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da Silva-Júnior AHP, de Oliveira Silva RC, Gurgel APAD, Barros-Júnior MR, Nascimento KCG, Santos DL, Pena LJ, Lima RDCP, Batista MVDA, Chagas BS, de Freitas AC. Identification and Functional Implications of the E5 Oncogene Polymorphisms of Human Papillomavirus Type 16. Trop Med Infect Dis 2024; 9:140. [PMID: 39058182 PMCID: PMC11281449 DOI: 10.3390/tropicalmed9070140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Revised: 06/12/2024] [Accepted: 06/21/2024] [Indexed: 07/28/2024] Open
Abstract
The persistence of the human papillomavirus type 16 (HPV16) infection on the cervical epithelium contributes to the progression of cervical cancer. Studies have demonstrated that HPV16 genetic variants may be associated with different risks of developing cervical cancer. However, the E5 oncoprotein of HPV16, which is related to several cellular mechanisms in the initial phases of the infection and thus contributes to carcinogenesis, is still little studied. Here we investigate the HPV16 E5 oncogene variants to assess the effects of different mutations on the biological function of the E5 protein. We detected and analyzed the HPV16 E5 oncogene polymorphisms and their phylogenetic relationships. After that, we proposed a tertiary structure analysis of the protein variants, preferential codon usage, and functional activity of the HPV16 E5 protein. Intra-type variants were grouped in the lineages A and D using in silico analysis. The mutations in E5 were located in the T-cell epitopes region. We therefore analyzed the interference of the HPV16 E5 protein in the NF-kB pathway. Our results showed that the variants HPV16E5_49PE and HPV16E5_85PE did not increase the potential of the pathway activation capacity. This study provides additional knowledge about the mechanisms of dispersion of the HPV16 E5 variants, providing evidence that these variants may be relevant to the modulation of the NF-κB signaling pathway.
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Affiliation(s)
- Antônio Humberto P. da Silva-Júnior
- Laboratory of Molecular Studies and Experimental Therapy (LEMTE), Department of Genetics, Federal University of Pernambuco, Recife 50670-901, Pernambuco, Brazil; (A.H.P.d.S.-J.); (R.C.d.O.S.); (M.R.B.-J.); (K.C.G.N.); (D.L.S.); (R.d.C.P.L.); (B.S.C.)
| | - Ruany Cristyne de Oliveira Silva
- Laboratory of Molecular Studies and Experimental Therapy (LEMTE), Department of Genetics, Federal University of Pernambuco, Recife 50670-901, Pernambuco, Brazil; (A.H.P.d.S.-J.); (R.C.d.O.S.); (M.R.B.-J.); (K.C.G.N.); (D.L.S.); (R.d.C.P.L.); (B.S.C.)
| | - Ana Pavla A. Diniz Gurgel
- Department of Engineering and Environment, Federal University of Paraiba, João Pessoa 58033-455, Paraíba, Brazil;
| | - Marconi Rêgo Barros-Júnior
- Laboratory of Molecular Studies and Experimental Therapy (LEMTE), Department of Genetics, Federal University of Pernambuco, Recife 50670-901, Pernambuco, Brazil; (A.H.P.d.S.-J.); (R.C.d.O.S.); (M.R.B.-J.); (K.C.G.N.); (D.L.S.); (R.d.C.P.L.); (B.S.C.)
| | - Kamylla Conceição Gomes Nascimento
- Laboratory of Molecular Studies and Experimental Therapy (LEMTE), Department of Genetics, Federal University of Pernambuco, Recife 50670-901, Pernambuco, Brazil; (A.H.P.d.S.-J.); (R.C.d.O.S.); (M.R.B.-J.); (K.C.G.N.); (D.L.S.); (R.d.C.P.L.); (B.S.C.)
| | - Daffany Luana Santos
- Laboratory of Molecular Studies and Experimental Therapy (LEMTE), Department of Genetics, Federal University of Pernambuco, Recife 50670-901, Pernambuco, Brazil; (A.H.P.d.S.-J.); (R.C.d.O.S.); (M.R.B.-J.); (K.C.G.N.); (D.L.S.); (R.d.C.P.L.); (B.S.C.)
| | - Lindomar J. Pena
- Laboratory of Virology and Experimental Therapy, Instituto Aggeu Magalhães (IAM), Oswaldo Cruz Foundation, Recife 50670-901, Pernambuco, Brazil;
| | - Rita de Cássia Pereira Lima
- Laboratory of Molecular Studies and Experimental Therapy (LEMTE), Department of Genetics, Federal University of Pernambuco, Recife 50670-901, Pernambuco, Brazil; (A.H.P.d.S.-J.); (R.C.d.O.S.); (M.R.B.-J.); (K.C.G.N.); (D.L.S.); (R.d.C.P.L.); (B.S.C.)
| | - Marcus Vinicius de Aragão Batista
- Laboratory of Molecular Genetics and Biotechnology (GMBio), Department of Biology, Federal University of Sergipe, São Cristóvão 49107-230, Sergipe, Brazil
| | - Bárbara Simas Chagas
- Laboratory of Molecular Studies and Experimental Therapy (LEMTE), Department of Genetics, Federal University of Pernambuco, Recife 50670-901, Pernambuco, Brazil; (A.H.P.d.S.-J.); (R.C.d.O.S.); (M.R.B.-J.); (K.C.G.N.); (D.L.S.); (R.d.C.P.L.); (B.S.C.)
| | - Antonio Carlos de Freitas
- Laboratory of Molecular Studies and Experimental Therapy (LEMTE), Department of Genetics, Federal University of Pernambuco, Recife 50670-901, Pernambuco, Brazil; (A.H.P.d.S.-J.); (R.C.d.O.S.); (M.R.B.-J.); (K.C.G.N.); (D.L.S.); (R.d.C.P.L.); (B.S.C.)
