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The Unfolded-Protein Response Triggers the Arthropod Immune Deficiency Pathway. mBio 2022; 13:e0070322. [PMID: 35862781 PMCID: PMC9426425 DOI: 10.1128/mbio.00703-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The insect immune deficiency (IMD) pathway is a defense mechanism that senses and responds to Gram-negative bacteria. Ticks lack genes encoding upstream components that initiate the IMD pathway. Despite this deficiency, core signaling molecules are present and functionally restrict tick-borne pathogens. The molecular events preceding activation remain undefined. Here, we show that the unfolded-protein response (UPR) initiates the IMD network. The endoplasmic reticulum (ER) stress receptor IRE1α is phosphorylated in response to tick-borne bacteria but does not splice the mRNA encoding XBP1. Instead, through protein modeling and reciprocal pulldowns, we show that Ixodes IRE1α complexes with TRAF2. Disrupting IRE1α-TRAF2 signaling blocks IMD pathway activation and diminishes the production of reactive oxygen species. Through in vitro, in vivo, and ex vivo techniques, we demonstrate that the UPR-IMD pathway circuitry limits the Lyme disease-causing spirochete Borrelia burgdorferi and the rickettsial agents Anaplasma phagocytophilum and A. marginale (anaplasmosis). Altogether, our study uncovers a novel linkage between the UPR and the IMD pathway in arthropods. IMPORTANCE The ability of an arthropod to harbor and transmit pathogens is termed "vector competency." Many factors influence vector competency, including how arthropod immune processes respond to the microbe. Divergences in innate immunity between arthropods are increasingly being reported. For instance, although ticks lack genes encoding key upstream molecules of the immune deficiency (IMD) pathway, it is still functional and restricts causative agents of Lyme disease (Borrelia burgdorferi) and anaplasmosis (Anaplasma phagocytophilum). How the IMD pathway is activated in ticks without classically defined pathway initiators is not known. Here, we found that a cellular stress response network, the unfolded-protein response (UPR), functions upstream to induce the IMD pathway and restrict transmissible pathogens. Collectively, this explains how the IMD pathway can be activated in the absence of canonical pathway initiators. Given that the UPR is highly conserved, UPR-initiated immunity may be a fundamental principle impacting vector competency across arthropods.
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202
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Wu X, Qiu R, Yi W, Chen J, Zhang Z, Zhang J, Zhu Z. Structure-based analysis and rational design of human peroxiredoxin-1's C-terminus-derived peptides to target sulfiredoxin-1 in pancreatic cancer. Biophys Chem 2022; 288:106857. [PMID: 35901662 DOI: 10.1016/j.bpc.2022.106857] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 07/04/2022] [Accepted: 07/14/2022] [Indexed: 11/18/2022]
Abstract
Human peroxiredoxin (PRX) family of antioxidant enzymes reduces hydrogen peroxide and alkyl hydroperoxide involved in the redox signaling, among which the widely documented PRX1 is a versatile molecule regulating cell growth, differentiation and apoptosis, and has been implicated in the tumorigensis of pancreatic cancer. In this study, we systematically examined the complex crystal structure of PRX1 with its cognate interacting partner sulfiredoxin-1 (SRX1) at molecular level, and found that the PRX1-SRX1 association is a typical peptide-mediated protein-protein interaction, where a 18-mer C-terminal tail (CTT) segment of PRX1 was identified to be primarily responsible for the interaction, which contributes ~80% and ~ 55% to the total binding potency of SRX1 to PRX1 monomer and homodimer, respectively. We also demonstrated that the SRX1 exhibits a strong global selectivity for PRX1 CTT tail over other PRX family proteins. Next, the intermolecular interaction between PRX1 CTT tail and SRX1 was investigated at structural, energetic and dynamic levels, from which a 9-mer core region of PRX1 CTT tail was defined as the SRX1-binding hotspot. Biophysical assays substantiated that the CTT and CTTc peptides (out of PRX1 protein context) can bind in an independent manner and possess a close affinity to SRX1. Based on the CTTc sketch a computational combinatorial library consisting of 216 designed peptide derivatives was rationally generated, from which the top-5 hits were found to have comparable affinity with CTT peptide and improved affinity relative to CTTc peptide. They can be used as structurally reduced lead molecular entities to further develop new peptidic agents for therapeutic purpose to disrupt the native PRX1-SRX1 interaction by competing with PRX1 CTT tail for the peptide-binding pocket of SRX1.
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Affiliation(s)
- Xiaoqiong Wu
- Department of Gastroenterology, Yueyang People's Hospital, the Affilinated Hospital of Hunan Normal University, Yueyang 414022, China.
| | - Rongyuan Qiu
- Department of Gastroenterology, Yueyang People's Hospital, the Affilinated Hospital of Hunan Normal University, Yueyang 414022, China
| | - Wei Yi
- Department of Gastroenterology, Yueyang People's Hospital, the Affilinated Hospital of Hunan Normal University, Yueyang 414022, China
| | - Juan Chen
- Department of Gastroenterology, Yueyang People's Hospital, the Affilinated Hospital of Hunan Normal University, Yueyang 414022, China
| | - Zhou Zhang
- Department of Gastroenterology, Yueyang People's Hospital, the Affilinated Hospital of Hunan Normal University, Yueyang 414022, China
| | - Ji Zhang
- Department of Gastroenterology, Yueyang People's Hospital, the Affilinated Hospital of Hunan Normal University, Yueyang 414022, China
| | - Zhiyuan Zhu
- Suzhou QingYaQiRui Biotechonology Co. Ltd, Suzhou 215100, China
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203
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Mitra A, Acharya K, Bhattacharya A. Evolutionary analysis of globin domains from kinetoplastids. Arch Microbiol 2022; 204:493. [PMID: 35841431 DOI: 10.1007/s00203-022-03107-1] [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: 02/14/2022] [Revised: 06/14/2022] [Accepted: 06/24/2022] [Indexed: 11/25/2022]
Abstract
Globin (Gb) domains function in sensing gaseous ligands like oxygen and nitric oxide. In recent years, Gb domain containing heme binding adenylate cyclases (OsAC or GbAC) emerged as significant modulator of Leishmania response to hypoxia and oxidative stress. During progression of life cycle stages, kinetoplastids experience altered condition in insect vectors or other hosts. Moreover, marked diversity in life style has been accounted among kinetoplastids. Distribution and abundance of Gb-domains vary between different groups of kinetoplastids. While in bodonoids, Gbs are not combined with any other functional domains, in trypanosomatids it is either fused with adenylate cyclase (AC) or oxidoreductase (OxR) domains. In salivarian trypanosomatids and Leishmania (Viannia) subtypes, no gene product featuring Gbs can be identified. In this context, evolution of Gb-domains in kinetoplastids was explored. GbOxR derived Gbs clustered with bacterial flavohemoglobins (fHb) including one fHb from Advenella, an endosymbiont of monoxeneous trypanosomatids. Codon adaptation and other evolutionary analysis suggested that OsAC (LmjF.28.0090), the solitary Gb-domain featuring gene product in Leishmania, was acquired via possible horizontal gene transfer. Substantial functional divergence was estimated between orthologues of genes encoding GbAC or GbOxR; an observation also reflected in structural alignment and heme-binding residue predictions. Orthologue-paralogue and synteny analysis indicated genomic reduction in GbOxR and GbAC loci for dixeneous trypanosomatids.
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Affiliation(s)
- Akash Mitra
- Department of Microbiology, Adamas University, Barasat-Barrackpore Rd, Kolkata, 700126, India.,Stem Cells and Regenerative Medicine Centre, Yenepoya Research Centre, Mangalore, 575018, India
| | - Kusumita Acharya
- Department of Microbiology, Adamas University, Barasat-Barrackpore Rd, Kolkata, 700126, India
| | - Arijit Bhattacharya
- Department of Microbiology, Adamas University, Barasat-Barrackpore Rd, Kolkata, 700126, India.
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Combing Immunoinformatics with Pangenome Analysis To Design a Multiepitope Subunit Vaccine against Klebsiella pneumoniae K1, K2, K47, and K64. Microbiol Spectr 2022; 10:e0114822. [PMID: 35863000 PMCID: PMC9431259 DOI: 10.1128/spectrum.01148-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Klebsiella pneumoniae is an opportunistic Gram-negative bacterium that has become a leading causative agent of nosocomial infections, mainly infecting patients with immunosuppressive diseases. Capsular (K) serotypes K1, K2, K47, and K64 are commonly associated with higher virulence (hypervirulent Klebsiella pneumoniae), and more threateningly, isolates belonging to the last two K serotypes are also frequently associated with resistance to carbapenem (hypervirulent carbapenem-resistant Klebsiella pneumoniae). The prevalence of these isolates has posed significant threats to human health, and there are no appropriate therapies available against them. Therefore, in this study, a method combining immunoinformatics and pangenome analysis was applied for contriving a multiepitope subunit vaccine against these four threatening serotypes. To obtain cross-protection, 12 predicted conserved antigens were screened from the core genome of 274 complete Klebsiella pneumoniae genomes (KL1, KL2, KL47, and KL64), from which the epitopes of T and B cells were extracted for vaccine construction. In addition, the immunological properties, the interaction with Toll-like receptors, and the stability in a simulative humoral environment were evaluated by immunoinformatics methods, molecular docking, and molecular dynamics simulation. All of these evaluations indicated the potency of this constructed vaccine to be an effective therapeutic agent. Lastly, the cDNA of the designed vaccine was optimized and ligated to pET-28a(+) for expression vector construction. Overall, our research provides a newly cross-protective control strategy against these troublesome pathogens and paves the way for the development of a safe and effective vaccine. IMPORTANCEKlebsiella pneumoniae is an opportunistic Gram-negative bacterium that has become a leading causative agent of nosocomial infections. Among the numerous capsular serotypes, K1, K2, K47, and K64 are commonly associated with higher virulence (hypervirulent K. pneumoniae). More threateningly, the last two serotypes are frequently associated with resistance to carbapenem (hypervirulent carbapenem-resistant K. pneumoniae). However, there is currently no therapeutic agent or vaccine specifically against these isolates. Therefore, development of a vaccine against these pathogens is very essential. In this study, for the first time, a method combining pangenome analysis, reverse vaccinology, and immunoinformatics was applied for contriving a multiepitope subunit vaccine against K. pneumoniae isolates of K1, K2, K47, and K64. Also, the immunological properties of the constructed vaccine were evaluated and its high potency was revealed. Overall, our research will pave the way for the vaccine development against these four threatening capsular serotypes of K. pneumoniae.
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Choi YJ, Lee Y, Lin Y, Heo Y, Lee YH, Song K. The Multivalent Polyampholyte Domain of Nst1, a P-Body-Associated Saccharomyces cerevisiae Protein, Provides a Platform for Interacting with P-Body Components. Int J Mol Sci 2022; 23:ijms23137380. [PMID: 35806385 PMCID: PMC9266425 DOI: 10.3390/ijms23137380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/29/2022] [Accepted: 06/29/2022] [Indexed: 12/10/2022] Open
Abstract
The condensation of nuclear promyelocytic leukemia bodies, cytoplasmic P-granules, P-bodies (PBs), and stress granules is reversible and dynamic via liquid–liquid phase separation. Although each condensate comprises hundreds of proteins with promiscuous interactions, a few key scaffold proteins are required. Essential scaffold domain sequence elements, such as poly-Q, low-complexity regions, oligomerizing domains, and RNA-binding domains, have been evaluated to understand their roles in biomolecular condensation processes. However, the underlying mechanisms remain unclear. We analyzed Nst1, a PB-associated protein that can intrinsically induce PB component condensations when overexpressed. Various Nst1 domain deletion mutants with unique sequence distributions, including intrinsically disordered regions (IDRs) and aggregation-prone regions, were constructed based on structural predictions. The overexpression of Nst1 deletion mutants lacking the aggregation-prone domain (APD) significantly inhibited self-condensation, implicating APD as an oligomerizing domain promoting self-condensation. Remarkably, cells overexpressing the Nst1 deletion mutant of the polyampholyte domain (PD) in the IDR region (Nst1∆PD) rarely accumulate endogenous enhanced green fluorescent protein (EGFP)-tagged Dcp2. However, Nst1∆PD formed self-condensates, suggesting that Nst1 requires PD to interact with Dcp2, regardless of its self-condensation. In Nst1∆PD-overexpressing cells treated with cycloheximide (CHX), Dcp2, Xrn1, Dhh1, and Edc3 had significantly diminished condensation compared to those in CHX-treated Nst1-overexpressing cells. These observations suggest that the PD of the IDR in Nst1 functions as a hub domain interacting with other PB components.
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Affiliation(s)
- Yoon-Jeong Choi
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea; (Y.-J.C.); (Y.L.)
| | - Yujin Lee
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea; (Y.-J.C.); (Y.L.)
| | - Yuxi Lin
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute (KBSI), Chungbuk 28119, Korea; (Y.L.); (Y.H.); (Y.-H.L.)
| | - Yunseok Heo
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute (KBSI), Chungbuk 28119, Korea; (Y.L.); (Y.H.); (Y.-H.L.)
| | - Young-Ho Lee
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute (KBSI), Chungbuk 28119, Korea; (Y.L.); (Y.H.); (Y.-H.L.)
- Department of Bio-Analytical Science, University of Science and Technology (UST), Daejeon 34113, Korea
- Graduate School of Analytical Science and Technology (GRAST), Chungnam National University (CNU), Daejeon 34134, Korea
| | - Kiwon Song
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea; (Y.-J.C.); (Y.L.)
- Correspondence: ; Tel.: +82-2-2123-2705; Fax: +82-2-362-9897
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206
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Arias‐Gaguancela O, Adhikari B, Aziz M, Chapman KD. Enhanced seedling growth by 3- n-pentadecylphenolethanolamide is mediated by fatty acid amide hydrolases in upland cotton ( Gossypium hirsutum L.). PLANT DIRECT 2022; 6:e421. [PMID: 35844778 PMCID: PMC9277032 DOI: 10.1002/pld3.421] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 06/16/2022] [Accepted: 06/19/2022] [Indexed: 05/25/2023]
Abstract
Fatty acid amide hydrolase (FAAH) is a conserved amidase that is known to modulate the levels of endogenous N-acylethanolamines (NAEs) in both plants and animals. The activity of FAAH is enhanced in vitro by synthetic phenoxyacylethanolamides resulting in greater hydrolysis of NAEs. Previously, 3-n-pentadecylphenolethanolamide (PDP-EA) was shown to exert positive effects on the development of Arabidopsis seedlings by enhancing Arabidopsis FAAH (AtFAAH) activity. However, there is little information regarding FAAH activity and the impact of PDP-EA in the development of seedlings of other plant species. Here, we examined the effects of PDP-EA on growth of upland cotton (Gossypium hirsutum L. cv Coker 312) seedlings including two lines of transgenic seedlings overexpressing AtFAAH. Independent transgenic events showed accelerated true-leaf emergence compared with non-transgenic controls. Exogenous applications of PDP-EA led to increases in overall seedling growth in AtFAAH transgenic lines. These enhanced-growth phenotypes coincided with elevated FAAH activities toward NAEs and NAE oxylipins. Conversely, the endogenous contents of NAEs and NAE-oxylipin species, especially linoleoylethanolamide and 9-hydroxy linoleoylethanolamide, were lower in PDP-EA treated seedlings than in controls. Further, transcripts for endogenous cotton FAAH genes were increased following PDP-EA exposure. Collectively, our data corroborate that the enhancement of FAAH enzyme activity by PDP-EA stimulates NAE-hydrolysis and that this results in enhanced growth in seedlings of a perennial crop species, extending the role of NAE metabolism in seedling development beyond the model annual plant species, Arabidopsis thaliana.
