high population coverage for each, while FYRQGAFEL has shown promising results in terms of its binding profile to MHC-II and MHC-I alleles and good strength of binding when docked with HLA-C∗12:03. In addition, there is massive global population coverage in the three coverage modes. Accordingly, our in silico vaccine is expected to be the future epitope-based peptide vaccine against Cryptococcus neoformans var. grubii that covers a significant figure of the entire world citizens.
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Soltan MA, Eldeen MA, Elbassiouny N, Mohamed I, El-damasy DA, Fayad E, Abu Ali OA, Raafat N, Eid RA, Al-Karmalawy AA. Proteome Based Approach Defines Candidates for Designing a Multitope Vaccine against the Nipah Virus. Int J Mol Sci 2021; 22:ijms22179330. [PMID: 34502239 PMCID: PMC8431361 DOI: 10.3390/ijms22179330] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 08/24/2021] [Accepted: 08/26/2021] [Indexed: 02/05/2023] Open
Abstract
Nipah virus is one of the most harmful emerging viruses with deadly effects on both humans and animals. Because of the severe outbreaks, in 2018, the World Health Organization focused on the urgent need for the development of effective solutions against the virus. However, up to date, there is no effective vaccine against the Nipah virus in the market. In the current study, the complete proteome of the Nipah virus (nine proteins) was analyzed for the antigenicity score and the virulence role of each protein, where we came up with fusion glycoprotein (F), glycoprotein (G), protein (V), and protein (W) as the candidates for epitope prediction. Following that, the multitope vaccine was designed based on top-ranking CTL, HTL, and BCL epitopes from the selected proteins. We used suitable linkers, adjuvant, and PADRE peptides to finalize the constructed vaccine, which was analyzed for its physicochemical features, antigenicity, toxicity, allergenicity, and solubility. The designed vaccine passed these assessments through computational analysis and, as a final step, we ran a docking analysis between the designed vaccine and TLR-3 and validated the docked complex through molecular dynamics simulation, which estimated a strong binding and supported the nomination of the designed vaccine as a putative solution for Nipah virus. Here, we describe the computational approach for design and analysis of this vaccine.
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Affiliation(s)
- Mohamed A. Soltan
- Department of Microbiology and Immunology, Faculty of Pharmacy, Sinai University, Ismailia 41611, Egypt;
| | - Muhammad Alaa Eldeen
- Cell Biology, Histology & Genetics Division, Zoology Department, Faculty of Science, Zagazig University, Zagazig 44519, Egypt;
| | - Nada Elbassiouny
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Sinai University, Ismailia 41611, Egypt;
| | - Ibrahim Mohamed
- Department of Microbiology and Immunology, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt;
| | - Dalia A. El-damasy
- Department of Microbiology and Immunology, Faculty of Pharmacy, Egyptian Russian University, Cairo 11829, Egypt;
| | - Eman Fayad
- Department of Biotechnology, Faculty of Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia;
| | - Ola A. Abu Ali
- Department of Chemistry, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia;
| | - Nermin Raafat
- Department of Medical Biochemistry, Faculty of Medicine, Zagazig University, Zagazig 44519, Egypt;
| | - Refaat A. Eid
- Department of Pathology, College of Medicine, King Khalid University, Abha 12573, Saudi Arabia;
| | - Ahmed A. Al-Karmalawy
- Department of Pharmaceutical Medicinal Chemistry, Faculty of Pharmacy, Horus University-Egypt, New Damietta 34518, Egypt
- Correspondence: ; Tel.: +20-109-214-7330
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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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HMP-S7 Is a Novel Anti-Leukemic Peptide Discovered from Human Milk. Biomedicines 2021; 9:biomedicines9080981. [PMID: 34440185 PMCID: PMC8394283 DOI: 10.3390/biomedicines9080981] [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: 07/12/2021] [Revised: 07/29/2021] [Accepted: 08/06/2021] [Indexed: 01/17/2023] Open
Abstract
Chemotherapy in childhood leukemia is associated with late morbidity in leukemic survivors, while certain patient subsets are relatively resistant to standard chemotherapy. It is therefore important to identify new agents with sensitivity and selectivity towards leukemic cells, while having less systemic toxicity. Peptide-based therapeutics has gained a great deal of attention during the last few years. Here, we used an integrative workflow combining mass spectrometric peptide library construction, in silico anticancer peptide screening, and in vitro leukemic cell studies to discover a novel anti-leukemic peptide having 3+ charges and an alpha helical structure, namely HMP-S7, from human breast milk. HMP-S7 showed cytotoxic activity against four distinct leukemic cell lines in a dose-dependent manner but had no effect on solid malignancies or representative normal cells. HMP-S7 induced leukemic cell death by penetrating the plasma membrane to enter the cytoplasm and cause the leakage of lactate dehydrogenase, thus acting in a membranolytic manner. Importantly, HMP-S7 exhibited anti-leukemic effects against patient-derived leukemic cells ex vivo. In conclusion, HMP-S7 is a selective anti-leukemic peptide with promise, which requires further validation in preclinical and clinical studies.