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Rabaan AA, Alshahrani FS, Garout M, Alissa M, Mashraqi MM, Alshehri AA, Alsaleh AA, Alwarthan S, Sabour AA, Alfaraj AH, AlShehail BM, Alotaibi N, Abduljabbar WA, Aljeldah M, Alestad JH. Repositioning of anti-infective compounds against monkeypox virus core cysteine proteinase: a molecular dynamics study. Mol Divers 2024:10.1007/s11030-023-10802-8. [PMID: 38652365 DOI: 10.1007/s11030-023-10802-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 12/26/2023] [Indexed: 04/25/2024]
Abstract
Monkeypox virus (MPXV) core cysteine proteinase (CCP) is one of the major drug targets used to examine the inhibitory action of chemical moieties. In this study, an in silico technique was applied to screen 1395 anti-infective compounds to find out the potential molecules against the MPXV-CCP. The top five hits were selected after screening and processed for exhaustive docking based on the docked score of ≤ -9.5 kcal/mol. Later, the top three hits based on the exhaustive-docking score and interaction profile were selected to perform MD simulations. The overall RMSD suggested that two compounds, SC75741 and ammonium glycyrrhizinate, showed a highly stable complex with a standard deviation of 0.18 and 0.23 nm, respectively. Later, the MM/GBSA binding free energies of complexes showed significant binding strength with ΔGTOTAL from -21.59 to -15 kcal/mol. This report reported the potential inhibitory activity of SC75741 and ammonium glycyrrhizinate against MPXV-CCP by competitively inhibiting the binding of the native substrate.
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Affiliation(s)
- Ali A Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, 31311, Dhahran, Saudi Arabia.
- College of Medicine, Alfaisal University, 11533, Riyadh, Saudi Arabia.
- Department of Public Health and Nutrition, The University of Haripur, Haripur, 22610, Pakistan.
| | - Fatimah S Alshahrani
- Department of Internal Medicine, College of Medicine, King Saud University, 11362, Riyadh, Saudi Arabia
- Division of Infectious Diseases, Department of Internal Medicine, College of Medicine, King Saud University and King Saud University Medical City, 11451, Riyadh, Saudi Arabia
| | - Mohammed Garout
- Department of Community Medicine and Health Care for Pilgrims, Faculty of Medicine, Umm Al-Qura University, 21955, Makkah, Saudi Arabia
| | - Mohammed Alissa
- Department of Medical Laboratory, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, 11942, Al-Kharj, Saudi Arabia
| | - Mutaib M Mashraqi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, 61441, Najra, Saudi Arabia
| | - Ahmad A Alshehri
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, 61441, Najra, Saudi Arabia
| | - Abdulmonem A Alsaleh
- Clinical Laboratory Science Department, Mohammed Al-Mana College for Medical Sciences, 34222, Dammam, Saudi Arabia
| | - Sara Alwarthan
- Department of Internal Medicine, College of Medicine, Imam Abdulrahman Bin Faisal University, 34212, Dammam, Saudi Arabia
| | - Amal A Sabour
- Department of Botany and Microbiology, College of Science, King Saud University, 11451, Riyadh, Saudi Arabia
| | - Amal H Alfaraj
- Pediatric Department, Abqaiq General Hospital, First Eastern Health Cluster, 33261, Abqaiq, Saudi Arabia
| | - Bashayer M AlShehail
- Pharmacy Practice Department, College of Clinical Pharmacy, Imam Abdulrahman Bin Faisal University, 31441, Dammam, Saudi Arabia
| | - Nouf Alotaibi
- Clinical pharmacy Department, College of Pharmacy, Umm Al-Qura University, 21955, Makkah, Saudi Arabia
| | - Wesam A Abduljabbar
- Department of Medical laboratory sciences, Fakeeh College for Medical Science, 21134, Jeddah, Saudi Arabia
| | - Mohammed Aljeldah
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hafr Al Batin, 39831, Hafr Al Batin, Saudi Arabia
| | - Jeehan H Alestad
- Immunology and Infectious Microbiology Department, University of Glasgow, Glasgow, G1 1XQ, UK.
- Microbiology Department, Collage of Medicine, 46300, Jabriya, Kuwait.
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Struwe H, Droste J, Dhar D, Davari MD, Kirschning A. Chemoenzymatic Synthesis of a New Germacrene Derivative Named Germacrene F. Chembiochem 2024; 25:e202300599. [PMID: 37910783 DOI: 10.1002/cbic.202300599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 10/20/2023] [Accepted: 10/30/2023] [Indexed: 11/03/2023]
Abstract
The new farnesyl pyrophosphate (FPP) derivative with a shifted olefinic double bond from C6-C7 to C7-C8 is accepted and converted by the sesquiterpene cyclases protoilludene synthase (Omp7) as well as viridiflorene synthase (Tps32). In both cases, a so far unknown germacrene derivative was found to be formed, which we name "germacrene F". Both cases are examples in which a modification around the central olefinic double bond in FPP leads to a change in the mode of initial cyclization (from 1→11 to 1→10). For Omp7 a rationale for this behaviour was found by carrying out molecular docking studies. Temperature-dependent NMR experiments, accompanied by NOE studies, show that germacrene F adopts a preferred mirror-symmetric conformation with both methyl groups oriented in the same directions in the cyclodecane ring.
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Affiliation(s)
- Henry Struwe
- Organic Chemistry, Leibniz University Hannover, Schneiderberg 1B, 30167, Hannover, Germany
| | - Jörn Droste
- Organic Chemistry, Leibniz University Hannover, Schneiderberg 1B, 30167, Hannover, Germany
| | - Dipendu Dhar
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle, Germany
| | - Mehdi D Davari
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle, Germany
| | - Andreas Kirschning
- Organic Chemistry, Leibniz University Hannover, Schneiderberg 1B, 30167, Hannover, Germany
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Borovsky D, Rougé P. Heliothis virescens chymotrypsin is translationally controlled by AeaTMOF binding ABC putative receptor. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2023; 114:1-24. [PMID: 37526204 DOI: 10.1002/arch.22042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 07/19/2023] [Accepted: 07/22/2023] [Indexed: 08/02/2023]
Abstract
Heliothis virescens larval chymotrypsin (GenBank accession number AF43709) was cloned, sequenced and its three dimensional (3D) conformation modeled. The enzyme's transcript was first detected 6 days after larval emergence and the transcript level was shown to fall between larval ecdysis periods. Comparisons between the activities of larval gut chymotrypsin and trypsin shows that chymotrypsin activity is only 16% of the total trypsin activity and the pH optimum of the larval chymotrypsin is between pH 9-10, however the enzyme also exhibited a broad activity between pH 4-6. Injections of AeaTMOF and several shorter analogues into 3rd instar larvae followed by Northern blot analyses showed that although the chymotrypsins activities were inhibited by 60%-80% the transcript level of the sequenced chymotrypsin was not reduced and was similar to controls in which the chymotrypsin activity was not inhibited, indicating that AeaTMOF and its analogues exert a translational control. Based on these observations a putative AeaTMOF receptor (ABCC4) homologous to the Ae. aegypti ABC receptor sequence was found in the H. virescens genome. 3D molecular modeling and docking of the AeaTMOF and several of its analogues to the ABCC4 receptor showed that it can bind AeaTMOF and its analogues as was shown before for the Ae. aegypti receptor.