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Affiliation(s)
- Omar Arias‐Gaguancela
- BioDiscovery Institute, Department of Biological SciencesUniversity of North TexasDentonTXUSA
| | | | - Mina Aziz
- BioDiscovery Institute, Department of Biological SciencesUniversity of North TexasDentonTXUSA
| | - Kent D. Chapman
- BioDiscovery Institute, Department of Biological SciencesUniversity of North TexasDentonTXUSA
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207
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Design of a Multiepitope Vaccine against Chicken Anemia Virus Disease. Viruses 2022; 14:v14071456. [PMID: 35891436 PMCID: PMC9318905 DOI: 10.3390/v14071456] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/22/2022] [Accepted: 06/24/2022] [Indexed: 11/23/2022] Open
Abstract
Chicken anemia virus (CAV) causes severe clinical and sub-clinical infection in poultry globally and thus leads to economic losses. The drawbacks of the commercially available vaccines against CAV disease signal the need for a novel, safe, and effective vaccine design. In this study, a multiepitope vaccine (MEV) consisting of T-cell and B-cell epitopes from CAV viral proteins (VP1 and VP2) was computationally constructed with the help of linkers and adjuvant. The 3D model of the MEV construct was refined and validated by different online bioinformatics tools. Molecular docking showed stable interaction of the MEV construct with TLR3, and this was confirmed by Molecular Dynamics Simulation. Codon optimization and in silico cloning of the vaccine in pET-28a (+) vector also showed its potential expression in the E. coli K12 system. The immune simulation also indicated the ability of this vaccine to induce an effective immune response against this virus. Although the vaccine in this study was computationally constructed and still requires further in vivo study to confirm its effectiveness, this study marks a very important step towards designing a potential vaccine against CAV disease.
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208
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Rahbar MR, Mubarak SMH, Hessami A, Khalesi B, Pourzardosht N, Khalili S, Zanoos KA, Jahangiri A. A unique antigen against SARS-CoV-2, Acinetobacter baumannii, and Pseudomonas aeruginosa. Sci Rep 2022; 12:10852. [PMID: 35760825 PMCID: PMC9237110 DOI: 10.1038/s41598-022-14877-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 06/14/2022] [Indexed: 02/07/2023] Open
Abstract
The recent outbreak of COVID-19 has increased hospital admissions, which could elevate the risk of nosocomial infections, such as A. baumannii and P. aeruginosa infections. Although effective vaccines have been developed against SARS-CoV-2, no approved treatment option is still available against antimicrobial-resistant strains of A. baumannii and P. aeruginosa. In the current study, an all-in-one antigen was designed based on an innovative, state-of-the-art strategy. In this regard, experimentally validated linear epitopes of spike protein (SARS-CoV-2), OmpA (A. baumannii), and OprF (P. aeruginosa) were selected to be harbored by mature OmpA as a scaffold. The selected epitopes were used to replace the loops and turns of the barrel domain in OmpA; OprF311–341 replaced the most similar sequence within the OmpA, and three validated epitopes of OmpA were retained intact. The obtained antigen encompasses five antigenic peptides of spike protein, which are involved in SARS-CoV-2 pathogenicity. One of these epitopes, viz. QTQTNSPRRARSV could trigger antibodies preventing super-antigenic characteristics of spike and alleviating probable autoimmune responses. The designed antigen could raise antibodies neutralizing emerging variants of SARS-CoV-2 since at least two epitopes are consensus. In conclusion, the designed antigen is expected to raise protective antibodies against SARS-CoV-2, A. baumannii, and P. aeruginosa.
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Affiliation(s)
- Mohammad Reza Rahbar
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Shaden M H Mubarak
- Department of Clinical Laboratory Science, Faculty of Pharmacy, University of Kufa, Najaf, Iraq
| | - Anahita Hessami
- School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Bahman Khalesi
- Department of Research and Production of Poultry Viral Vaccine, Razi Vaccine and Serum Research Institute, Agricultural Research Education and Extension Organization, Karaj, Iran
| | - Navid Pourzardosht
- Biochemistry Department, Guilan University of Medical Sciences, Rasht, Iran
| | - Saeed Khalili
- Department of Biology Sciences, Shahid Rajaee Teacher Training University, Tehran, Iran
| | - Kobra Ahmadi Zanoos
- Young Researchers Club, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Abolfazl Jahangiri
- Applied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Vanak Sq. Molasadra St., P.O. Box 1435915371, Tehran, Iran.
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209
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Gomes LGR, Rodrigues TCV, Jaiswal AK, Santos RG, Kato RB, Barh D, Alzahrani KJ, Banjer HJ, Soares SDC, Azevedo V, Tiwari S. In Silico Designed Multi-Epitope Immunogen “Tpme-VAC/LGCM-2022” May Induce Both Cellular and Humoral Immunity against Treponema pallidum Infection. Vaccines (Basel) 2022; 10:vaccines10071019. [PMID: 35891183 PMCID: PMC9320004 DOI: 10.3390/vaccines10071019] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/21/2022] [Accepted: 06/23/2022] [Indexed: 01/16/2023] Open
Abstract
Syphilis, a sexually transmitted infection caused by the spirochete Treponema pallidum, has seen a resurgence over the past years. T. pallidum is capable of early dissemination and immune evasion, and the disease continues to be a global healthcare burden. The purpose of this study was to design a multi-epitope immunogen through an immunoinformatics-based approach. Multi-epitope immunogens constitute carefully selected epitopes belonging to conserved and essential bacterial proteins. Several physico-chemical characteristics, such as antigenicity, allergenicity, and stability, were determined. Further, molecular docking and dynamics simulations were performed, ensuring binding affinity and stability between the immunogen and TLR-2. An in silico cloning was performed using the pET-28a(+) vector and codon adaptation for E. coli. Finally, an in silico immune simulation was performed. The in silico predictions obtained in this work indicate that this construct would be capable of inducing the requisite immune response to elicit protection against T. pallidum. Through this methodology we have designed a promising potential vaccine candidate for syphilis, namely Tpme-VAC/LGCM-2022. However, it is necessary to validate these findings in in vitro and in vivo assays.
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Affiliation(s)
- Lucas Gabriel Rodrigues Gomes
- Laboratory of Cellular and Molecular Genetics (LGCM), PG Program in Bioinformatics, Department of Genetics, Ecology, and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte 31270-901, Brazil; (L.G.R.G.); (T.C.V.R.); (A.K.J.); (R.G.S.); (R.B.K.); (D.B.)
| | - Thaís Cristina Vilela Rodrigues
- Laboratory of Cellular and Molecular Genetics (LGCM), PG Program in Bioinformatics, Department of Genetics, Ecology, and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte 31270-901, Brazil; (L.G.R.G.); (T.C.V.R.); (A.K.J.); (R.G.S.); (R.B.K.); (D.B.)
| | - Arun Kumar Jaiswal
- Laboratory of Cellular and Molecular Genetics (LGCM), PG Program in Bioinformatics, Department of Genetics, Ecology, and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte 31270-901, Brazil; (L.G.R.G.); (T.C.V.R.); (A.K.J.); (R.G.S.); (R.B.K.); (D.B.)
| | - Roselane Gonçalves Santos
- Laboratory of Cellular and Molecular Genetics (LGCM), PG Program in Bioinformatics, Department of Genetics, Ecology, and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte 31270-901, Brazil; (L.G.R.G.); (T.C.V.R.); (A.K.J.); (R.G.S.); (R.B.K.); (D.B.)
| | - Rodrigo Bentes Kato
- Laboratory of Cellular and Molecular Genetics (LGCM), PG Program in Bioinformatics, Department of Genetics, Ecology, and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte 31270-901, Brazil; (L.G.R.G.); (T.C.V.R.); (A.K.J.); (R.G.S.); (R.B.K.); (D.B.)
| | - Debmalya Barh
- Laboratory of Cellular and Molecular Genetics (LGCM), PG Program in Bioinformatics, Department of Genetics, Ecology, and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte 31270-901, Brazil; (L.G.R.G.); (T.C.V.R.); (A.K.J.); (R.G.S.); (R.B.K.); (D.B.)
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur 721172, West Bengal, India
| | - Khalid J. Alzahrani
- Department of Clinical Laboratories Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia; (K.J.A.); (H.J.B.)
| | - Hamsa Jameel Banjer
- Department of Clinical Laboratories Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia; (K.J.A.); (H.J.B.)
| | - Siomar de Castro Soares
- Department of Immunology, Microbiology, and Parasitology, Institute of Biological and Natural Sciences, Federal University of Triângulo Mineiro (UFTM), Uberaba 38025-180, Brazil;
| | - Vasco Azevedo
- Laboratory of Cellular and Molecular Genetics (LGCM), PG Program in Bioinformatics, Department of Genetics, Ecology, and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte 31270-901, Brazil; (L.G.R.G.); (T.C.V.R.); (A.K.J.); (R.G.S.); (R.B.K.); (D.B.)
- Correspondence: (V.A.); (S.T.)
| | - Sandeep Tiwari
- Laboratory of Cellular and Molecular Genetics (LGCM), PG Program in Bioinformatics, Department of Genetics, Ecology, and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte 31270-901, Brazil; (L.G.R.G.); (T.C.V.R.); (A.K.J.); (R.G.S.); (R.B.K.); (D.B.)
- Correspondence: (V.A.); (S.T.)
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Zhang J, Li J, Hu K, Zhou Q, Chen X, He J, Yin S, Chi Y, Liao X, Xiao Y, Qin H, Zheng Z, Chen J. Screening Novel Vaccine Candidates for Leishmania Donovani by Combining Differential Proteomics and Immunoinformatics Analysis. Front Immunol 2022; 13:902066. [PMID: 35812381 PMCID: PMC9260594 DOI: 10.3389/fimmu.2022.902066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 05/25/2022] [Indexed: 11/18/2022] Open
Abstract
Visceral leishmaniasis (VL), also known as kala-azar, is the most dangerous form of leishmaniasis. Currently no effective vaccine is available for clinical use. Since the pathogenicity of different Leishmania strains is inconsistent, the differentially expressed proteins in Leishmania strains may play an important role as virulence factors in pathogenesis. Therefore, effective vaccine candidate targets may exist in the differentially expressed proteins. In this study, we used differential proteomics analysis to find the differentially expressed proteins in two Leishmania donovani strains, and combined with immunoinformatics analysis to find new vaccine candidates. The differentially expressed proteins from L. DD8 (low virulent) and L. 9044 (virulent) strains were analyzed by LC-MS/MS, and preliminarily screened by antigenicity, allergenicity and homology evaluation. The binding peptides of MHC II, IFN-γ and MHC I from differentially expressed proteins were then predicted and calculated for the second screening. IFN-γ/IL-10 ratios and conserved domain prediction were performed to choose more desirable differentially expressed proteins. Finally, the 3D structures of three vaccine candidate proteins were produced and submitted for molecular dynamics simulation and molecular docking interaction with TLR4/MD2. The results showed that 396 differentially expressed proteins were identified by LC-MS/MS, and 155 differentially expressed proteins were selected through antigenicity, allergenicity and homology evaluation. Finally, 16 proteins whose percentages of MHC II, IFN-γ and MHC I binding peptides were greater than those of control groups (TSA, LmSTI1, LeIF, Leish-111f) were considered to be suitable vaccine candidates. Among the 16 candidates, amino acid permease, amastin-like protein and the hypothetical protein (XP_003865405.1) simultaneously had the large ratios of IFN-γ/IL-10 and high percentages of MHC II, IFN-γ and MHC I, which should be focused on. In conclusion, our comprehensive work provided a methodological basis to screen new vaccine candidates for a better intervention against VL and associated diseases.
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Affiliation(s)
- Jianhui Zhang
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Jiao Li
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Kaifeng Hu
- Department of Clinical Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Qi Zhou
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Xiaoxiao Chen
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Jinlei He
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Shuangshuang Yin
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Yangjian Chi
- Department of Urinary Surgery, Jianou Municipal Hospital of Fujian Province, Jianou, China
| | - Xuechun Liao
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Yuying Xiao
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Hanxiao Qin
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Zhiwan Zheng
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
- *Correspondence: Zhiwan Zheng, ; Jianping Chen,
| | - Jianping Chen
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Sichuan University, Chengdu, China
- *Correspondence: Zhiwan Zheng, ; Jianping Chen,
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211
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Park JH, Kim MH, Sutanto E, Na SW, Kim MJ, Yeom JS, Nyunt MH, Abbas Elfaki MM, Abdel Hamid MM, Cha SH, Alemu SG, Sriprawat K, Anstey NM, Grigg MJ, Barber BE, William T, Gao Q, Liu Y, Pearson RD, Price RN, Nosten F, Yoon SI, No JH, Han ET, Auburn S, Russell B, Han JH. Geographical distribution and genetic diversity of Plasmodium vivax reticulocyte binding protein 1a correlates with patient antigenicity. PLoS Negl Trop Dis 2022; 16:e0010492. [PMID: 35737709 PMCID: PMC9258880 DOI: 10.1371/journal.pntd.0010492] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 07/06/2022] [Accepted: 05/12/2022] [Indexed: 01/12/2023] Open
Abstract
Plasmodium vivax is the most widespread cause of human malaria. Recent reports of drug resistant vivax malaria and the challenge of eradicating the dormant liver forms increase the importance of vaccine development against this relapsing disease. P. vivax reticulocyte binding protein 1a (PvRBP1a) is a potential vaccine candidate, which is involved in red cell tropism, a crucial step in the merozoite invasion of host reticulocytes. As part of the initial evaluation of the PvRBP1a vaccine candidate, we investigated its genetic diversity and antigenicity using geographically diverse clinical isolates. We analysed pvrbp1a genetic polymorphisms using 202 vivax clinical isolates from six countries. Pvrbp1a was separated into six regions based on specific domain features, sequence conserved/polymorphic regions, and the reticulocyte binding like (RBL) domains. In the fragmented gene sequence analysis, PvRBP1a region II (RII) and RIII (head and tail structure homolog, 152-625 aa.) showed extensive polymorphism caused by random point mutations. The haplotype network of these polymorphic regions was classified into three clusters that converged to independent populations. Antigenicity screening was performed using recombinant proteins PvRBP1a-N (157-560 aa.) and PvRBP1a-C (606-962 aa.), which contained head and tail structure region and sequence conserved region, respectively. Sensitivity against PvRBP1a-N (46.7%) was higher than PvRBP1a-C (17.8%). PvRBP1a-N was reported as a reticulocyte binding domain and this study identified a linear epitope with moderate antigenicity, thus an attractive domain for merozoite invasion-blocking vaccine development. However, our study highlights that a global PvRBP1a-based vaccine design needs to overcome several difficulties due to three distinct genotypes and low antigenicity levels.