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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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148
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Hydrophobic Residues Confer the Helicity and Membrane Permeability of Ocellatin-1 Antimicrobial Peptide Scaffold Towards Therapeutics. Int J Pept Res Ther 2021. [DOI: 10.1007/s10989-021-10265-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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149
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Tiwari P, Wu R, Metternich JB, Zenobi R. Transition Metal Ion FRET in the Gas Phase: A 10-40 Å Range Molecular Ruler for Mass-Selected Biomolecular Ions. J Am Chem Soc 2021; 143:11291-11295. [PMID: 34291949 DOI: 10.1021/jacs.1c01915] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Structural studies of mass-selected biomolecules in the gas phase can reveal their intrinsic properties and provide useful benchmarks for biomolecular modeling. Here, we report the first evidence of transition metal ion FRET (tmFRET) in the gas phase and its application to measure short (10-40 Å) biomolecular backbone distances. The measured FRET efficiencies in rhodamine dye (donor) labeled helical peptides complexed with Cu2+ ions (acceptor) decreased with increasing donor - acceptor distances, confirming the occurrence of tmFRET. The distances estimated for similar peptide sequences from the FRET efficiencies were consistently longer in the gas phase compared to those reported in solution, indicating an expanded structure and a possible loss of helicity.
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Affiliation(s)
- Prince Tiwari
- Department of Chemistry and Applied Biosciences, ETH Zürich Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Ri Wu
- Department of Chemistry and Applied Biosciences, ETH Zürich Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Jonas B Metternich
- Department of Chemistry and Applied Biosciences, ETH Zürich Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences, ETH Zürich Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
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150
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Kanumuri R, Chelluboyina AK, Biswal J, Vignesh R, Pandian J, Venu A, Vaishnavi B, Leena DJ, Jeyaraman J, Ganesan K, Aradhyam GK, Venkatraman G, Rayala SK. Small peptide inhibitor from the sequence of RUNX3 disrupts PAK1-RUNX3 interaction and abrogates its phosphorylation-dependent oncogenic function. Oncogene 2021; 40:5327-5341. [PMID: 34253860 DOI: 10.1038/s41388-021-01927-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 06/09/2021] [Accepted: 06/24/2021] [Indexed: 02/06/2023]
Abstract
P21 Activated Kinase 1 (PAK1) is an oncogenic serine/threonine kinase known to play a significant role in the regulation of cytoskeleton and cell morphology. Runt-related transcription factor 3 (RUNX3) was initially known for its tumor suppressor function, but recent studies have reported the oncogenic role of RUNX3 in various cancers. Previous findings from our laboratory provided evidence that Threonine 209 phosphorylation of RUNX3 acts as a molecular switch in dictating the tissue-specific dualistic functions of RUNX3 for the first time. Based on these proofs and to explore the translational significance of these findings, we designed a small peptide (RMR) from the protein sequence of RUNX3 flanking the Threonine 209 phosphorylation site. The selection of this specific peptide from multiple possible peptides was based on their binding energies, hydrogen bonding, docking efficiency with the active site of PAK1 and their ability to displace PAK1-RUNX3 interaction in our prediction models. We found that this peptide is stable both in in vitro and in vivo conditions, not toxic to normal cells and inhibits the Threonine 209 phosphorylation in RUNX3 by PAK1. We also tested the efficacy of this peptide to block the RUNX3 Threonine 209 phosphorylation mediated tumorigenic functions in in vitro cell culture models, patient-derived explant (PDE) models and in in vivo tumor xenograft models. These results proved that this peptide has the potential to be developed as an efficient therapeutic molecule for targeting RUNX3 Threonine 209 phosphorylation-dependent tumor phenotypes.
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Affiliation(s)
- Rahul Kanumuri
- Department of Biotechnology, Indian Institute of technology Madras (IITM), Chennai, Tamilnadu, India
- Department of Human Genetics, Sri Ramachandra Faculty of Biomedical Sciences & Technology, Sri Ramachandra Institute of Higher Education & Research (Deemed to be University), Porur, Chennai, Tamilnadu, India
| | - Aruna Kumar Chelluboyina
- Department of Biotechnology, Indian Institute of technology Madras (IITM), Chennai, Tamilnadu, India
- Division of General Medical Sciences - Oncology, Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Jayashree Biswal
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, India
| | - Ravichandran Vignesh
- Department of Biotechnology, Indian Institute of technology Madras (IITM), Chennai, Tamilnadu, India
| | - Jaishree Pandian
- Unit of Excellence in Cancer Genetics, Department of Genetics, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
| | - Akkanapally Venu
- Department of Human Genetics, Sri Ramachandra Faculty of Biomedical Sciences & Technology, Sri Ramachandra Institute of Higher Education & Research (Deemed to be University), Porur, Chennai, Tamilnadu, India
| | - B Vaishnavi
- Department of Human Genetics, Sri Ramachandra Faculty of Biomedical Sciences & Technology, Sri Ramachandra Institute of Higher Education & Research (Deemed to be University), Porur, Chennai, Tamilnadu, India
| | - D J Leena
- Department of Pathology, Sri Ramachandra Institute of Higher Education & Research (Deemed to be University), Porur, Chennai, Tamilnadu, India
| | - Jeyakanthan Jeyaraman
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, India
| | - Kumaresan Ganesan
- Unit of Excellence in Cancer Genetics, Department of Genetics, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
| | - Gopala Krishna Aradhyam
- Department of Biotechnology, Indian Institute of technology Madras (IITM), Chennai, Tamilnadu, India
| | - Ganesh Venkatraman
- Department of Human Genetics, Sri Ramachandra Faculty of Biomedical Sciences & Technology, Sri Ramachandra Institute of Higher Education & Research (Deemed to be University), Porur, Chennai, Tamilnadu, India.
| | - Suresh K Rayala
- Department of Biotechnology, Indian Institute of technology Madras (IITM), Chennai, Tamilnadu, India.
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