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Affiliation(s)
- Dov Borovsky
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz School of Medicine, Aurora, Colorado, USA
| | - Pierre Rougé
- UMR 152 Pharma-Dev, Faculté des Sciences Pharmaceutiques, Institut de Recherche et Développement, Université Toulouse 3, Toulouse, France
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Borovsky D, Rougé P. Cloning and characterization of Aedes aegypti blood downregulated chymotrypsin II. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2023; 113:e22018. [PMID: 37106507 DOI: 10.1002/arch.22018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 04/12/2023] [Accepted: 04/13/2023] [Indexed: 06/17/2023]
Abstract
Aedes aegypti adult and larval blood downregulated chymotrypsin II was cloned, sequenced and its 3D conformation modeled. Cloning of the enzymes from adult and larval guts indicated that both genes sit at the same location on Chromosome 2. Genomic analyses showed that larval and adult genes are the same and both have four exons and three introns that are located on an 8.32 Kb DNA in direction with the Ae. aegypti genome. The adult and larval transcript synthesis is controlled by alternative splicing explaining small difference in the amino acids sequences. Chymotrypsin II that was extracted from guts of sugar-fed and at 48 after blood feeding showed a pH optimum of 4-5 with a broad shoulder of activity from pH 6 to 10. Dot blot analyses show that the enzyme's transcript is downregulated after females take a blood meal and upregulated at 48 h after the blood meal. A Chymotrypsin II transcript was also detected in the larval gut during different times of larval developmental stages, indication that Ae. aegypti chymotrypsin II is synthesized by adults and larval guts. The possibility that JH III and 20HE play an active role in the regulation is discussed.
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Affiliation(s)
- Dov Borovsky
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz School of Medicine, Aurora, Colorado, USA
| | - Pierre Rougé
- UMR 152 Pharma-Dev, Faculté des Sciences Pharmaceutiques, Institut de Recherche et Développement, Université Toulouse 3, Toulouse, France
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Guimarães Santana BC, de Almeida Marques DP, Dos Santos Freitas A, Ferreira MM, de Sousa Lopes D, Bagno FF, Guimarães da Fonseca F, Dos Reis JGAC, Oliveira Mendes TAD, Santos JLD, Pirovani CP. Protease inhibitors from Theobroma cacao impair SARS-CoV-2 replication in vitro. Heliyon 2023; 9:e15860. [PMID: 37153407 PMCID: PMC10155420 DOI: 10.1016/j.heliyon.2023.e15860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 04/21/2023] [Accepted: 04/24/2023] [Indexed: 05/09/2023] Open
Abstract
SARS-CoV-2 is a newly emerging virus from the Coronaviridae family that has already infected over 700 million people worldwide and killed over 6 million. This virus uses protease molecules to replicate and infect the host, which makes these molecules targets for therapeutic substances to eliminate the virus and treat infected people. Through the protein-protein molecular docking approach, we detected two cystatins from Theobroma cacao, TcCYS3 and TcCYS4, described as papain-like protease inhibitors. These inhibitors decreased SARS-CoV-2 genomic copies without toxicity to Vero cells. There is a need to perform comprehensive studies in relevant animal models and to investigate the action mechanisms of protease inhibitors from Theobroma cacao that control the replication of SARS-CoV-2 in human cells.
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Affiliation(s)
| | - Daisymara Priscila de Almeida Marques
- Laboratório de Virologia Básica e Aplicada, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Andria Dos Santos Freitas
- Laboratório de Proteômica, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, BA, Brazil
| | - Monaliza Macêdo Ferreira
- Laboratório de Proteômica, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, BA, Brazil
| | - Danielle de Sousa Lopes
- Laboratório de Imunobiologia, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, BA, Brazil
| | - Flávia Fonseca Bagno
- Centro de Tecnologia de Vacinas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Jordana Grazziela Alves Coelho Dos Reis
- Laboratório de Virologia Básica e Aplicada, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | | | - Jane Lima Dos Santos
- Laboratório de Imunobiologia, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, BA, Brazil
| | - Carlos Priminho Pirovani
- Laboratório de Proteômica, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, BA, Brazil
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Impacts of Sourdough Technology on the Availability of Celiac Peptides from Wheat α- and γ-Gliadins: In Silico Approach. ALLERGIES 2023. [DOI: 10.3390/allergies3010004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Celiac peptide-generating α- and γ-gliadins consist of a disordered N-terminal domain extended by an α-helical-folded C-terminal domain. Celiac peptides, primarily located along the disordered part of α- and γ-gliadin molecules, are nicely exposed and directly accessible to proteolytic enzymes occurring in the gastric (pepsin) and intestinal (trypsin, chymotrypsin) fluids. More than half of the potential celiac peptides identified so far in gliadins exhibit cleavage sites for pepsin. However, celiac peptides proteolytically truncated by one or two amino acid residues could apparently retain some activity toward HLA-DQ2 and HLA-DQ8 receptors in docking experiments. Together with the uncleaved peptides, these still active partially degraded CD peptides account for the incapacity of the digestion process to inactivate CD peptides from gluten proteins. In contrast, sourdough fermentation processes involve other proteolytic enzymes susceptible to the deep degradation of celiac peptides. In particular, sourdough supplemented by fungal prolyl endoproteases enhances the degrading capacities of the sourdough fermentation process toward celiac peptides. Nevertheless, since tiny amounts of celiac peptides sufficient to trigger deleterious effects on CD people can persist in sourdough-treated bread and food products, it is advisable to avoid consumption of sourdough-treated food products for people suffering from celiac disease. As an alternative, applying the supplemented sourdough process to genetically modified low gluten or celiac-safe wheat lines should result in food products that are safer for susceptible and CD people.