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Affiliation(s)
- Ji-Hoon Park
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon, Republic of Korea
| | - Min-Hee Kim
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon, Republic of Korea
| | - Edwin Sutanto
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | - Seok-Won Na
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon, Republic of Korea
| | - Min-Jae Kim
- Department of Infectious Diseases, Asan Medical Center, Seoul, Republic of Korea
| | - Joon Sup Yeom
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | | | - Mohammed Mohieldien Abbas Elfaki
- Department of Parasitology and Medical Entomology, Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan
- Department of Microbiology and Parasitology, Faculty of Medicine, Jazan University, Jizan, Saudi Arabia
| | - Muzamil Mahdi Abdel Hamid
- Department of Parasitology and Medical Entomology, Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan
| | - Seok Ho Cha
- Department of Parasitology and Tropical Medicine, Inha University School of Medicine, Incheon, Republic of Korea
| | - Sisay Getachew Alemu
- College of Natural Sciences, Addis Ababa University, Addis Ababa, Ethiopia
- Armauer Hansen Research Institute, Jimma Road, Addis Ababa, Ethiopia
- Bioreliance, Rockville, Maryland, United States of America
| | - Kanlaya Sriprawat
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Tak, Thailand
| | - Nicholas M. Anstey
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Australia
| | - Matthew J. Grigg
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Australia
- Infectious Diseases Society Sabah-Menzies School of Health Research Clinical Research Unit, Sabah, Malaysia
| | - Bridget E. Barber
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Australia
- Infectious Diseases Society Sabah-Menzies School of Health Research Clinical Research Unit, Sabah, Malaysia
| | - Timothy William
- Infectious Diseases Society Sabah-Menzies School of Health Research Clinical Research Unit, Sabah, Malaysia
- Clinical Research Centre, Queen Elizabeth Hospital, Sabah, Malaysia
- Gleneagles Hospital, Sabah, Malaysia
| | - Qi Gao
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, China
| | - Yaobao Liu
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, China
- School of Public Health, Nanjing Medical University, Nanjing, China
| | | | - Ric N. Price
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Australia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine Research Building, University of Oxford, Oxford, United Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Francois Nosten
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Tak, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine Research Building, University of Oxford, Oxford, United Kingdom
| | - Sung-Il Yoon
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, Republic of Korea
| | - Joo Hwan No
- Host-Parasite Research Laboratory, Institut Pasteur Korea, Seongnam, Republic of Korea
| | - Eun-Taek Han
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon, Republic of Korea
| | - Sarah Auburn
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Australia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine Research Building, University of Oxford, Oxford, United Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Bruce Russell
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Jin-Hee Han
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon, Republic of Korea
- * E-mail:
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212
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Kurskova AO, Dotsenko VV, Frolov KA, Aksenov NA, Aksenova IV, Krivokolysko BS, Peresypkina AA, Chigorina EA, Krivokolysko SG. Synthesis and Aminomethylation of 2-Amino-4-(2-chlorophenyl)-6-(dicyanomethyl)-1,4-dihydropyridine-3,5-dicarbonitrile N-Methylmorpholinium Salt. RUSS J GEN CHEM+ 2022; 92:779-790. [PMID: 35729943 PMCID: PMC9197094 DOI: 10.1134/s1070363222050061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 02/15/2022] [Accepted: 02/17/2022] [Indexed: 12/01/2022]
Abstract
Sequential reaction of 2-chlorobenzaldehyde, cyanothioacetamide, and malononitrile dimer in the presence of an excess of N-methylmorpholine resulted in the formation of N-methylmorphlinium salt of 2-amino-4-(2-chlorophenyl)-6-(dicyanomethyl)-1,4-dihydropyridine-3,5-dicarbonitrile. The resulting salt reacts under Mannich conditions with primary amines and an excess of formaldehyde to form substituted 2-alkylamino-4-(dicyanomethylene)-3,7-diazabicyclo[3.3.1]non-2-ene-1,5-dicarbonitriles. Structure of the key compound was confirmed by single crystal X-ray diffraction analysis.
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Affiliation(s)
- A O Kurskova
- ChemEx Laboratory, V. Dahl Lugansk State University, 91034 Lugansk, Ukraine
| | - V V Dotsenko
- Kuban State University, 350040 Krasnodar, Russia.,North Caucasian Federal University, 355009 Stavropol, Russia
| | - K A Frolov
- ChemEx Laboratory, V. Dahl Lugansk State University, 91034 Lugansk, Ukraine
| | - N A Aksenov
- North Caucasian Federal University, 355009 Stavropol, Russia
| | - I V Aksenova
- North Caucasian Federal University, 355009 Stavropol, Russia
| | - B S Krivokolysko
- Lugansk State Medical University named after St. Luke, 91045 Lugansk, Ukraine
| | - A A Peresypkina
- Belgorod State National Research University, 308015 Belgorod, Russia
| | - E A Chigorina
- National Research Center "Kurchatov Institute" - IREA, 107076 Moscow, Russia.,National Research Center "Kurchatov Institute", 123182 Moscow, Russia
| | - S G Krivokolysko
- ChemEx Laboratory, V. Dahl Lugansk State University, 91034 Lugansk, Ukraine.,Lugansk State Medical University named after St. Luke, 91045 Lugansk, Ukraine
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213
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Characterization of the RNA-dependent RNA polymerase from Chikungunya virus and discovery of a novel ligand as a potential drug candidate. Sci Rep 2022; 12:10601. [PMID: 35732685 PMCID: PMC9217121 DOI: 10.1038/s41598-022-14790-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 06/13/2022] [Indexed: 11/08/2022] Open
Abstract
Chikungunya virus (CHIKV) is the causative agent of Chikungunya fever, an acute febrile and arthritogenic illness with no effective treatments available. The development of effective therapeutic strategies could be significantly accelerated with detailed knowledge of the molecular components behind CHIKV replication. However, drug discovery is hindered by our incomplete understanding of their main components. The RNA-dependent RNA-polymerase (nsP4-CHIKV) is considered the key enzyme of the CHIKV replication complex and a suitable target for antiviral therapy. Herein, the nsP4-CHIKV was extensively characterized through experimental and computational biophysical methods. In the search for new molecules against CHIKV, a compound designated LabMol-309 was identified as a strong ligand of the nsp4-CHIKV and mapped to bind to its active site. The antiviral activity of LabMol-309 was evaluated in cellular-based assays using a CHIKV replicon system and a reporter virus. In conclusion, this study highlights the biophysical features of nsP4-CHIKV and identifies a new compound as a promising antiviral agent against CHIKV infection.
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214
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Araf Y, Moin AT, Timofeev VI, Faruqui NA, Saiara SA, Ahmed N, Parvez MSA, Rahaman TI, Sarkar B, Ullah MA, Hosen MJ, Zheng C. Immunoinformatic Design of a Multivalent Peptide Vaccine Against Mucormycosis: Targeting FTR1 Protein of Major Causative Fungi. Front Immunol 2022; 13:863234. [PMID: 35720422 PMCID: PMC9204303 DOI: 10.3389/fimmu.2022.863234] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 04/12/2022] [Indexed: 12/14/2022] Open
Abstract
Mucormycosis is a potentially fatal illness that arises in immunocompromised people due to diabetic ketoacidosis, neutropenia, organ transplantation, and elevated serum levels of accessible iron. The sudden spread of mucormycosis in COVID-19 patients engendered massive concern worldwide. Comorbidities including diabetes, cancer, steroid-based medications, long-term ventilation, and increased ferritin serum concentration in COVID-19 patients trigger favorable fungi growth that in turn effectuate mucormycosis. The necessity of FTR1 gene-encoded ferrous permease for host iron acquisition by fungi has been found in different studies recently. Thus, targeting the transit component could be a potential solution. Unfortunately, no appropriate antifungal vaccine has been constructed as of yet. To date, mucormycosis has been treated with antiviral therapy and surgical treatment only. Thus, in this study, the FTR1 protein has been targeted to design a convenient and novel epitope-based vaccine with the help of immunoinformatics against four different virulent fungal species. Furthermore, the vaccine was constructed using 8 CTL, 2 HTL, and 1 LBL epitopes that were found to be highly antigenic, non-allergenic, non-toxic, and fully conserved among the fungi under consideration. The vaccine has very reassuring stability due to its high pI value of 9.97, conclusive of a basic range. The vaccine was then subjected to molecular docking, molecular dynamics, and immune simulation studies to confirm the biological environment’s safety, efficacy, and stability. The vaccine constructs were found to be safe in addition to being effective. Finally, we used in-silico cloning to develop an effective strategy for vaccine mass production. The designed vaccine will be a potential therapeutic not only to control mucormycosis in COVID-19 patients but also be effective in general mucormycosis events. However, further in vitro, and in vivo testing is needed to confirm the vaccine’s safety and efficacy in controlling fungal infections. If successful, this vaccine could provide a low-cost and effective method of preventing the spread of mucormycosis worldwide.
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Affiliation(s)
- Yusha Araf
- Department of Genetic Engineering and Biotechnology, School of Life Sciences, Shahjalal University of Science and Technology, Sylhet, Bangladesh.,Department of Immunology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China.,Department of Research and Development, Community of Biotechnology, Dhaka, Bangladesh
| | - Abu Tayab Moin
- Department of Research and Development, Community of Biotechnology, Dhaka, Bangladesh.,Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram, Bangladesh
| | - Vladimir I Timofeev
- Shubnikov Institute of Crystallography, Federal Scientific Research Centre, Crystallography and Photonics, Russian Academy of Sciences, Moscow, Russia
| | - Nairita Ahsan Faruqui
- Department of Research and Development, Community of Biotechnology, Dhaka, Bangladesh.,Biotechnology Program, Department of Mathematics and Natural Sciences, School of Data and Sciences, Brac University, Dhaka, Bangladesh
| | - Syeda Afra Saiara
- Department of Research and Development, Community of Biotechnology, Dhaka, Bangladesh
| | - Nafisa Ahmed
- Department of Research and Development, Community of Biotechnology, Dhaka, Bangladesh.,Biotechnology Program, Department of Mathematics and Natural Sciences, School of Data and Sciences, Brac University, Dhaka, Bangladesh
| | - Md Sorwer Alam Parvez
- Department of Genetic Engineering and Biotechnology, School of Life Sciences, Shahjalal University of Science and Technology, Sylhet, Bangladesh.,Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Tanjim Ishraq Rahaman
- Department of Research and Development, Community of Biotechnology, Dhaka, Bangladesh.,Department of Biotechnology and Genetic Engineering, Faculty of Life Sciences, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Bangladesh
| | - Bishajit Sarkar
- Department of Research and Development, Community of Biotechnology, Dhaka, Bangladesh.,Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Jahangirnagar University, Dhaka, Bangladesh
| | - Md Asad Ullah
- Department of Research and Development, Community of Biotechnology, Dhaka, Bangladesh.,Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Jahangirnagar University, Dhaka, Bangladesh
| | - Mohammad Jakir Hosen
- Department of Genetic Engineering and Biotechnology, School of Life Sciences, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Chunfu Zheng
- Department of Immunology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China.,Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada
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215
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Krivokolysko DS, Dotsenko VV, Bibik EY, Samokish AA, Venidiktova YS, Frolov KA, Krivokolysko SG, Pankov AA, Aksenov NA, Aksenova IV. New Hybrid Molecules Based on Sulfur-Containing Nicotinonitriles: Synthesis, Analgesic Activity in Acetic Acid-Induced Writhing Test, and Molecular Docking Studies. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2022. [DOI: 10.1134/s1068162022030104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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216
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Mangal P, Jha RK, Jain M, Singh AK, Muthukumaran J. Identification and prioritization of promising lead molecules from Syzygium aromaticum against Sortase C from Streptococcus pyogenes: an in silico investigation. J Biomol Struct Dyn 2022:1-18. [PMID: 35706070 DOI: 10.1080/07391102.2022.2086921] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Sortases are extracellular transpeptidases that play an essential role in the adhesion of secreted proteins to the peptidoglycan layer of the cell wall of Gram-negative bacteria. Sortases are an important drug target protein due to their involvement in synthesizing the peptidoglycan cell wall of Streptococcus pyogenes, and these are not found in Homo sapiens. In this study, initially, we have performed protein sequence analysis to understand the sequential properties of Sortase C. Next, a comparative protein modeling approach was used to predict the three-dimensional model of Sortase C based on the crystal structure of Sortase C from Streptococcus pneumoniae. Virtual screening with an in-house library of phytochemicals from Syzygium aromaticum and molecular docking studies were performed to identify the promising lead molecules. These compounds were also analyzed for their drug-like and pharmacokinetic properties. Subsequently, the protein-ligand complexes of the selected ligands were subjected to molecular dynamics (MD) simulations to investigate their dynamic behavior in physiological conditions. The global and essential dynamics analyses result implied that the Sortase C complexes of the proposed three lead candidates exhibited adequate stability during the MD simulations. Additionally, the three proposed molecules showed favorable MM/PBSA binding free energy values ranging from -13.8 +/- 9.41 to -56.6 +/- 8.82 kcal/mol. After an extensive computational investigation, we have identified three promising lead candidates (CID:13888122, CID:3694932 and CID:102445430) against Sortase C from S. pyogenes. The result obtained from these computational studies can be used to screen and develop the inhibitors against Sortase C from S. pyogenes. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Purti Mangal
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, India
| | - Rajat Kumar Jha
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, India
| | - Monika Jain
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, India
| | - Amit Kumar Singh
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, India
| | - Jayaraman Muthukumaran
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, India
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217
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Al-Megrin WAI, Karkashan A, Alnuqaydan AM, Aba Alkhayl FF, Alrumaihi F, Almatroudi A, Allemailem KS. Design of a Multi-Epitopes Based Chimeric Vaccine against Enterobacter cloacae Using Pan-Genome and Reverse Vaccinology Approaches. Vaccines (Basel) 2022; 10:vaccines10060886. [PMID: 35746494 PMCID: PMC9227637 DOI: 10.3390/vaccines10060886] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/13/2022] [Accepted: 05/22/2022] [Indexed: 01/27/2023] Open
Abstract
Enterobacter cloacae (EC) is a significant emerging pathogen that is occasionally associated with lung infection, surgical site infection, urinary infection, sepsis, and outbreaks in neonatal intensive care units. In light of the fact that there is currently no approved vaccine or therapeutic option for the treatment of EC, the current study was developed to concentrate on applications based on modern computational approaches to design a multi-epitope-based E. cloacae peptide vaccine (MEBEPV) expressing the antigenic determinants prioritized from the EC genome. Integrated computational analyses identified two potential protein targets (phosphoporin protein-PhoE and putative outer-membrane porin protein) for further exploration on the basis of pangenome subtractive proteomics and immunoinformatic in-depth examination of the core proteomes. Then, a multi-epitope peptide vaccine was designed, which comprised shortlisted epitopes that were capable of eliciting both innate and adaptive immunity, as well as the cholera toxin’s B-subunit, which was used as an adjuvant in the vaccine formulation. To ensure maximum expression, the vaccine’s 3D structure was developed and the loop was refined, improving the stability by disulfide engineering, and the physicochemical characteristics of the recombinant vaccine sequence were found to be ideal for both in vitro and in vivo experimentation. Blind docking was then used for the prediction of the MEBEPV predominant blinding mode with MHCI, MHCII, and TLR3 innate immune receptors, with lowest global energy of −18.64 kJ/mol, −48.25 kJ/mol, and −5.20 kJ/mol for MHC-I, MHC-II, and TLR-4, respectively, with docked complexes considered for simulation. In MD and MMGBSA investigations, the docked models of MEBEPV-TLR3, MEBEPV-MHCI, and MEBEPV-MHCII were found to be stable during the course of the simulation. MM-GBSA analysis calculated −122.17 total net binding free energies for the TLR3-vaccine complex, −125.4 for the MHC I-vaccine complex, and −187.94 for the MHC II-vaccine complex. Next, MM-PBSA analysis calculated −115.63 binding free energy for the TLR3-vaccine complex, −118.19 for the MHC I-vaccine complex, and −184.61 for the MHC II-vaccine complex. When the vaccine was tested in silico, researchers discovered that it was capable of inducing both types of immune responses (cell mediated and humoral) at the same time. Even though the suggested MEBEPV has the potential to be a powerful contender against E. cloacae-associated illnesses, further testing in the laboratory will be required before it can be declared safe and immunogenic.