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Structural Basis for the IgE-Binding Cross-Reacting Epitopic Peptides of Cup s 3, a PR-5 Thaumatin-like Protein Allergen from Common Cypress (Cupressus sempervirens) Pollen. ALLERGIES 2023. [DOI: 10.3390/allergies3010002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The present work was aimed at identifying the IgE-binding epitopic regions on the surface of the Cup s 3 allergen from the common cypress Cupressus sempervirens, that are possibly involved in the IgE-binding cross-reactivity reported between Cupressaceae species. Three main IgE-binding epitopic regions were mapped on the molecular surface of Cup s 3, the PR-5 thaumatin-like allergen of common cypress Cupressus sempervirens. They correspond to exposed areas containing either electropositive (R, K) or electronegative (D, E) residues. A coalescence occurs between epitopes #1 and #2, that creates an extended IgE-binding regions on the surface of the allergen. Epitope #3 contains a putative N-glycosylation site which is actually glycosylated and could therefore comprise a glycotope. However, most of the allergenic potency of Cup s 3 depends on non-glycosylated epitopic peptides. The corresponding regions of thaumatin-like allergens from other closely related Cupressaceae (Cryptomeria, Juniperus, Thuja) exhibit a very similar conformation that should account for the IgE-binding cross-reactivity observed among the Cupressaceae allergens.
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Shahzadi A, Tariq N, Sonmez H, Waquar S, Zahid A, Javed MA, Ashraf MY, Malik A, Ozturk M. Potential effect of luteolin, epiafzelechin, and albigenin on rats under cadmium-induced inflammatory insult: In silico and in vivo approach. Front Chem 2023; 11:1036478. [PMID: 36936530 PMCID: PMC10016615 DOI: 10.3389/fchem.2023.1036478] [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: 09/04/2022] [Accepted: 01/19/2023] [Indexed: 03/06/2023] Open
Abstract
Introduction: Cadmium(Cd) an industrial poison present abundantly in the environment, causes human toxicity by an inflammatory process. Chronic exposure of cadmium can cause a number of molecular lesions that could be relevant to oncogenesis, through indirect or epigenetic mechanisms, potentially including abnormal activation of oncogenes and suppression of apoptosis by depletion of antioxidants. As induction of cyclooxygenase (COX)-2 is linked to inflammatory processes, use of luteolin, epiafzelechin, and albigenin alone or in different combinations may be used as anti-inflammatory therapeutic agents. Methods: We, herein, performed in silico experiments to check the binding affinity of phytochemicals and their therapeutic effect against COX-2 in cadmium administered rats. Wistar albino rats were given phytochemicals in different combinations to check their anti-inflammatory activities against cadmium intoxication. The level of alanine aminotransferases (ALT), 4-hydroxynonenal (4HNE), 8-hydroxy-2-deoxyguanosine (8-OHdG), tumor necrosis factor-alpha (TNF-α), isoprostanes (IsoP-2α), COX-2, and malondialdehyde (MDA) were estimated with their respective ELISA and spectrophotometric methods. Results: The generated results show that phytocompounds possessed good binding energy potential against COX-2, and common interactive behavior was observed in all docking studies. Moreover, the level of ALT, 4HNE, 8-OHdG, TNF-α, IsoP-2α, malondialdehyde, and COX-2 were significantly increased in rats with induced toxicity compared to the control group, whereas in combinational therapy of phytocompounds, the levels were significantly decreased in the group. Discussion: Taken together, luteolin, epiafzelechin, and albigenin can be used as anti-inflammatory therapeutic agents for future novel drug design, and thus it may have therapeutic importance against cadmium toxicity.
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Affiliation(s)
- Andleeb Shahzadi
- Department of Medical Pharmacology, Cerrahpasa Medical Faculty, Istanbul University-Cerrahpasa, Istanbul, Turkiye
| | - Nusrat Tariq
- Department of Physiology, M. Islam Medical and Dental College, Gujranwala, Pakistan
| | - Haktan Sonmez
- Department of Medical Pharmacology, Cerrahpasa Medical Faculty, Istanbul University-Cerrahpasa, Istanbul, Turkiye
| | - Sulayman Waquar
- School of Biochemistry, Minhaj University Lahore, Lahore, Pakistan
| | - Ayesha Zahid
- Institute of Molecular Biology and Biotechnology (IMBB), The University of Lahore, Lahore, Pakistan
| | | | - Muhammad Yasin Ashraf
- Institute of Molecular Biology and Biotechnology (IMBB), The University of Lahore, Lahore, Pakistan
| | - Arif Malik
- Institute of Molecular Biology and Biotechnology (IMBB), The University of Lahore, Lahore, Pakistan
| | - Munir Ozturk
- Centre for Environmental Studies, Ege University, Izmir, Turkiye
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Borovsky D, Rougé P, Shatters RG. Bactericidal Properties of Proline-Rich Aedes aegypti Trypsin Modulating Oostatic Factor ( AeaTMOF). LIFE (BASEL, SWITZERLAND) 2022; 13:life13010019. [PMID: 36675967 PMCID: PMC9862690 DOI: 10.3390/life13010019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/16/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022]
Abstract
The antimicrobial properties of proline-rich Aedes aegypti decapeptide TMOF (AeaTMOF) and oncocin112 (1-13) were compared. Incubations with multidrug-resistant Escherichia coli cells showed that AeaTMOF (5 mM) was able to completely inhibit bacterial cell growth, whereas oncocin112 (1-13) (20 mM) partially inhibited bacterial growth as compared with bacterial cells that were not multidrug-resistant cells. AeaTMOF (5 mM) was very effective against Acinetobacter baumannii and Pseudomonas aeruginosa, completely inhibiting cell growth during 15 h incubations. AeaTMOF (5 mM) completely inhibited the Gram-positive bacteria Staphylococcus aureus and Bacillus thurengiensis sups. Israelensis cell growth, whereas oncocin112 (1-13) (10 and 20 mM) failed to affect bacterial cell growth. E. coli cells that lack the SbmA transporter were inhibited by AeaTMOF (5 mM) and not by oncocin112 (1-13) (10 to 20 mM), indicating that AeaTMOF can use other bacterial transporters than SbmA that is mainly used by proline-rich antimicrobial peptides. Incubation of E. coli cells with NaAzide showed that AeaTMOF does not use ABC-like transporters that use ATP hydrolysis to import molecules into bacterial cells. Three-dimensional modeling and docking of AeaTMOF to SbmA and MdtM transporters showed that AeaTMOF can bind these proteins, and the binding location of AeaTMOF inside these protein transporters allows AeaTMOF to be transported into the bacterial cytosol. These results show that AeaTMOF can be used as a future antibacterial agent against both multidrug-resistant Gram-positive and -negative bacteria.
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Affiliation(s)
- Dov Borovsky
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Correspondence:
| | - Pierre Rougé
- Faculte des Sciences Pharmaceutiques, 3106 Toulouse, France
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Rivera-Márquez K, Núñez-Muñoz LA, Calderón-Pérez B, De La Torre-Almaraz R, Vargas-Hernández BY, Ruiz-Medrano R, Xoconostle-Cázares B. Bioinformatic-based approach for mutagenesis of plant immune Tm-2 2 receptor to confer resistance against tomato brown rugose fruit virus (ToBRFV). FRONTIERS IN PLANT SCIENCE 2022; 13:984846. [PMID: 36247646 PMCID: PMC9562835 DOI: 10.3389/fpls.2022.984846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 09/13/2022] [Indexed: 06/16/2023]
Abstract
Nucleotide-binding leucine-rich repeat (NLR) plant immune receptors mediate the recognition and activation of defense signaling pathways in response to intra- and extracellular pathogens. Several NLR such as Tm-2 and Tm-22 have been introgressed into commercial solanaceous varieties to confer protection against different tobamoviruses. Particularly, Tm-22 was used during recent decades to confer resistance against tobacco mosaic virus, tomato mottle mosaic virus and tomato mosaic virus, which recognizes the viral movement protein (MP). However, tomato brown rugose fruit virus(ToBRFV), a novel tobamovirus, can avoid the protection conferred by Tm-22 due to the presence of key substitutions in the MP. The aim of this work was to identify the key amino acid residues involved in the interaction between Tm-22 and ToBRFV MP through bioinformatic analyses, and to identify potential Tm-22 mutations that could generate greater binding affinity. In silico 3D structure prediction, molecular docking, and computational affinity methods were performed. We predicted that R350, H384 and K385 Tm-22 residues are relevant for the interaction with MP, and two mutations (H384W and K385L) were identified as putative sites to increase the affinity of Tm-22 to the MP with the potential elicitation of resistance against ToBRFV.
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Affiliation(s)
- Karla Rivera-Márquez
- Departamento de Biotecnología y Bioingeniería, Centro de Investigación y de Estudios Avanzados, Mexico City, Mexico
| | - Leandro Alberto Núñez-Muñoz
- Departamento de Biotecnología y Bioingeniería, Centro de Investigación y de Estudios Avanzados, Mexico City, Mexico
- Unidad de Biotecnología y Prototipos, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Mexico, Mexico
| | - Berenice Calderón-Pérez
- Departamento de Biotecnología y Bioingeniería, Centro de Investigación y de Estudios Avanzados, Mexico City, Mexico
| | - Rodolfo De La Torre-Almaraz
- Unidad de Biotecnología y Prototipos, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, Mexico, Mexico
| | | | - Roberto Ruiz-Medrano
- Departamento de Biotecnología y Bioingeniería, Centro de Investigación y de Estudios Avanzados, Mexico City, Mexico
| | - Beatriz Xoconostle-Cázares
- Departamento de Biotecnología y Bioingeniería, Centro de Investigación y de Estudios Avanzados, Mexico City, Mexico
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12
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Bayrak A, Mohr F, Kolb K, Szpakowska M, Shevchenko E, Dicenta V, Rohlfing AK, Kudolo M, Pantsar T, Günther M, Kaczor AA, Poso A, Chevigné A, Pillaiyar T, Gawaz M, Laufer SA. Discovery and Development of First-in-Class ACKR3/CXCR7 Superagonists for Platelet Degranulation Modulation. J Med Chem 2022; 65:13365-13384. [PMID: 36150079 DOI: 10.1021/acs.jmedchem.2c01198] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The atypical chemokine receptor 3 (ACKR3), formerly known as CXC-chemokine receptor 7 (CXCR7), has been postulated to regulate platelet function and thrombus formation. Herein, we report the discovery and development of first-in-class ACKR3 agonists, which demonstrated superagonistic properties with Emax values of up to 160% compared to the endogenous reference ligand CXCL12 in a β-arrestin recruitment assay. Initial in silico screening using an ACKR3 homology model identified two hits, C10 (EC50 19.1 μM) and C11 (EC50 = 11.4 μM). Based on these hits, extensive structure-activity relationship studies were conducted by synthesis and testing of derivatives. It resulted in the identification of the novel thiadiazolopyrimidinone-based compounds 26 (LN5972, EC50 = 3.4 μM) and 27 (LN6023, EC50 = 3.5 μM). These compounds are selective for ACKR3 versus CXCR4 and show metabolic stability. In a platelet degranulation assay, these agonists effectively reduced P-selectin expression by up to 97%, suggesting potential candidates for the treatment of platelet-mediated thrombosis.