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Affiliation(s)
- Wafa Abdullah I. Al-Megrin
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
- Correspondence: (W.A.I.A.-M.); (K.S.A.)
| | - Alaa Karkashan
- Department of Biology, College of Sciences, University of Jeddah, Jeddah 21959, Saudi Arabia;
| | - Abdullah M. Alnuqaydan
- Department of Medical Biotechnology, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia;
| | - Faris F. Aba Alkhayl
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia; (F.F.A.A.); (F.A.); (A.A.)
- Department of Pharmaceutical Chemistry and Pharmacognosy, College of Dentistry and Pharmacy, Buraydah Colleges, Buraydah 51418, Saudi Arabia
| | - Faris Alrumaihi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia; (F.F.A.A.); (F.A.); (A.A.)
| | - Ahmad Almatroudi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia; (F.F.A.A.); (F.A.); (A.A.)
| | - Khaled S. Allemailem
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia; (F.F.A.A.); (F.A.); (A.A.)
- Correspondence: (W.A.I.A.-M.); (K.S.A.)
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218
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Paiva VDA, Gomes IDS, Monteiro CR, Mendonça MV, Martins PM, Santana CA, Gonçalves-Almeida V, Izidoro SC, Melo-Minardi RCD, Silveira SDA. Protein structural bioinformatics: An overview. Comput Biol Med 2022; 147:105695. [DOI: 10.1016/j.compbiomed.2022.105695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 06/01/2022] [Accepted: 06/02/2022] [Indexed: 11/27/2022]
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219
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Aslam S, Ashfaq UA, Zia T, Aslam N, Alrumaihi F, Shahid F, Noor F, Qasim M. Proteome based mapping and reverse vaccinology techniques to contrive multi-epitope based subunit vaccine (MEBSV) against Streptococcus pyogenes. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 100:105259. [PMID: 35231667 DOI: 10.1016/j.meegid.2022.105259] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 12/01/2021] [Accepted: 02/23/2022] [Indexed: 06/14/2023]
Abstract
Streptococcus pyogenes is a root cause of human infection like pharyngitis, tonsillitis, scarlet fever, impetigo, and respiratory tract infections. About 11 million individuals in the US suffer from pharyngitis every year. Unfortunately, no vaccine against S. pyogenes is available yet. The purpose of this study is to create a multiepitope-based subunit vaccine (MEBSV) targeting S. pyogenes top four highly antigenic proteins by using a combination of immunological techniques and molecular docking to tackle term group A streptococcal (GAS) infections. T-cell (HTL & CTL), B-cell, and IFN-γ of target proteins were forecasted and epitopes having high antigenic properties being selected for subsequent research. For designing of final vaccine, 5LBL, 9CTL, and 4HTL epitopes were joined by the KK, AAY, and GPGPG linkers. To enhance the immune response, the N-end of the vaccine was linked by adjuvant (Cholera enterotoxin subunit B) with a linker named EAAAK. With the addition of adjuvants and linkers, the construct size was 421 amino acids. IFN-γ and B-cell epitopes illustrate that the modeled construct is optimized for cell-mediated immune or humoral responses. The developed MEBSV structure was assessed to be highly antigenic, non-toxic, and non-allergenic. Moreover, disulphide engineering further enhanced the stability of the final vaccine protein. Molecular docking of the MEBSV with toll-like receptor 4 (TLR4) was conducted to check the vaccine's compatibility with the receptor. Besides, in-silico cloning has been carried out for credibility validation and proper expression of vaccine construct. These findings suggested that the multi-epitope vaccine produced might be a potential immunogenic against Group A streptococcus infections but further experimental testing is required to validate this study.
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Affiliation(s)
- Sidra Aslam
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Pakistan
| | - Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Pakistan
| | - Tuba Zia
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Pakistan
| | - Nosheen Aslam
- Department of Biochemistry, Government College University Faisalabad, Pakistan
| | - Faris Alrumaihi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia
| | - Farah Shahid
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Pakistan
| | - Fatima Noor
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Pakistan
| | - Muhammad Qasim
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Pakistan.
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220
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Levan-type fructooligosaccharides synthesis by novel levansucrase-inulosucrase fusion enzyme. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2022.108524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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221
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Tan C, Zhu F, Xiao Y, Wu Y, Meng X, Liu S, Liu T, Chen S, Zhou J, Li C, Wu A. Immunoinformatics Approach Toward the Introduction of a Novel Multi-Epitope Vaccine Against Clostridium difficile. Front Immunol 2022; 13:887061. [PMID: 35720363 PMCID: PMC9204425 DOI: 10.3389/fimmu.2022.887061] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 04/05/2022] [Indexed: 11/13/2022] Open
Abstract
Clostridium difficile (C.difficile) is an exclusively anaerobic, spore-forming, and Gram-positive pathogen that is the most common cause of nosocomial diarrhea and is becoming increasingly prevalent in the community. Because C. difficile is strictly anaerobic, spores that can survive for months in the external environment contribute to the persistence and diffusion of C. difficile within the healthcare environment and community. Antimicrobial therapy disrupts the natural intestinal flora, allowing spores to develop into propagules that colonize the colon and produce toxins, thus leading to antibiotic-associated diarrhea and pseudomembranous enteritis. However, there is no licensed vaccine to prevent Clostridium difficile infection (CDI). In this study, a multi-epitope vaccine was designed using modern computer methods. Two target proteins, CdeC, affecting spore germination, and fliD, affecting propagule colonization, were chosen to construct the vaccine so that it could simultaneously induce the immune response against two different forms (spore and propagule) of C. difficile. We obtained the protein sequences from the National Center for Biotechnology Information (NCBI) database. After the layers of filtration, 5 cytotoxic T-cell lymphocyte (CTL) epitopes, 5 helper T lymphocyte (HTL) epitopes, and 7 B-cell linear epitopes were finally selected for vaccine construction. Then, to enhance the immunogenicity of the designed vaccine, an adjuvant was added to construct the vaccine. The Prabi and RaptorX servers were used to predict the vaccine's two- and three-dimensional (3D) structures, respectively. Additionally, we refined and validated the structures of the vaccine construct. Molecular docking and molecular dynamics (MD) simulation were performed to check the interaction model of the vaccine-Toll-like receptor (TLR) complexes, vaccine-major histocompatibility complex (MHC) complexes, and vaccine-B-cell receptor (BCR) complex. Furthermore, immune stimulation, population coverage, and in silico molecular cloning were also conducted. The foregoing findings suggest that the final formulated vaccine is promising against the pathogen, but more researchers are needed to verify it.
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Affiliation(s)
- Caixia Tan
- Infection Control Center, Xiangya Hospital, Central South University, Changsha, China
| | - Fei Zhu
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, China
| | - Yuanyuan Xiao
- Infection Control Center, Xiangya Hospital, Central South University, Changsha, China
| | - Yuqi Wu
- Infection Control Center, Xiangya Hospital, Central South University, Changsha, China
| | - Xiujuan Meng
- Infection Control Center, Xiangya Hospital, Central South University, Changsha, China
| | - Sidi Liu
- Infection Control Center, Xiangya Hospital, Central South University, Changsha, China
| | - Ting Liu
- Infection Control Center, Xiangya Hospital, Central South University, Changsha, China
| | - Siyao Chen
- Infection Control Center, Xiangya Hospital, Central South University, Changsha, China
| | - Juan Zhou
- Infection Control Center, Xiangya Hospital, Central South University, Changsha, China
| | - Chunhui Li
- Infection Control Center, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders (XiangYa Hospital), Changsha, China
| | - Anhua Wu
- Infection Control Center, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders (XiangYa Hospital), Changsha, China
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222
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Omoniyi AA, Adebisi SS, Musa SA, Nzalak JO, Bauchi ZM, Bako KW, Olatomide OD, Zachariah R, Nyengaard JR. In silico design and analyses of a multi-epitope vaccine against Crimean-Congo hemorrhagic fever virus through reverse vaccinology and immunoinformatics approaches. Sci Rep 2022; 12:8736. [PMID: 35610299 PMCID: PMC9127496 DOI: 10.1038/s41598-022-12651-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 05/12/2022] [Indexed: 12/16/2022] Open
Abstract
Crimean Congo Hemorrhagic Fever virus (CCHFV) is a deadly human pathogen that causes an emerging zoonotic disease with a broad geographic spread, especially in Africa, Asia, and Europe, and the second most common viral hemorrhagic fever and widely transmitted tick-borne viral disease. Following infection, the patients are presented with a variety of clinical manifestations and a fatality rate of 40%. Despite the high fatality rate, there are unmet clinical interventions, as no antiviral drugs or vaccines for CCHF have been approved. Immunoinformatics pipeline and reverse vaccinology were used in this study to design a multi-epitope vaccine that may elicit a protective humoral and cellular immune response against Crimean-Congo hemorrhagic fever virus infection. Three essential virulent and antigenic proteins (S, M, and L) were used to predict seven CTL and 18 HTL epitopes that were non-allergenic, antigenic, IFN-γ inducing, and non-toxic. The epitopes were connected using linkers and 50S ribosomal protein L7/L12 was used as an adjuvant and raised a multi-epitope vaccine (MEV) that is 567 amino acids long. Molecular docking and simulation of the predicted 3D structure of the MEV with the toll-like (TLR2, TLR3, and TLR4) receptors and major histocompatibility complex (MCH-I and MCH-II) indicate high interactions and stability of the complexes, MM-GBSA free binding energy calculation revealed a favourable protein-protein complex. Maximum MEV expression was achieved with a CAI value of 0.98 through in silico cloning in the Drosophila melanogaster host. According to the immune simulation, IgG1, T-helper cells, T-cytotoxic cells, INF-γ, and IL-2 were predicted to be significantly elevated. These robust computational analyses demonstrated that the proposed MEV is effective in preventing CCHFV infections. However, it is still necessary to conduct both in vitro and in vivo experiments to validate the potential of the vaccine.
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Affiliation(s)
- Akinyemi Ademola Omoniyi
- Department of Human Anatomy, Faculty of Basic Medical Science, College of Medical Sciences, Ahmadu Bello University, Zaria, Nigeria.
- Department of Clinical Medicine, Core Centre for Molecular Morphology, Section for Stereology and Microscopy, Aarhus University, Aarhus, Denmark.
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark.
| | - Samuel Sunday Adebisi
- Department of Human Anatomy, Faculty of Basic Medical Science, College of Medical Sciences, Ahmadu Bello University, Zaria, Nigeria
| | - Sunday Abraham Musa
- Department of Human Anatomy, Faculty of Basic Medical Science, College of Medical Sciences, Ahmadu Bello University, Zaria, Nigeria
| | - James Oliver Nzalak
- Department of Veterinary Anatomy, Faculty of Veterinary Medicine, Ahmadu Bello University, Zaria, Nigeria
| | - Zainab Mahmood Bauchi
- Department of Human Anatomy, Faculty of Basic Medical Sciences, Abubakar Tafawa Balewa University, Bauchi, Nigeria
| | - Kerkebe William Bako
- Department of Human Anatomy, Faculty of Basic Medical Science, College of Medical Sciences, Ahmadu Bello University, Zaria, Nigeria
| | - Oluwasegun Davis Olatomide
- Department of Human Anatomy, Faculty of Basic Medical Science, College of Medical Sciences, Ahmadu Bello University, Zaria, Nigeria
| | - Richard Zachariah
- Department of Human Anatomy, Faculty of Basic Medical Science, College of Medical Sciences, Ahmadu Bello University, Zaria, Nigeria
| | - Jens Randel Nyengaard
- Department of Clinical Medicine, Core Centre for Molecular Morphology, Section for Stereology and Microscopy, Aarhus University, Aarhus, Denmark
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
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223
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Nguyen HL, Linh HQ, Krupa P, La Penna G, Li MS. Amyloid β Dodecamer Disrupts the Neuronal Membrane More Strongly than the Mature Fibril: Understanding the Role of Oligomers in Neurotoxicity. J Phys Chem B 2022; 126:3659-3672. [PMID: 35580354 PMCID: PMC9150093 DOI: 10.1021/acs.jpcb.2c01769] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
![]()
The amyloid cascade
hypothesis states that senile plaques, composed
of amyloid β (Aβ) fibrils, play a key role in Alzheimer’s
disease (AD). However, recent experiments have shown that Aβ
oligomers are more toxic to neurons than highly ordered fibrils. The
molecular mechanism underlying this observation remains largely unknown.
One of the possible scenarios for neurotoxicity is that Aβ peptides
create pores in the lipid membrane that allow Ca2+ ions
to enter cells, resulting in a signal of cell apoptosis. Hence, one
might think that oligomers are more toxic due to their higher ability
to create ion channels than fibrils. In this work, we study the effect
of Aβ42 dodecamer and fibrils on a neuronal membrane, which
is similar to that observed in AD patients, using all-atom molecular
dynamics simulations. Due to short simulation times, we cannot observe
the formation of pores, but useful insight on the early events of
this process has been obtained. Namely, we showed that dodecamer distorts
the lipid membrane to a greater extent than fibrils, which may indicate
that ion channels can be more easily formed in the presence of oligomers.
Based on this result, we anticipate that oligomers are more toxic
than mature fibrils, as observed experimentally. Moreover, the Aβ–membrane
interaction was found to be governed by the repulsive electrostatic
interaction between Aβ and the ganglioside GM1 lipid. We calculated
the bending and compressibility modulus of the membrane in the absence
of Aβ and obtained good agreement with the experiment. We predict
that the dodecamer will increase the compressibility modulus but has
little effect on the bending modulus. Due to the weak interaction
with the membrane, fibrils insignificantly change the membrane elastic
properties.