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Affiliation(s)
- Alp Bayrak
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Florian Mohr
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Kyra Kolb
- Department of Internal Medicine III, Cardiology and Angiology, University Hospital Tübingen, Otfried-Müller-Strasse 10, 72076 Tübingen, Germany
| | - Martyna Szpakowska
- Department of Infection and Immunity, Immuno-Pharmacology and Interactomics, Luxembourg Institute of Health (LIH), L-4354 Esch-sur-Alzette, Luxembourg
| | - Ekaterina Shevchenko
- Department of Internal Medicine VIII, Oncology and Pneumology, University Hospital Tübingen, Otfried-Müller-Strasse 14, 72076 Tübingen, Germany
| | - Valerie Dicenta
- Department of Internal Medicine III, Cardiology and Angiology, University Hospital Tübingen, Otfried-Müller-Strasse 10, 72076 Tübingen, Germany
| | - Anne-Katrin Rohlfing
- Department of Internal Medicine III, Cardiology and Angiology, University Hospital Tübingen, Otfried-Müller-Strasse 10, 72076 Tübingen, Germany
| | - Mark Kudolo
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Tatu Pantsar
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.,School of Pharmacy, University of Eastern Finland, P.O. BOX 1627, 70211 Kuopio, Finland
| | - Marcel Günther
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Agnieszka A Kaczor
- School of Pharmacy, University of Eastern Finland, P.O. BOX 1627, 70211 Kuopio, Finland.,Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modeling Laboratory, Faculty of Pharmacy, Medical University of Lublin, 4A Chodzki St., PL-20093 Lublin, Poland
| | - Antti Poso
- School of Pharmacy, University of Eastern Finland, P.O. BOX 1627, 70211 Kuopio, Finland.,Department of Internal Medicine VIII, Oncology and Pneumology, University Hospital Tübingen, Otfried-Müller-Strasse 14, 72076 Tübingen, Germany
| | - Andy Chevigné
- Department of Infection and Immunity, Immuno-Pharmacology and Interactomics, Luxembourg Institute of Health (LIH), L-4354 Esch-sur-Alzette, Luxembourg
| | - Thanigaimalai Pillaiyar
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Meinrad Gawaz
- Department of Internal Medicine III, Cardiology and Angiology, University Hospital Tübingen, Otfried-Müller-Strasse 10, 72076 Tübingen, Germany
| | - Stefan A Laufer
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
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13
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Identification of Potential IgE-Binding Epitopes Contributing to the Cross-Reactivity of the Major Cupressaceae Pectate-Lyase Pollen Allergens (Group 1). ALLERGIES 2022. [DOI: 10.3390/allergies2030010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Pectate-lyase allergens, the group 1 of allergens from Cupressaceae pollen, consist of glycoproteins exhibiting an extremely well-conserved three-dimensional structure and sequential IgE-binding epitopes. Up to 10 IgE-binding epitopic regions were identified on the molecular surface, which essentially cluster at both extremities of the long, curved β-prism-shaped allergens. Most of these IgE-binding epitopes possess very similar conformations that provide insight into the IgE-binding cross-reactivity and cross-allergenicity commonly observed among Cupressaceae pollen allergens. Some of these epitopic regions coincide with putative N-glycosylation sites that most probably consist of glycotopes or cross-reactive carbohydrate determinants, recognized by the corresponding IgE antibodies from allergic patients. Pectate-lyase allergens of Cupressaceae pollen offer a nice example of structurally conserved allergens that are widely distributed in closely-related plants (Chamæcyparis, Cryptomeria, Cupressus, Hesperocyparis, Juniperus, Thuja) and responsible for frequent cross-allergenicity.
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14
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Mondal A, Paul D, Dastidar SG, Saha T, Goswami AM. In silico analyses of Wnt1 nsSNPs reveal structurally destabilizing variants, altered interactions with Frizzled receptors and its deregulation in tumorigenesis. Sci Rep 2022; 12:14934. [PMID: 36056132 PMCID: PMC9440047 DOI: 10.1038/s41598-022-19299-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 08/26/2022] [Indexed: 11/26/2022] Open
Abstract
Wnt1 is the first mammalian Wnt gene, which is discovered as proto-oncogene and in human the gene is located on the chromosome 12q13. Mutations in Wnt1 are reported to be associated with various cancers and other human diseases. The structural and functional consequences of most of the non-synonymous SNPs (nsSNPs), present in the human Wnt1 gene, are not known. In the present work, extensive bioinformatics analyses are used to screen 292 nsSNPs of Wnt1 for predicting pathogenic and harmless polymorphisms. We have identified 10 highly deleterious nsSNPs among which 7 are located within the highly conserved areas. These 10 nsSNPs are also predicted to affect the post-translational modifications of Wnt1. Further, structure based stability analyses of these 10 highly deleterious nsSNPs revealed 8 variants as highly destabilizing. These 8 highly destabilizing variants were shown to have high BC score and high RMSIP score from normal mode analyses. Based on the deformation energies, obtained from the normal mode analyses, variants like G169A, G169S, G331R and G331S were found to be unstable. Molecular Dynamics (MD) simulations revealed structural stability and fluctuation of WT Wnt1 and its prioritized variants. RMSD remained fluctuating mostly between 4 and 5 Å and occasionally between 3.5 and 5.5 Å ranges. RMSF in the CTD region (residues 330-360) of the binding pocket were lower compared to that of WT. Studying the impacts of nsSNPs on the binding interface of Wnt1 and seven Frizzled receptors have predicted substitutions which can stabilize or destabilize the binding interface. We have found that Wnt1 and FZD8-CRD is the best docked complex in our study. MD simulation based analyses of wild type Wnt1-FZD8-CRD complex and the 8 prioritized variants revealed that RMSF was higher in the unstructured regions and RMSD remained fluctuating in the region of 5 Å ± 1 Å. We have also observed differential Wnt1 gene expression pattern in normal, tumor and metastatic conditions across different tissues. Wnt1 gene expression was significantly higher in metastatic tissues of lungs, colon and skin; and was significantly lower in metastatic tissues of breast, esophagus and kidney. We have also found that Wnt1 deregulation is associated with survival outcome in patients with gastric and breast cancer. Furthermore, these computationally screened highly deleterious nsSNPs of Wnt1 can be analyzed in population based genetic studies and may help understand the Wnt1 associated diseases.