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Affiliation(s)
- Hoang Linh Nguyen
- Institute for Computational Science and Technology, SBI Building, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City 729110, Vietnam.,Ho Chi Minh City University of Technology (HCMUT), Ho Chi Minh City 740500, Vietnam.,Vietnam National University, Ho Chi Minh City 71300, Vietnam
| | - Huynh Quang Linh
- Ho Chi Minh City University of Technology (HCMUT), Ho Chi Minh City 740500, Vietnam.,Vietnam National University, Ho Chi Minh City 71300, Vietnam
| | - Pawel Krupa
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, Warsaw 02-668, Poland
| | - Giovanni La Penna
- National Research Council of Italy (CNR), Institute for Chemistry of Organometallic Compounds (ICCOM), Florence 50019, Italy.,National Institute for Nuclear Physics (INFN), Section of Roma-Tor Vergata, Rome 00815, Italy
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, Warsaw 02-668, Poland
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224
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Dwivedi M, Mukhopadhyay S, Yadav S, Dubey KD. A multidrug efflux protein in Mycobacterium tuberculosis; tap as a potential drug target for drug repurposing. Comput Biol Med 2022; 146:105607. [PMID: 35617724 DOI: 10.1016/j.compbiomed.2022.105607] [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: 02/26/2022] [Revised: 05/02/2022] [Accepted: 05/09/2022] [Indexed: 11/27/2022]
Abstract
Tuberculosis (TB) is a serious communicative disease caused by Mycobacterium tuberculosis. Although there are vaccines and drugs available to treat the disease, they are not efficient, moreover, multidrug-resistant TB (MDR-TB) become a major hurdle in its therapy. These MDR strains utilize the multidrug efflux pump as a decisive weapon to fight against antitubercular drugs. Tap membrane protein was observed as a crucial multidrug efflux pump in M. tuberculosis and its critical implication in MDR-MTB development makes it an effective drug target. In the present study, we have utilized various in silico approaches to predict the applicability of FDA-approved ion channel inhibitors and blockers as therapeutic leads against Tuberculosis by targeting multidrug efflux protein; Tap in MTB. Tap protein structure is predicted by Phyre2 server followed by model refinement, validation, physio-chemical catheterization and target prediction. Further, the interaction between Tap protein and ligands were analysed by molecular docking and MD simulation run of 100 ns. Based on implication and compatibility, 18 FDA-approved ion channel inhibitors and blockers are selected as a ligand against the Tap protein and eventually observed five ligands; Glimepiride, Flecainide, Flupiritine, Nimodipine and Amlodipine as promising compounds which have exhibited the significant stable interaction with Tap protein and are proposed to modulate or interfere with its activity. These compounds illustrated the substantial docking score and total binding enthalpy more than -7 kcal/mol and -42 kcal/mol respectively which implies that the selected FDA-approved compounds can spontaneously interact with the Tap protein to modulate its function. This study proposed Tap protein as a prominent drug target in MTB and investigated compounds that show considerable interaction with the Tap protein as potential therapeutic molecules. These interactions may lead to modulating or inhibit the activity of drug efflux protein thereby making MTB susceptible to antitubercular drugs.
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Affiliation(s)
- Manish Dwivedi
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow, 226028, India.
| | - Sutanu Mukhopadhyay
- Department of Chemistry, Ramakrishna Mission Vivekananda Centenary College, West Bengal, India
| | - Shalini Yadav
- Department of Chemistry, Shiv Nadar University, Greater Noida, 201314, India
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225
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Ezzemani W, Kettani A, Sappati S, Kondaka K, El Ossmani H, Tsukiyama-Kohara K, Altawalah H, Saile R, Kohara M, Benjelloun S, Ezzikouri S. Reverse vaccinology-based prediction of a multi-epitope SARS-CoV-2 vaccine and its tailoring to new coronavirus variants. J Biomol Struct Dyn 2022:1-22. [PMID: 35549819 DOI: 10.1080/07391102.2022.2075468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The genome feature of SARS-CoV-2 leads the virus to mutate and creates new variants of concern. Tackling viral mutations is also an important challenge for the development of a new vaccine. Accordingly, in the present study, we undertook to identify B- and T-cell epitopes with immunogenic potential for eliciting responses to SARS-CoV-2, using computational approaches and its tailoring to coronavirus variants. A total of 47 novel epitopes were identified as immunogenic triggering immune responses and no toxic after investigation with in silico tools. Furthermore, we found these peptide vaccine candidates showed a significant binding affinity for MHC I and MHC II alleles in molecular docking investigations. We consider them to be promising targets for developing peptide-based vaccines against SARS-CoV-2. Subsequently, we designed two efficient multi-epitopes vaccines against the SARS-CoV-2, the first one based on potent MHC class I and class II T-cell epitopes of S (FPNITNLCPF-NYNYLYRLFR-MFVFLVLLPLVSSQC), M (MWLSYFIASF-GLMWLSYFIASFRLF), E (LTALRLCAY-LLFLAFVVFLLVTLA), and N (SPRWYFYYL-AQFAPSASAFFGMSR). The second candidate is the result of the tailoring of the first designed vaccine according to three classes of SARS-CoV-2 variants. Molecular docking showed that the protein-protein binding interactions between the vaccines construct and TLR2-TLR4 immune receptors are stable complexes. These findings confirmed that the final multi-epitope vaccine could be easily adapted to new viral variants. Our study offers a shortlist of promising epitopes that can accelerate the development of an effective and safe vaccine against the virus and its adaptation to new variants.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Wahiba Ezzemani
- Virology Unit, Viral Hepatitis Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco.,Laboratoire de Biologie et Santé (URAC34), Départment de Biologie, Faculté des Sciences Ben Msik, Hassan II University of Casablanca, Casablanca, Morocco
| | - Anass Kettani
- Laboratoire de Biologie et Santé (URAC34), Départment de Biologie, Faculté des Sciences Ben Msik, Hassan II University of Casablanca, Casablanca, Morocco
| | - Subrahmanyam Sappati
- Department of Pharmaceutical Technology and Biochemistry, Gdańsk University of Technology, Gdańsk, Poland.,BioTechMed Center, Gdańsk University of Technology, Gdańsk, Poland
| | - Kavya Kondaka
- Department of Pharmaceutical Technology and Biochemistry, Gdańsk University of Technology, Gdańsk, Poland
| | - Hicham El Ossmani
- Institut de Criminalistique de la Gendarmerie Royale, AMSSNuR, Rabat, Morocco
| | - Kyoko Tsukiyama-Kohara
- Transboundary Animal Diseases Centre, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Japan
| | - Haya Altawalah
- Department of Microbiology, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait.,Virology Unit, Yacoub Behbehani Center, Sabah Hospital, Ministry of Health, Kuwait City, Kuwait
| | - Rachid Saile
- Laboratoire de Biologie et Santé (URAC34), Départment de Biologie, Faculté des Sciences Ben Msik, Hassan II University of Casablanca, Casablanca, Morocco
| | - Michinori Kohara
- Department of Microbiology and Cell Biology, The Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Soumaya Benjelloun
- Virology Unit, Viral Hepatitis Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Sayeh Ezzikouri
- Virology Unit, Viral Hepatitis Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
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226
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Islam E. Development of epitope-based chimeric protein as a vaccine against Lujo virus by utilizing immunoinformatic tools. Future Virol 2022. [DOI: 10.2217/fvl-2021-0105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aim: Lujo is a modern zoonotic virus that is potentially fatal and spreads by bodily fluids. In this research, immunoinformatic tools are used to build a vaccine. Methodology: The epitopes of cytotoxic T-lymphocytes, helper T-lymphocytes and linear B-lymphocytes were predicted from the most antigenic protein. The designed vaccine's physiochemical properties and 3D structure have been forecasted. Low free energy and strong binding affinity estimated in molecular docking against toll-like receptor 4 (TLR4) and dynamic simulation. Furthermore, in silico cloning in the Escherichia coli K12 host system was performed for high level of expression. Conclusion: Finally, immune simulation was used to determine immune responses to the vaccine that was formulated confirming the developed vaccine as a good candidate against Lujo virus.
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Affiliation(s)
- Enayetul Islam
- Department of Genetic Engineering & Biotechnology, University of Chittagong, Chittagong, Bangladesh
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227
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Designing a novel E2-IFN-γ fusion protein against CSFV by immunoinformatics and structural vaccinology approaches. Appl Microbiol Biotechnol 2022; 106:3611-3623. [PMID: 35524776 DOI: 10.1007/s00253-022-11919-w] [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: 02/27/2022] [Revised: 04/01/2022] [Accepted: 04/08/2022] [Indexed: 11/02/2022]
Abstract
Subunit vaccines with high purity and safety are gradually becoming a main trend in vaccinology. However, adjuvants such as interferon-gamma (IFN-γ) are required to enhance immune responses of subunit vaccines due to their poor immunogenicity. The conjugation of antigen with adjuvant can induce more potent immune responses compared to the mixture of antigen and adjuvant. At the same time, the selection of linker, indispensable in the construction of the stable and bioactive fusion proteins, is complicated and time-consuming. The development of immunoinformatics and structural vaccinology approaches provides a means to address the abovementioned problem. Therefore, in this study, a E2-IFN-γ fusion protein with an optimal linker (E2-R2-PIFN) was designed by bioinformatics approaches to improve the immunogenicity of the classical swine fever virus (CSFV) E2 subunit vaccine. Moreover, the E2-R2-PIFN fusion protein was expressed in HEK293T cells and the biological effects of IFN-γ in E2-R2-PIFN were confirmed in vitro via Western blotting. Here, an alternative method is utilized to simplify the design and validation of the antigen-adjuvant fusion protein, providing a potential subunit vaccine candidate against CSFV. KEY POINTS: • An effective and simple workflow of antigen-adjuvant fusion protein design and validation was established by immunoinformatics and structural vaccinology. • A novel E2-IFN-γ fusion protein with an optimal linker was designed as a potential CSFV vaccine. • The bioactivity of the newly designed fusion protein was preliminarily validated through in vitro experiments.
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228
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Yu M, Zhu Y, Li Y, Chen Z, Li Z, Wang J, Li Z, Zhang F, Ding J. Design of a Recombinant Multivalent Epitope Vaccine Based on SARS-CoV-2 and Its Variants in Immunoinformatics Approaches. Front Immunol 2022; 13:884433. [PMID: 35603198 PMCID: PMC9120605 DOI: 10.3389/fimmu.2022.884433] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 04/12/2022] [Indexed: 01/08/2023] Open
Abstract
The development of an effective multivalent vaccine against SARS-CoV-2 variants is an important means to improve the global public health situation caused by COVID-19. In this study, we identified the antigen epitopes of the main global epidemic SARS-CoV-2 and mutated virus strains using immunoinformatics approach, and screened out 8 cytotoxic T lymphocyte epitopes (CTLEs), 17 helper T lymphocyte epitopes (HTLEs), 9 linear B-cell epitopes (LBEs) and 4 conformational B-cell epitopes (CBEs). The global population coverage of CTLEs and HTLEs was 93.16% and 99.9% respectively. These epitopes were spliced together by corresponding linkers and recombined into multivalent vaccine. In silico tests, the vaccine protein was a non-allergen and the docking with TLR-3 molecule showed a strong interaction. The results of immune simulation showed that the vaccine may be helpful to initiate both cellular and humoral immunity against all VOC. The optimistic immunogenicity of the vaccine was confirmed in vivo and in vitro finally. Therefore, our vaccine may have potential protection against SARS-CoV-2 and its variants.
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Affiliation(s)
- Mingkai Yu
- Department of Immunology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, China
- Xinjiang Key Molecular Biology Laboratory of Endemic Disease, Xinjiang Medical University, Urumqi, China
| | - Yuejie Zhu
- Reproductive Medicine Center, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Yujiao Li
- Department of Blood Transfusion, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Zhiqiang Chen
- Department of Immunology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, China
- Xinjiang Key Molecular Biology Laboratory of Endemic Disease, Xinjiang Medical University, Urumqi, China
| | - Zhiwei Li
- Clinical Laboratory Center, Xinjiang Uygur Autonomous Region People’s Hospital, Urumqi, China
| | - Jing Wang
- Xinjiang Laboratory of Respiratory Disease Research, Traditional Chinese Medicine Hospital Affiliated to Xinjiang Medical University, Urumqi, China
| | - Zheng Li
- Xinjiang Laboratory of Respiratory Disease Research, Traditional Chinese Medicine Hospital Affiliated to Xinjiang Medical University, Urumqi, China
| | - Fengbo Zhang
- Department of Clinical Laboratory, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
- State Key Laboratory of Pathogenesis, Prevention, Treatment of Central Asian High Incidence Diseases, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
- *Correspondence: Jianbing Ding, ; Fengbo Zhang,
| | - Jianbing Ding
- Department of Immunology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, China
- Xinjiang Key Molecular Biology Laboratory of Endemic Disease, Xinjiang Medical University, Urumqi, China
- *Correspondence: Jianbing Ding, ; Fengbo Zhang,
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229
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Kaushal N, Jain S, Baranwal M. Computational design of immunogenic peptide constructs comprising multiple HLA restricted Dengue virus envelope epitopes. J Mol Recognit 2022; 35:e2961. [PMID: 35514257 DOI: 10.1002/jmr.2961] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 02/01/2022] [Accepted: 05/02/2022] [Indexed: 11/09/2022]
Abstract
Dengue virus (DENV) is endemic in 100 countries with ability to impact nearly 50% of world population. DENV envelope (E) protein is responsible for viral attachment to host cells and has been target of various countermeasure development efforts. The current study focuses on a consensus computational approach to identify cross-reactive, immunogenic DENV-2 E peptides displaying promiscuity with a wide array of HLA molecules. Four conserved peptides (FP-1, FP-2, FP-3 and FP-4) containing multiple CD8+ and CD4+ T cell epitopes were identified by employment of various immunoinformatics tools. FP-1, FP-2, FP-3 and FP-4 were estimated to bind with 227, 1787, 1008 and 834 HLA alleles respectively. RMSD values obtained by Molecular docking (CABS-Dock) with 20 HLA alleles (10 each of HLA class I and II) resulted into comparable RMSD values of identified epitopes with native peptides which represents the natural presentation of epitopes to HLA molecules. These peptides were also found to be part of previous experimentally validated immunogenic peptides. Further, a dengue immunogenic peptide construct was generated by linking the four peptides, an adjuvant and a 6x histidine tag. The construct showed strong binding and stability with Toll-like receptor (TLR4). Collectively, these results provide strong evidence in the support of the immunogenic potential of the dengue immunogenic peptide construct. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Neha Kaushal
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, Punjab, India
| | - Sahil Jain
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, Punjab, India.,University Institute of Biotechnology, Chandigarh University, Mohali, India
| | - Manoj Baranwal
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, Punjab, India
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Münch J, Engesser M, Schönauer R, Hamm JA, Hartig C, Hantmann E, Akay G, Pehlivan D, Mitani T, Coban Akdemir Z, Tüysüz B, Shirakawa T, Dateki S, Claus LR, van Eerde AM, Smol T, Devisme L, Franquet H, Attié-Bitach T, Wagner T, Bergmann C, Höhn AK, Shril S, Pollack A, Wenger T, Scott AA, Paolucci S, Buchan J, Gabriel GC, Posey JE, Lupski JR, Petit F, McCarthy AA, Pazour GJ, Lo CW, Popp B, Halbritter J. Biallelic pathogenic variants in roundabout guidance receptor 1 associate with syndromic congenital anomalies of the kidney and urinary tract. Kidney Int 2022; 101:1039-1053. [PMID: 35227688 PMCID: PMC10010616 DOI: 10.1016/j.kint.2022.01.028] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 11/30/2021] [Accepted: 01/11/2022] [Indexed: 11/16/2022]
Abstract
Congenital anomalies of the kidney and urinary tract (CAKUT) represent the most common cause of chronic kidney failure in children. Despite growing knowledge of the genetic causes of CAKUT, the majority of cases remain etiologically unsolved. Genetic alterations in roundabout guidance receptor 1 (ROBO1) have been associated with neuronal and cardiac developmental defects in living individuals. Although Slit-Robo signaling is pivotal for kidney development, diagnostic ROBO1 variants have not been reported in viable CAKUT to date. By next-generation-sequencing methods, we identified six unrelated individuals and two non-viable fetuses with biallelic truncating or combined missense and truncating variants in ROBO1. Kidney and genitourinary manifestation included unilateral or bilateral kidney agenesis, vesicoureteral junction obstruction, vesicoureteral reflux, posterior urethral valve, genital malformation, and increased kidney echogenicity. Further clinical characteristics were remarkably heterogeneous, including neurodevelopmental defects, intellectual impairment, cerebral malformations, eye anomalies, and cardiac defects. By in silico analysis, we determined the functional significance of identified missense variants and observed absence of kidney ROBO1 expression in both human and murine mutant tissues. While its expression in multiple tissues may explain heterogeneous organ involvement, variability of the kidney disease suggests gene dosage effects due to a combination of null alleles with mild hypomorphic alleles. Thus, comprehensive genetic analysis in CAKUT should include ROBO1 as a new cause of recessively inherited disease. Hence, in patients with already established ROBO1-associated cardiac or neuronal disorders, screening for kidney involvement is indicated.