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Affiliation(s)
- Amalesh Mondal
- Department of Physiology, Katwa College, Purba Bardhaman, Katwa, West Bengal, 713130, India
- Department of Molecular Biology and Biotechnology, University of Kalyani, Nadia, Kalyani, India
| | - Debarati Paul
- Division of Bioinformatics, Bose Institute, P-1/12 CIT Scheme VII M, Kolkata, 700054, India
| | - Shubhra Ghosh Dastidar
- Division of Bioinformatics, Bose Institute, P-1/12 CIT Scheme VII M, Kolkata, 700054, India
| | - Tanima Saha
- Department of Molecular Biology and Biotechnology, University of Kalyani, Nadia, Kalyani, India.
| | - Achintya Mohan Goswami
- Department of Physiology, Krishnagar Govt. College, Nadia, Krishnagar, West Bengal, 741101, India.
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15
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Borovsky D, Breyssens H, Buytaert E, Peeters T, Laroye C, Stoffels K, Rougé P. Cloning and Characterization of Drosophila melanogaster Juvenile Hormone Epoxide Hydrolases (JHEH) and Their Promoters. Biomolecules 2022; 12:biom12070991. [PMID: 35883546 PMCID: PMC9313241 DOI: 10.3390/biom12070991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/12/2022] [Accepted: 07/14/2022] [Indexed: 02/05/2023] Open
Abstract
Juvenile hormone epoxide hydrolase (JHEH) plays an important role in the metabolism of JH III in insects. To study the control of JHEH in female Drosophila melanogaster, JHEH 1, 2 and 3 cDNAs were cloned and sequenced. Northern blot analyses showed that the three transcripts are expressed in the head thorax, the gut, the ovaries and the fat body of females. Molecular modeling shows that the enzyme is a homodimer that binds juvenile hormone III acid (JH IIIA) at the catalytic groove better than JH III. Analyses of the three JHEH promoters and expressing short promoter sequences behind a reporter gene (lacZ) in D. melanogaster cell culture identified a JHEH 3 promoter sequence (626 bp) that is 10- and 25-fold more active than the most active promoter sequences of JHEH 2 and JHEH 1, respectively. A transcription factor (TF) Sp1 that is involved in the activation of JHEH 3 promoter sequence was identified. Knocking down Sp1 using dsRNA inhibited the transcriptional activity of this promoter in transfected D. melanogaster cells and JH III and 20HE downregulated the JHEH 3 promoter. On the other hand, JH IIIA and farnesoic acid did not affect the promoter, indicating that JH IIIA is JHEH's preferred substrate. A transgenic D. melanogaster expressing a highly activated JHEH 3 promoter behind a lacZ reporter gene showed promoter transcriptional activity in many D. melanogaster tissues.
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Affiliation(s)
- Dov Borovsky
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Correspondence:
| | - Hilde Breyssens
- Zoological Institute, KU Leuven, 3000 Leuven, Belgium; (H.B.); (E.B.); (T.P.); (C.L.); (K.S.)
| | - Esther Buytaert
- Zoological Institute, KU Leuven, 3000 Leuven, Belgium; (H.B.); (E.B.); (T.P.); (C.L.); (K.S.)
| | - Tom Peeters
- Zoological Institute, KU Leuven, 3000 Leuven, Belgium; (H.B.); (E.B.); (T.P.); (C.L.); (K.S.)
- Open BioLab Brussels, Erasmushogeschool Brussels, 1210 Brussels, Belgium
| | - Carole Laroye
- Zoological Institute, KU Leuven, 3000 Leuven, Belgium; (H.B.); (E.B.); (T.P.); (C.L.); (K.S.)
| | - Karolien Stoffels
- Zoological Institute, KU Leuven, 3000 Leuven, Belgium; (H.B.); (E.B.); (T.P.); (C.L.); (K.S.)
| | - Pierre Rougé
- Faculte des Sciences Pharmaceutiques, 31400 Tolouse, France;
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16
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Mallikarjuna MG, Sharma R, Veeraya P, Tyagi A, Rao AR, Hirenallur Chandappa L, Chinnusamy V. Evolutionary and functional characterisation of glutathione peroxidases showed splicing mediated stress responses in Maize. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 178:40-54. [PMID: 35276595 DOI: 10.1016/j.plaphy.2022.02.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 02/02/2022] [Accepted: 02/27/2022] [Indexed: 06/14/2023]
Abstract
Maize (Zea mays L) is an important cereal with extensive adaptability and multifaceted usages. However, various abiotic and biotic stresses limit the productivity of maize across the globe. Exposure of plant to stresses disturb the balance between reactive oxygen species (ROS) production and scavenging, which subsequently increases cellular damage and death of plants. Tolerant genotypes have evolved higher output of scavenging antioxidative defence compounds (ADCs) during stresses as one of the protective mechanisms. The glutathione peroxidases (GPXs) are the broad class of ADCs family. The plant GPXs catalyse the reduction of hydrogen peroxide (H2O2), lipid hydroperoxides and organic hydroperoxides to the corresponding alcohol, and facilitate the regulation of stress tolerance mechanisms. The present investigation was framed to study the maize GPXs using evolutionary and functional analyses. Seven GPX genes with thirteen splice-variants and sixty-three types of cis-acting elements were identified through whole-genome scanning in maize. Evolutionary analysis of GPXs in monocots and dicots revealed mixed and lineage-specific grouping patterns in phylogeny. The expression of ZmGPX splice variants was studied in drought and waterlogging tolerant (L1621701) and sensitive (PML10) genotypes in root and shoot tissues. Further, the differential expression of splice variants of ZmGPX1, ZmGPX3, ZmGPX6 and ZmGPX7 and regulatory network analysis suggested the splicing and regulatory elements mediated stress responses. The present investigation suggests targeting the splicing machinery of GPXs as an approach to enhance the stress tolerance in maize.