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Affiliation(s)
- Johannes Münch
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, Berlin, Germany; Division of Nephrology, University of Leipzig Medical Center, Leipzig, Germany
| | - Marie Engesser
- Division of Nephrology, University of Leipzig Medical Center, Leipzig, Germany
| | - Ria Schönauer
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, Berlin, Germany; Division of Nephrology, University of Leipzig Medical Center, Leipzig, Germany
| | - J Austin Hamm
- East Tennessee Children's Hospital, Genetic Center, Knoxville, Tennessee, USA
| | - Christin Hartig
- Division of Nephrology, University of Leipzig Medical Center, Leipzig, Germany
| | - Elena Hantmann
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, Berlin, Germany; Division of Nephrology, University of Leipzig Medical Center, Leipzig, Germany
| | - Gulsen Akay
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA; Department of Pediatrics, University of Utah, Salt Lake, Utah, USA
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA; Division of Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA; Texas Children's Hospital, Houston, Texas, USA
| | - Tadahiro Mitani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Zeynep Coban Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA; Department of Epidemiology, Human Genetics, and Environmental Sciences, Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Beyhan Tüysüz
- Department of Pediatric Genetics, Istanbul University Cerrahpasa Medical Faculty, Istanbul, Turkey
| | | | - Sumito Dateki
- Department of Pediatrics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Laura R Claus
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - Thomas Smol
- Centre Hospitalier Universitaire de Lille, Institut de Génétique Médicale, Lille, France
| | - Louise Devisme
- Centre Hospitalier Universitaire de Lille, Institut de Pathologie, Lille, France
| | - Hélène Franquet
- Centre Hospitalier Universitaire de Lille, Institut de Pathologie, Lille, France
| | - Tania Attié-Bitach
- Laboratoire de biologie médicale multisites SeqOIA, Paris, France; Service de Médecine Génomique des Maladies Rares, APHP.Centre, Université de Paris, Paris, France
| | - Timo Wagner
- Medizinische Genetik Mainz, Limbach Genetics, Mainz, Germany
| | - Carsten Bergmann
- Medizinische Genetik Mainz, Limbach Genetics, Mainz, Germany; Department of Medicine, Nephrology, University Hospital Freiburg, Freiburg, Germany
| | - Anne Kathrin Höhn
- Division of Pathology, University of Leipzig Medical Center, Leipzig, Germany
| | - Shirlee Shril
- Division of Nephrology, Boston Children's Hospital, Boston, USA
| | - Ari Pollack
- Division of Genetic Medicine, University of Washington, Seattle, Washington, USA
| | - Tara Wenger
- Division of Genetic Medicine, University of Washington, Seattle, Washington, USA
| | - Abbey A Scott
- Division of Genetic Medicine, Seattle Children's Hospital, Seattle, Washington, USA
| | - Sarah Paolucci
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Jillian Buchan
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - George C Gabriel
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA; Texas Children's Hospital, Houston, Texas, USA; Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Florence Petit
- Centre Hospitalier Universitaire de Lille, Clinique de Génétique Guy Fontaine, Lille, France
| | | | - Gregory J Pazour
- Program in Molecular Medicine, University of Massachusetts Medical School, Biotech II, Worcester, USA
| | - Cecilia W Lo
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.
| | - Bernt Popp
- Institute for Human Genetics, University of Leipzig Medical Center, Leipzig, Germany.
| | - Jan Halbritter
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, Berlin, Germany; Division of Nephrology, University of Leipzig Medical Center, Leipzig, Germany.
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Sure F, Bertog M, Afonso S, Diakov A, Rinke R, Madej MG, Wittmann S, Gramberg T, Korbmacher C, Ilyaskin AV. Transmembrane serine protease 2 (TMPRSS2) proteolytically activates the epithelial sodium channel (ENaC) by cleaving the channel's γ-subunit. J Biol Chem 2022; 298:102004. [PMID: 35504352 PMCID: PMC9163703 DOI: 10.1016/j.jbc.2022.102004] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 04/21/2022] [Accepted: 04/27/2022] [Indexed: 01/09/2023] Open
Abstract
The epithelial sodium channel (ENaC) is a heterotrimer consisting of α-, β-, and γ-subunits. Channel activation requires proteolytic release of inhibitory tracts from the extracellular domains of α-ENaC and γ-ENaC; however, the proteases involved in the removal of the γ-inhibitory tract remain unclear. In several epithelial tissues, ENaC is coexpressed with the transmembrane serine protease 2 (TMPRSS2). Here, we explored the effect of human TMPRSS2 on human αβγ-ENaC heterologously expressed in Xenopus laevis oocytes. We found that coexpression of TMPRSS2 stimulated ENaC-mediated whole-cell currents by approximately threefold, likely because of an increase in average channel open probability. Furthermore, TMPRSS2-dependent ENaC stimulation was not observed using a catalytically inactive TMPRSS2 mutant and was associated with fully cleaved γ-ENaC in the intracellular and cell surface protein fractions. This stimulatory effect of TMPRSS2 on ENaC was partially preserved when inhibiting its proteolytic activity at the cell surface using aprotinin but was abolished when the γ-inhibitory tract remained attached to its binding site following introduction of two cysteine residues (S155C–Q426C) to form a disulfide bridge. In addition, computer simulations and site-directed mutagenesis experiments indicated that TMPRSS2 can cleave γ-ENaC at sites both proximal and distal to the γ-inhibitory tract. This suggests a dual role of TMPRSS2 in the proteolytic release of the γ-inhibitory tract. Finally, we demonstrated that TMPRSS2 knockdown in cultured human airway epithelial cells (H441) reduced baseline proteolytic activation of endogenously expressed ENaC. Thus, we conclude that TMPRSS2 is likely to contribute to proteolytic ENaC activation in epithelial tissues in vivo.
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Affiliation(s)
- Florian Sure
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Institute of Cellular and Molecular Physiology, Erlangen, Germany
| | - Marko Bertog
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Institute of Cellular and Molecular Physiology, Erlangen, Germany
| | - Sara Afonso
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Institute of Cellular and Molecular Physiology, Erlangen, Germany
| | - Alexei Diakov
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Institute of Cellular and Molecular Physiology, Erlangen, Germany
| | - Ralf Rinke
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Institute of Cellular and Molecular Physiology, Erlangen, Germany
| | - M Gregor Madej
- Department of Biophysics II/Structural Biology, University of Regensburg, Regensburg, Germany
| | - Sabine Wittmann
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Universitätsklinikum Erlangen, Institute of Clinical and Molecular Virology, Erlangen, Germany
| | - Thomas Gramberg
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Universitätsklinikum Erlangen, Institute of Clinical and Molecular Virology, Erlangen, Germany
| | - Christoph Korbmacher
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Institute of Cellular and Molecular Physiology, Erlangen, Germany.
| | - Alexandr V Ilyaskin
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Institute of Cellular and Molecular Physiology, Erlangen, Germany
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232
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Design of a Multi-Epitope Vaccine against Tropheryma whipplei Using Immunoinformatics and Molecular Dynamics Simulation Techniques. Vaccines (Basel) 2022; 10:vaccines10050691. [PMID: 35632446 PMCID: PMC9147804 DOI: 10.3390/vaccines10050691] [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: 03/07/2022] [Revised: 04/13/2022] [Accepted: 04/20/2022] [Indexed: 12/15/2022] Open
Abstract
Whipple’s disease is caused by T. whipplei, a Gram-positive pathogenic bacterium. It is considered a persistent infection affecting various organs, more likely to infect males. There is currently no licensed vaccination available for Whipple’s disease; thus, the development of a chimeric peptide-based vaccine against T. whipplei has the potential to be tremendously beneficial in preventing Whipple’s disease in the future. The present study aimed to apply modern computational approaches to generate a multi-epitope-based vaccine that expresses antigenic determinants prioritized from the core proteome of two T. whipplei whole proteomes. Using an integrated computational approach, four immunodominant epitopes were found from two extracellular proteins. Combined, these epitopes covered 89.03% of the global population. The shortlisted epitopes exhibited a strong binding affinity for the B- and T-cell reference set of alleles, high antigenicity score, nonallergenic nature, high solubility, nontoxicity, and excellent binders of DRB1*0101. Through the use of appropriate linkers and adjuvation with a suitable adjuvant molecule, the epitopes were designed into a chimeric vaccine. An adjuvant was linked to the connected epitopes to boost immunogenicity and efficiently engage both innate and adaptive immunity. The physiochemical properties of the vaccine were observed favorable, leading toward the 3D modeling of the construct. Furthermore, the vaccine’s binding confirmation to the TLR-4 critical innate immune receptor was also determined using molecular docking and molecular dynamics (MD) simulations, which shows that the vaccine has a strong binding affinity for TLR4 (−29.4452 kcal/mol in MM-GBSA and −42.3229 kcal/mol in MM-PBSA). Overall, the vaccine described here has a promising potential for eliciting protective and targeted immunogenicity, subject to further experimental testing.
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233
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Designing of a Novel Multi-Antigenic Epitope-Based Vaccine against E. hormaechei: An Intergraded Reverse Vaccinology and Immunoinformatics Approach. Vaccines (Basel) 2022; 10:vaccines10050665. [PMID: 35632421 PMCID: PMC9143018 DOI: 10.3390/vaccines10050665] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/15/2022] [Accepted: 04/20/2022] [Indexed: 12/14/2022] Open
Abstract
Enterobacter hormaechei is involved in multiple hospital-associated infections and is resistant to beta-lactam and tetracycline antibiotics. Due to emerging antibiotics resistance in E. hormaechei and lack of licensed vaccine availability, efforts are required to overcome the antibiotics crisis. In the current research study, a multi-epitope-based vaccine against E. hormaechei was designed using reverse vaccinology and immunoinformatic approaches. A total number of 50 strains were analyzed from which the core proteome was extracted. One extracellular (curlin minor subunit CsgB) and two periplasmic membrane proteins (flagellar basal-body rod protein (FlgF) and flagellar basal body P-ring protein (FlgI) were prioritized for B and T-cell epitope prediction. Only three filtered TPGKMDYTS, GADMTPGKM and RLSAESQAT epitopes were used when designing the vaccine construct. The epitopes were linked via GPGPG linkers and EAAAK linker-linked cholera toxin B-subunit adjuvant was used to enhance the immune stimulation efficacy of the vaccine. Docking studies of the vaccine construct with immune cell receptors revealed better interactions, vital for generating proper immune reactions. Docked complexes of vaccine with MHC-I, MHC-II and Tool-like receptor 4 (TLR-4) reported the lowest binding energy of −594.1 kcal/mol, −706.7 kcal/mol, −787.2 kcal/mol, respectively, and were further subjected to molecular dynamic simulations. Net binding free energy calculations also confirmed that the designed vaccine has a strong binding affinity for immune receptors and thus could be a good vaccine candidate for future experimental investigations.
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234
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D. S. P, Chaturvedi PK, Krishnamoorthy D, Seo YS, Thippana M, Park WY. Fused toes homolog, a potential molecular regulator of human papillomavirus type 16 E6 and E7 oncoproteins in cervical cancer. PLoS One 2022; 17:e0266532. [PMID: 35421154 PMCID: PMC9009596 DOI: 10.1371/journal.pone.0266532] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 03/22/2022] [Indexed: 11/19/2022] Open
Abstract
Human papillomavirus type 16 (HPV16) plays a major role in the development of cervical cancer. The oncogenic potential of HPV16 is attributed to E6 and E7 oncoproteins. Here, we investigated the relationship between fused toes homolog (FTS) and HPV16 E6 and E7 in cervical cancer cells. HPV16-positive CaSki and SiHa cell lines were used for in vitro studies. FTS silencing was performed using a small interfering RNA (siRNA)-based approach, and western blotting was performed to determine the protein expression of tumor suppressors and cell survival markers. Immunoprecipitation, immunofluorescence, in silico analysis, and immunohistochemistry were performed to determine the interaction between, and intracellular co-localization of, FTS and both the E6 and E7 proteins. Silencing of FTS reduced the expression of the E6 and E7 proteins in cervical cancer cell lines and conversely increased the expression of the tumor suppressor proteins p53 and retinoblastoma protein. However, the primary transcripts of HPV16 E6 and E7 were unaffected by FTS silencing; furthermore, FTS transcription was unaffected by silencing of either E6 or E7, suggesting their interaction occurs post-translationally. Immunofluorescence and immunohistochemistry analysis demonstrated co-localization of FTS with the HPV16 E6 and E7 proteins, while immunoprecipitation results suggested that FTS interacts with both E6 and E7. Furthermore, in silico structural analysis identified putative residues involved in the binding of FTS with E6 and E7. Taken together, these results show that FTS affects both HPV16 E6 and E7 oncogenes in cervical cancer. We propose FTS as a target for the prevention of cervical cancer development and progression.
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Affiliation(s)
- Prabakaran D. S.
- Department of Radiation Oncology, Chungbuk National University Hospital, Cheongju, Republic of Korea
| | - Pankaj Kumar Chaturvedi
- Department of Radiation Oncology, Chungbuk National University Hospital, Cheongju, Republic of Korea
| | | | - Young-Seok Seo
- Department of Radiation Oncology, Chungbuk National University Hospital, Cheongju, Republic of Korea
| | - Mallikarjuna Thippana
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, India
| | - Woo-Yoon Park
- Department of Radiation Oncology, Chungbuk National University Hospital, Cheongju, Republic of Korea
- Department of Radiation Oncology, Chungbuk National University College of Medicine, Cheongju, Republic of Korea
- * E-mail:
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235
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Kootery KP, Sarojini S. Structural and functional characterization of a hypothetical protein in the RD7 region in clinical isolates of Mycobacterium tuberculosis - an in silico approach to candidate vaccines. J Genet Eng Biotechnol 2022; 20:55. [PMID: 35394551 PMCID: PMC8993957 DOI: 10.1186/s43141-022-00340-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 03/30/2022] [Indexed: 11/29/2022]
Abstract
Background Mycobacterium tuberculosis has been ravaging humans by inflicting respiratory tuberculosis since centuries. Bacillus Calmette Guerine (BCG) is the only vaccine available for tuberculosis, and it is known to be poorly effective against adult tuberculosis. Proteins belonging to the ESAT-6 family and PE/PPE family show immune responses and are included in different vaccine trials. Herein, we study the functional and structural characterization of a 248 amino acid long putative protein novel hypothetical protein 1 (NHP1) present in the RD7 region of Mycobacterium tuberculosis (identified first by subtractive hybridization in the clinical isolate RGTB123) using bioinformatics tools. Results Physicochemical properties were studied using Expasy ProtParam and SMS software. We predicted different B-cell and T-cell epitopes by using the immune epitope database (IEDB) and also tested antigenicity, immunogenicity, and allergenicity. Secondary structure of the protein predicted 30% alpha helices, 20% beta strands, and 48% random coils. Tertiary structure of the protein was predicted using the Robetta server using the Mycobacterium smegmatis protein as the putative protein with homology. Structural evaluations were done with Ramachandran plot analysis, ProSA-web, and VERIFY3D, and with GalaxyWEB server, a more stable structure was validated with good stereo chemical properties. Conclusion The present study of a subtracted genomic locus using various bioinformatics tools indicated good immunological properties of the putative mycobacterial protein, NHP1. Evidence obtained from the analyses of NHP1 using structure prediction tools strongly point to the fact that NHP1 is an ancient protein having flavodoxin folding structure with ATP binding sites. Positive scores were obtained for antigenicity, immunogenicity, and virulence too, implying the possibility of NHP1 to be a potential vaccine candidate. Such computational studies might give clues for developing newer vaccines for tuberculosis, which is the need of the hour. Supplementary Information The online version contains supplementary material available at 10.1186/s43141-022-00340-5.
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Affiliation(s)
- Kaviya Parambath Kootery
- Department of Lifesciences, CHRIST (Deemed to be University), Bengaluru, Karnataka, 560029, India
| | - Suma Sarojini
- Department of Lifesciences, CHRIST (Deemed to be University), Bengaluru, Karnataka, 560029, India.
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Semenova AM, Gadzhiakhmedova YR, Bespalov AV, Dotsenko VV, Aksenov NA, Aksenova IV. New Heterocyclisation Reactions of 5-Amino-3-(cyanomethyl)-1H-pyrazole-4-carbonitrile with Some 1,3-Dielectrophilic Agents. RUSS J GEN CHEM+ 2022. [DOI: 10.1134/s1070363222030057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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237
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Castrosanto MA, Clemente AJN, Whitfield AE, Alviar KB. In silico analysis of the predicted protein-protein interaction of syntaxin-18, a putative receptor of Peregrinus maidis Ashmead (Hemiptera: Delphacidae) with Maize mosaic virus glycoprotein. J Biomol Struct Dyn 2022; 41:3956-3963. [PMID: 35377265 DOI: 10.1080/07391102.2022.2059569] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The corn planthopper, Peregrinus maidis Ashmead (Hemiptera:Delphacidae), is a widely distributed insect pest which serves as a vector of two phytopathogenic viruses, Maize mosaic virus (MMV) and Maize stripe virus (MStV). It transmits the viruses in a persistent and propagative manner. MMV is an alphanucleorhabdovirus with a negative-sense, single-stranded RNA unsegmented genome. One identified insect vector protein that may serve as receptor to MMV is Syntaxin-18 (PmStx18) which belongs to the SNAREs (soluble N-ethylmaleimide-sensitive factor attachment protein receptors) proteins. SNAREs play major roles in the final stage of docking and subsequent fusion of diverse vesicle-mediated transport events. In this work, in silico analysis of the interaction of MMV glycoprotein (MMV G) and PmStx18 was performed. Various freely available protein-protein docking web servers were used to predict the 3 D complex of MMV G and PmStx18. Analysis and protein-protein interaction (PPI) count showed that the complex predicted by the ZDOCK server has the highest number of interaction and highest affinity, as suggested by the calculated solvation free energy gain upon formation of the interface (ΔiG = -31 kcal/mol). Molecular dynamics simulation of the complex revealed important interactions at the interface over the course of 25 ns. This is the first in silico analysis performed for the interaction on a putative receptor of P. maidis and MMV G. The results of the PPI prediction provide novel information for studying the role of Stx18 in the transport, docking and fusion events involved in virus particle transport in the insect vector cells and its release.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Melvin A Castrosanto
- Institute of Chemistry, College of Arts and Sciences, University of the Philippines Los Baños, Los Baños, Laguna Philippines
| | - Apel Jae N Clemente
- Institute of Weed Science, Entomology and Plant Pathology, College of Agriculture and Food Science, University of the Philippines Los Baños, Los Baños, Laguna Philippines
| | - Anna E Whitfield
- Department of Entomology and Plant Pathology, North Carolina State University, NC, USA
| | - Karen B Alviar
- Institute of Weed Science, Entomology and Plant Pathology, College of Agriculture and Food Science, University of the Philippines Los Baños, Los Baños, Laguna Philippines
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Gülbüz M, Saral Sariyer A. Combined in silico approach and whole genome sequencing: Acinetobacter baumannii ST218 isolate harboring ADC-73 β-lactamase which has a similar C-loop with ADC-56 and ADC-68 β-lactamase. J Mol Graph Model 2022; 114:108195. [DOI: 10.1016/j.jmgm.2022.108195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 04/07/2022] [Accepted: 04/11/2022] [Indexed: 11/28/2022]
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239
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Analysis of rainbow trout TCRαβ/CD3 complex: An in-silico modeling approach. Mol Immunol 2022; 144:35-43. [DOI: 10.1016/j.molimm.2022.02.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/07/2022] [Accepted: 02/08/2022] [Indexed: 11/18/2022]
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240
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Movahedpour A, Mostafavi-Pour Z, Sarkari B, Taheri-Anganeh M, Nezafat N, Savardashtaki A, Ghasemi Y. Designing a Multi-Epitope Antigen for Serodiagnosis of Strongyloides stercoralis Based on L3Nie.01 and IgG Immunoreactive Epitopes. Avicenna J Med Biotechnol 2022; 14:114-124. [PMID: 35633984 PMCID: PMC9077661 DOI: 10.18502/ajmb.v14i2.8886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 10/30/2021] [Indexed: 11/24/2022] Open
Abstract
Background Serological diagnosis of Strongyloides stercoralis (S. stercoralis) is fre-quently challenging because of cross-reactivity with other parasitic nematodes. Therefore, it is necessary to introduce novel serological tests with high performance to properly diagnose this neglected parasitic infection. The purpose of the current study was to design a multi-epitope construct for the diagnosis of S. stercoralis. Methods For the purpose of this study, first, highly antigenic segments and potential immunodominant epitopes of S. stercoralis were identified from two antigenic proteins, and then all of the selected parts were linked by an appropriate linker. Next, the physicochemical features of the designed construct were analyzed. Then, tertiary structures of the construct were built and evaluated to find out the best one. Lastly, the amino acid sequence was reverse-translated and optimized for over-expression in Escherchia coli (E. coli). Results The bioinformatic evaluation indicated that the designed protein construct could be hydrophilic, thermostable, and acidic and the estimated half-life was more than 10 hr in E. coli. Conclusion According to the results of the study, the designed construct could be used as an efficient antigen in the ELISA system for serological diagnosis of human strong-yloidiasis.
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Affiliation(s)
- Ahmad Movahedpour
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences Shiraz, Iran
- Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zohreh Mostafavi-Pour
- Recombinant Protein Laboratory, Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
- Autophagy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Bahador Sarkari
- Department of Parasitology and Mycology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
- Basic Sciences in Infectious Diseases Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mortaza Taheri-Anganeh
- Cellular and Molecular Research Center, Cellular and Molecular Medicine Institute, Urmia University of Medical Sciences, Urmia, Iran
| | - Navid Nezafat
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Amir Savardashtaki
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences Shiraz, Iran
- Infertility Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Younes Ghasemi
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
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241
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In silico designed Staphylococcus aureus B-cell multi-epitope vaccine did not elicit antibodies against target antigens suggesting multi-domain approach. J Immunol Methods 2022; 504:113264. [PMID: 35341759 PMCID: PMC9040383 DOI: 10.1016/j.jim.2022.113264] [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: 11/16/2021] [Revised: 01/24/2022] [Accepted: 03/21/2022] [Indexed: 10/18/2022]
Abstract
The vaccine development strategies have evolved from using an entire organism as an immunogen to a single antigen and further towards an epitope. Since an epitope is a relatively tiny and immunologically relevant part of an antigen, it has the potential to stimulate more robust and specific immune responses while causing minimal adverse effects. As a result, the recent focus of vaccine development has been to develop multi-epitope vaccines that can target multiple virulence mechanisms. Accordingly, we designed multi-epitope vaccine candidates B (multi-B-cell epitope immunogen) and CTB-B (an adjuvant - cholera toxin subunit B (CTB) - attached to immunogen B) against S. aureus by employing immunoinformatics approaches. The designed vaccines are composed of B-cell epitope segments (20-mer) of the eight well-characterized S. aureus virulence factors, namely ClfB, FnbpA, Hla, IsdA, IsdB, LukE, SdrD, and SdrE connected in series. The designed vaccines were expressed, purified, and administered to C57BL/6 mice with Freund adjuvant to evaluate the immunogenicity and protective efficacy. The results revealed that the immunized mice showed high IgG titer for the immunogen, and the antibody titer increased significantly following the second immunization. However, the generated antibodies did not protect mice from infection. The interaction of anti-B antibodies with source virulence factors showed that the generated antibodies have no binding affinity with any of the corresponding virulence factors. Our results demonstrate the limitation of in silico designed B-cell multi-epitope vaccine and suggest that a protein domain carrying both linear and conformational B-cell epitopes might be a better choice for developing an effective multi-epitope vaccine against S. aureus.
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242
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Boumezber S, Yelekçi K. Screening of novel and selective inhibitors for neuronal nitric oxide synthase (nNOS) via structure-based drug design techniques. J Biomol Struct Dyn 2022; 41:3607-3629. [PMID: 35322764 DOI: 10.1080/07391102.2022.2054471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
NO, or nitric oxide, is produced by a family of enzymes called nitric oxide synthase (NOS) from L-arginine. NO regulates many physiological functions such as smooth muscle relaxation, immune defense, and memory function. The overproduction of NO by the neuronal isoform of nitric oxide synthase (nNOS) is implicated in neurodegeneration and neuropathic pain, making nNOS inhibition a promising therapeutic approach. Many developed nNOS inhibitors, generally L-arginine mimetics, have some issues in selectivity and bioavailability. According to earlier studies, targeting nNOS has the advantage of decreasing excess NO in the brain while avoiding the negative consequences of inhibiting the two isozymes: endothelial NOS (eNOS) and inducible NOS (iNOS). This study applied structure-based virtual screening, molecular docking, and molecular dynamics simulations to design potent and selective inhibitors against nNOS over related isoforms (eNOS and iNOS) using human X-ray crystal structures of the NOS isoforms. It was discovered that some compounds displayed a very good inhibitory potency for hnNOS and moderate selectivity for the other isozymes, eNOS and iNOS, in addition to good solubility and desirable physiochemical properties. The compounds which showed good stability and selectivity with nNOS, such as ZINC000013485422, can be interesting and informative guidance for designing more potent human nNOS inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sarah Boumezber
- Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University, Istanbul, Turkey
| | - Kemal Yelekçi
- Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University, Istanbul, Turkey
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243
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Gerlevik U, Ergoren MC, Sezerman OU, Temel SG. Structural analysis of M1AP variants associated with severely impaired spermatogenesis causing male infertility. PeerJ 2022; 10:e12947. [PMID: 35341049 PMCID: PMC8944341 DOI: 10.7717/peerj.12947] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 01/25/2022] [Indexed: 01/11/2023] Open
Abstract
Background Impaired meiosis can result in absence of sperm in the seminal fluid. This condition, namely non-obstructive azoospermia (NOA), is one of the reasons of male infertility. Despite the low number of studies on meiosis 1-associated protein (M1AP) in the literature, M1AP is known to be crucial for spermatogenesis. Recently, seven variants (five missense, one frameshift, one splice-site) have been reported in the M1AP gene as associated with NOA, cryptozoospermia and oligozoospermia in two separate studies. However, all missense variants were evaluated as variant of uncertain significance by these studies. Therefore, we aimed to analyze their structural impacts on the M1AP protein that could lead to NOA. Methods We firstly performed an evolutionary conservation analysis for the variant positions. Afterwards, a comprehensive molecular modelling study was performed for the M1AP structure. By utilizing this model, protein dynamics were sampled for the wild-type and variants by performing molecular dynamics (MD) simulations. Results All variant positions are highly conserved, indicating that they are potentially important for function. In MD simulations, none of the variants led to a general misfolding or loss of stability in the protein structure, but they did cause severe modifications in the conformational dynamics of M1AP, particularly through changes in local interactions affecting flexibility, hinge and secondary structure. Conclusions Due to critical perturbations in protein dynamics, we propose that these variants may cause NOA by affecting important interactions regulating meiosis, particularly in wild-type M1AP deficiency since the variants are reported to be homozygous or bi-allelic in the infertile individuals. Our results provided reasonable insights about the M1AP structure and the effects of the variants to the structure and dynamics, which should be further investigated by experimental studies to validate.
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Affiliation(s)
- Umut Gerlevik
- Department of Biostatistics and Bioinformatics, Institute of Health Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey,Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Mahmut Cerkez Ergoren
- Department of Medical Genetics, Faculty of Medicine, Near East University, Nicosia, Cyprus,DESAM Institute, Near East University, Nicosia, Cyprus
| | - Osman Uğur Sezerman
- Department of Biostatistics and Bioinformatics, Institute of Health Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey,Department of Biostatistics and Medical Informatics, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Sehime Gulsun Temel
- Department of Medical Genetics, Faculty of Medicine, Bursa Uludag University, Bursa, Turkey,Department of Histology & Embryology, Faculty of Medicine, Bursa Uludag University, Bursa, Turkey,Department of Translational Medicine, Health Sciences Institute, Bursa Uludag University, Bursa, Turkey
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244
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Kumar A, Sharma P, Arun A, Meena LS. Development of peptide vaccine candidate using highly antigenic PE-PGRS family proteins to stimulate the host immune response against Mycobacterium tuberculosis H 37Rv: an immuno-informatics approach. J Biomol Struct Dyn 2022; 41:3382-3404. [PMID: 35293852 DOI: 10.1080/07391102.2022.2048079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Tuberculosis (TB) is a fast spreading; transmissible disease caused by the Mycobacterium tuberculosis (M. tuberculosis). M. tuberculosis has a high death rate in its endemic regions due to a lack of appropriate treatment and preventative measures. We have used a vaccinomics strategy to create an effective multi-epitope vaccine against M. tuberculosis. The antigenic proteins with the highest antigenicity were utilised to predict cytotoxic T-lymphocyte (CTL), helper T-lymphocyte (HTL), and linear B-lymphocyte (LBL) epitopes. CTL and HTL epitopes were covered in 99.97% of the population. Seven epitopes each of CTL, HTL, and LBL were ultimately selected and utilised to develop a multi-epitope vaccine. A vaccine design was developed by combining these epitopes with suitable linkers and LprG adjuvant. The vaccine chimera was revealed to be highly immunogenic, non-allergenic, and non-toxic. To ensure a better expression within the Escherichia coli K12 (E. coli K12) host system, codon adaptation and in silico cloning were accomplished. Following that, various validation studies were conducted, including molecular docking, molecular dynamics simulation, and immunological simulation, all of which indicated that the designed vaccine would be stable in the biological environment and effective against M. tuberculosis infection. The immune simulation revealed higher levels of T-cell and B-cell activity, which corresponded to the actual immune response. Exposure simulations were repeated several times, resulting in increased clonal selection and faster antigen clearance. These results suggest that, if proposed vaccine chimera would test both in-vitro and in-vivo, it could be a viable treatment and preventive strategy for TB.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ajit Kumar
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC, Ghaziabad, Uttar Pradesh, India
| | - Priyanka Sharma
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Akanksha Arun
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC, Ghaziabad, Uttar Pradesh, India
| | - Laxman S Meena
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC, Ghaziabad, Uttar Pradesh, India
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245
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Savar NS, Shengjuler D, Doroudian F, Vallet T, Mac Kain A, Arashkia A, Khamesipour A, Lundstrom K, Vignuzzi M, Niknam HM. An alphavirus-derived self-amplifying mRNA encoding PpSP15-LmSTI1 fusion protein for the design of a vaccine against leishmaniasis. Parasitol Int 2022; 89:102577. [PMID: 35301120 DOI: 10.1016/j.parint.2022.102577] [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: 06/23/2021] [Revised: 02/27/2022] [Accepted: 03/09/2022] [Indexed: 10/18/2022]
Abstract
The main aims of the present study were to design a fusion protein of Leishmania major stress-inducible protein 1 (LmSTI1) and Phlebotomus papatasi SP15 (PpSP15), and to express it in the form of alphavirus packaged Self-amplifying mRNA (SAM). Two combinations, PpSP15-LmSTI1 and LmSTI1-PpSP15 fusion forms, were analyzed for folding and minimum free energies of the mRNA. Conformational studies on 3D modeled fusion and native forms were performed, and the Root-Mean-Square-distance (RMSD) of the Cα atomic coordinates were calculated. Antigenicity and stability were predicted using bioinformatics tools. The coding sequences of PpSP15-LmSTI1 fusion, PpSP15, and LmSTI1 were cloned into an alphavirus-based vector and used to produce the SAM constructs. All the subcloned constructs were then subjected to packaging in the form of viral replicon particles (VRPs),and were evaluated for their ability to infect BHK-21 cells and express the recombinant fusion proteins. The in-silico analysis indicated that the PpSP15-LmSTI1 combination could be a promising candidate based on lower folding ΔG of mRNA, higher protein antigenicity and lower instability indexes, and less conformational changes compared to the native proteins and the LmSTI1-PpSP15 fusion form. Packaged SAM encoding fusion and native antigens are used for infection of mammalian cells and for recombinant protein expression. This is the first study on in silico designing and successful packaging of an alphavirus-derived SAM in the form of the VRPs to target leishmaniasis.
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Affiliation(s)
| | - Djoshkun Shengjuler
- Institut Pasteur, Viral Populations and Pathogenesis Unit, Centre National de la Recherche Scientifique UMR 3569, Paris 75015, France
| | - Fatemeh Doroudian
- Immunology Department, Pasteur Institute of Iran, Tehran 1316943551, Iran
| | - Thomas Vallet
- Institut Pasteur, Viral Populations and Pathogenesis Unit, Centre National de la Recherche Scientifique UMR 3569, Paris 75015, France
| | - Alice Mac Kain
- Institut Pasteur, Viral Populations and Pathogenesis Unit, Centre National de la Recherche Scientifique UMR 3569, Paris 75015, France
| | - Arash Arashkia
- Virology Department, Pasteur Institute of Iran, Tehran 1316943551, Iran
| | - Ali Khamesipour
- Center for Research and Training in Skin Diseases and Leprosy, Tehran University of Medical Sciences, Tehran 1416613675, Iran
| | | | - Marco Vignuzzi
- Institut Pasteur, Viral Populations and Pathogenesis Unit, Centre National de la Recherche Scientifique UMR 3569, Paris 75015, France.
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Dolganov AA, Levchenko AG, Dahno PG, Guz’ DD, Chikava AR, Dotsenko VV, Aksenov NA, Aksenova IV. 7-Aryl-3-(hydroxymethyl)-5-oxo-1,2,3,5-tetrahydro[1,2,4]triazolo[1,5-a]pyridine-6,8-dicarbonitriles: Synthesis and Predicted Biological Activity. RUSS J GEN CHEM+ 2022. [DOI: 10.1134/s1070363222020074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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247
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Three new inhibitors of class A β-lactamases evaluated by molecular docking and dynamics simulations methods: relebactam, enmetazobactam, and QPX7728. J Mol Model 2022; 28:76. [PMID: 35243556 DOI: 10.1007/s00894-022-05073-3] [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: 09/01/2021] [Accepted: 02/26/2022] [Indexed: 10/18/2022]
Abstract
Antibiotic-resistant Acinetobacter baumannii, Pseudomonas aeruginosa, Mycobacterium tuberculosis, Staphylococcus aureus, and Enterobacterales infections are serious global health problems, and class A β-lactamases are one mechanism that leads to antibiotic resistance. QPX7728, relebactam, and enmetazobactam are new β-lactamase inhibitors to combat β-lactam resistance. in silico approach was used in the current study to find which of the three inhibitors would be more effective for all class A β-lactamases and to reveal molecular insights into the differences between their binding energies. The mutations in conserved residues of the active sites of β-lactamases were defined using BLDB and Clustal Omega. FastME and MMseq2 were used for cluster and phylogeny analysis. 3D protein structure models for β-lactamases were built using SWISS-MODEL. ERRAT and Galaxy Web Server were used to verify 42 β-lactamase protein structures. QPX7728, relebactam, and enmetazobactam were docked to β-lactamases by using AutoDock 4.2. The TEM76-relebactam, CTX-M-81-relebactam, TEM-76-enmetazobactam, and CTX-M-200-enmetazobactam complexes were simulated by molecular dynamics method for 500 ns. Based on molecular docking results, relebactam and QPX7728 were more favorable inhibitors for serine A β-lactamases. A 2D representation of the interactions between ligands and β-lactamases showed that S235, hydrogen bonded with TEM-76, might play a role in inhibitor design. A 500-ns MD analysis of complexes indicated that distance from S70, stability in the enzyme active cavity, and high atomic displacement would account for a significant difference in inhibitor binding affinity.
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248
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BAHA S, ZHANG M, BEHLOUL N, LIU Z, WEI W, MENG J. Efficient production and characterization of immunogenic HEV-PCV2 chimeric virus-like particles. Vet Microbiol 2022; 268:109410. [DOI: 10.1016/j.vetmic.2022.109410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 03/11/2022] [Accepted: 03/24/2022] [Indexed: 11/16/2022]
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249
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Rajpoot S, Srivastava G, Siddiqi MI, Saqib U, Parihar SP, Hirani N, Baig MS. Identification of novel inhibitors targeting TIRAP interactions with BTK and PKCδ in inflammation through an in silico approach. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2022; 33:141-166. [PMID: 35174746 DOI: 10.1080/1062936x.2022.2035817] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 01/26/2022] [Indexed: 06/14/2023]
Abstract
Advanced computational tools focusing on protein-protein interaction (PPI) based drug development is a powerful platform to accelerate the therapeutic development of small lead molecules and repurposed drugs. Toll/interleukin-1 receptor (TIR) domain-containing adapter protein (TIRAP) and its interactions with other proteins in macrophages signalling are crucial components of severe or persistent inflammation. TIRAP activation through Bruton's tyrosine kinase (BTK) and Protein Kinase C delta (PKCδ) is essential for downstream inflammatory signalling. We created homology-based structural models of BTK and PKCδ in MODELLER 9.24. TIRAP interactions with BTK and PKCδ in its non-phosphorylated and phosphorylated states were determined by multiple docking tools including HADDOCK 2.4, pyDockWEB and ClusPro 2.0. Food and Drug Administration (FDA)-approved drugs were virtually screened through Discovery Studio LibDock and Autodock Vina tools to target the common TIR domain residues of TIRAP, which interact with both BTK and PKC at the identified interfacial sites of the complexes. Four FDA-approved drugs were identified and found to have stable interactions over a range of 100 ns MD simulation timescales. These drugs block the interactions of both kinases with TIRAP in silico. Hence, these drugs have the potential to dampen downstream inflammatory signalling and inflammation-mediated disease.
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Affiliation(s)
- S Rajpoot
- Department of Biosciences and Biomedical Engineering (BSBE), Indian Institute of Technology Indore (IITI), Simrol, Indore, India
| | - G Srivastava
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute (CSIR-CDRI), Jankipuram Extension, Sitapur Road, Lucknow, India
| | - M I Siddiqi
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute (CSIR-CDRI), Jankipuram Extension, Sitapur Road, Lucknow, India
| | - U Saqib
- Department of Chemistry, Indian Institute of Technology Indore (IITI), Simrol, Indore, India
| | - S P Parihar
- Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa) and Institute of Infectious Diseases and Molecular Medicine (IDM), Division of Medical Microbiology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - N Hirani
- MRC Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - M S Baig
- Department of Biosciences and Biomedical Engineering (BSBE), Indian Institute of Technology Indore (IITI), Simrol, Indore, India
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250
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Srivastava S, Verma S, Kamthania M, Agarwal D, Saxena AK, Kolbe M, Singh S, Kotnis A, Rathi B, Nayar SA, Shin HJ, Vashisht K, Pandey KC. Computationally validated SARS-CoV-2 CTL and HTL Multi-Patch vaccines, designed by reverse epitomics approach, show potential to cover large ethnically distributed human population worldwide. J Biomol Struct Dyn 2022; 40:2369-2388. [PMID: 33155524 PMCID: PMC7651196 DOI: 10.1080/07391102.2020.1838329] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 10/13/2020] [Indexed: 02/07/2023]
Abstract
The SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) is responsible for the COVID-19 outbreak. The highly contagious COVID-19 disease has spread to 216 countries in less than six months. Though several vaccine candidates are being claimed, an effective vaccine is yet to come. A novel reverse epitomics approach, 'overlapping-epitope-clusters-to-patches' method is utilized to identify the antigenic regions from the SARS-CoV-2 proteome. These antigenic regions are named as 'Ag-Patch or Ag-Patches', for Antigenic Patch or Patches. The identification of Ag-Patches is based on the clusters of overlapping epitopes rising from SARS-CoV-2 proteins. Further, we have utilized the identified Ag-Patches to design Multi-Patch Vaccines (MPVs), proposing a novel method for the vaccine design. The designed MPVs were analyzed for immunologically crucial parameters, physiochemical properties and cDNA constructs. We identified 73 CTL (Cytotoxic T-Lymphocyte) and 49 HTL (Helper T-Lymphocyte) novel Ag-Patches from the proteome of SARS-CoV-2. The identified Ag-Patches utilized to design MPVs cover 768 overlapping epitopes targeting 55 different HLA alleles leading to 99.98% of world human population coverage. The MPVs and Toll-Like Receptor ectodomain complex shows stable complex formation tendency. Further, the cDNA analysis favors high expression of the MPVs constructs in a human cell line. We identified highly immunogenic novel Ag-Patches from the entire proteome of SARS CoV-2 by a novel reverse epitomics approach and utilized them to design MPVs. We conclude that the novel MPVs could be a highly potential novel approach to combat SARS-CoV-2, with greater effectiveness, high specificity and large human population coverage worldwide. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sukrit Srivastava
- Molecular Medicine Lab., School of Life Science, Jawaharlal Nehru University, New Delhi, India
- Infection Biology Group, Indian Foundation for Fundamental Research, RaeBareli, India
| | - Sonia Verma
- Parasite-Host Biology Group, Protein Biochemistry & Engineering Lab, ICMR-National Institute of Malaria Research, New Delhi, India
| | - Mohit Kamthania
- Infection Biology Group, Indian Foundation for Fundamental Research, RaeBareli, India
| | - Deepa Agarwal
- Infection Biology Group, Indian Foundation for Fundamental Research, RaeBareli, India
| | - Ajay Kumar Saxena
- Molecular Medicine Lab., School of Life Science, Jawaharlal Nehru University, New Delhi, India
| | - Michael Kolbe
- Department for Structural Infection Biology, Centre for Structural Systems Biology (CSSB) & Helmholtz-Centre for Infection Research, Hamburg, Germany
- Faculty of Mathematics, Informatics and Natural Sciences, University of Hamburg, Hamburg, Germany
| | - Sarman Singh
- Department of Microbiology, All India Institute of Medical Sciences (AIIMS), Bhopal, India
| | - Ashwin Kotnis
- Department of Biochemistry, All India Institute of Medical Sciences (AIIMS), Bhopal, India
| | - Brijesh Rathi
- Laboratory For Translational Chemistry and Drug Discovery, Hansraj College, University of Delhi, New Delhi, India
| | - Seema A. Nayar
- Department of Microbiology, Government Medical College, Trivandrum, India
- Department of Microbiology, Sree Gokulam Medical College, Trivandrum, India
| | - Ho-Joon Shin
- Department of Microbiology, School of Medicine, Ajou University, Suwon, South Korea
| | - Kapil Vashisht
- Parasite-Host Biology Group, Protein Biochemistry & Engineering Lab, ICMR-National Institute of Malaria Research, New Delhi, India
| | - Kailash C. Pandey
- Parasite-Host Biology Group, Protein Biochemistry & Engineering Lab, ICMR-National Institute of Malaria Research, New Delhi, India
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