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Affiliation(s)
| | - Rinku Sharma
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Palanisamy Veeraya
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Akshita Tyagi
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | | | | | - Viswanathan Chinnusamy
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
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17
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Dlamini Z, Skepu A, Kim N, Mkhabele M, Khanyile R, Molefi T, Mbatha S, Setlai B, Mulaudzi T, Mabongo M, Bida M, Kgoebane-Maseko M, Mathabe K, Lockhat Z, Kgokolo M, Chauke-Malinga N, Ramagaga S, Hull R. AI and precision oncology in clinical cancer genomics: From prevention to targeted cancer therapies-an outcomes based patient care. INFORMATICS IN MEDICINE UNLOCKED 2022. [DOI: 10.1016/j.imu.2022.100965] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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18
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rsRNASP: A residue-separation-based statistical potential for RNA 3D structure evaluation. Biophys J 2022; 121:142-156. [PMID: 34798137 PMCID: PMC8758408 DOI: 10.1016/j.bpj.2021.11.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/23/2021] [Accepted: 11/10/2021] [Indexed: 01/07/2023] Open
Abstract
Knowledge-based statistical potentials have been shown to be rather effective in protein 3-dimensional (3D) structure evaluation and prediction. Recently, several statistical potentials have been developed for RNA 3D structure evaluation, while their performances are either still at a low level for the test datasets from structure prediction models or dependent on the "black-box" process through neural networks. In this work, we have developed an all-atom distance-dependent statistical potential based on residue separation for RNA 3D structure evaluation, namely rsRNASP, which is composed of short- and long-ranged potentials distinguished by residue separation. The extensive examinations against available RNA test datasets show that rsRNASP has apparently higher performance than the existing statistical potentials for the realistic test datasets with large RNAs from structure prediction models, including the newly released RNA-Puzzles dataset, and is comparable to the existing top statistical potentials for the test datasets with small RNAs or near-native decoys. In addition, rsRNASP is superior to RNA3DCNN, a recently developed scoring function through 3D convolutional neural networks. rsRNASP and the relevant databases are available to the public.
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19
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Rezaei MA, Li Y, Wu D, Li X, Li C. Deep Learning in Drug Design: Protein-Ligand Binding Affinity Prediction. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022; 19:407-417. [PMID: 33360998 PMCID: PMC8942327 DOI: 10.1109/tcbb.2020.3046945] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Computational drug design relies on the calculation of binding strength between two biological counterparts especially a chemical compound, i.e., a ligand, and a protein. Predicting the affinity of protein-ligand binding with reasonable accuracy is crucial for drug discovery, and enables the optimization of compounds to achieve better interaction with their target protein. In this paper, we propose a data-driven framework named DeepAtom to accurately predict the protein-ligand binding affinity. With 3D Convolutional Neural Network (3D-CNN) architecture, DeepAtom could automatically extract binding related atomic interaction patterns from the voxelized complex structure. Compared with the other CNN based approaches, our light-weight model design effectively improves the model representational capacity, even with the limited available training data. We carried out validation experiments on the PDBbind v.2016 benchmark and the independent Astex Diverse Set. We demonstrate that the less feature engineering dependent DeepAtom approach consistently outperforms the other baseline scoring methods. We also compile and propose a new benchmark dataset to further improve the model performances. With the new dataset as training input, DeepAtom achieves Pearson's R=0.83 and RMSE=1.23 pK units on the PDBbind v.2016 core set. The promising results demonstrate that DeepAtom models can be potentially adopted in computational drug development protocols such as molecular docking and virtual screening.
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Affiliation(s)
- Mohammad A. Rezaei
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida
| | - Yanjun Li
- Large-scale Intelligent Systems Laboratory, NSF Center for Big Learning, University of Florida Gainesville, FL, USA
| | - Dapeng Wu
- Large-scale Intelligent Systems Laboratory, NSF Center for Big Learning, University of Florida Gainesville, FL, USA
| | - Xiaolin Li
- Cognization Lab, Palo Alto, California, USA
| | - Chenglong Li
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida
- Large-scale Intelligent Systems Laboratory, NSF Center for Big Learning, University of Florida Gainesville, FL, USA
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20
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Borovsky D, Verhaert P, Rougé P, Powell CA, De Loof A. Culex quinquefasciatus Late Trypsin Biosynthesis Is Translationally Regulated by Trypsin Modulating Oostatic Factor. Front Physiol 2021; 12:764061. [PMID: 34867469 PMCID: PMC8637831 DOI: 10.3389/fphys.2021.764061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 10/12/2021] [Indexed: 12/02/2022] Open
Abstract
Trypsin is a serine protease that is synthesized by the gut epithelial cells of female mosquitoes; it is the enzyme that digests the blood meal. To study its molecular regulation, Culex quinquefasciatus late trypsin was purified by diethylaminoethyl (DEAE), affinity, and C18 reverse-phase high performance liquid chromatography (HPLC) steps, and the N-terminal amino acid sequence was determined for molecular cloning. Five overlapping segments of the late trypsin cDNA were amplified by PCR, cloned, and the full sequence (855 bp) was characterized. Three-dimensional models of the pro-trypsin and activated trypsin were built and compared with other trypsin models. Trypsin modulating oostatic factor (TMOF) concentrations in the hemolymph were determined by ELISA and compared with trypsin activity in the gut after the blood meal. The results showed that there was an increase in TMOF concentrations circulating in the hemolymph which has correlated to the reduction of trypsin activity in the mosquito gut. Northern blot analysis of the trypsin transcripts after the blood meal indicated that trypsin activity also followed the increase and decrease of the trypsin transcript. Injections of different amounts of TMOF (0.025 to 50 μg) decreased the amounts of trypsin in the gut. However, Northern blot analysis showed that TMOF injections did not cause a decrease in trypsin transcript abundance, indicating that TMOF probably affected trypsin translation.
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Affiliation(s)
- Dov Borovsky
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | | | - Pierre Rougé
- UMR 152 Pharma-Dev, Institut de Recherche et Développement, Université Toulouse 3, Faculté des Sciences Pharmaceutiques, Toulouse, France
| | - Charles A Powell
- UF-IFAS Indian River Research and Education Center, Fort Pierce, FL, United States
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21
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The T/Tn-Specific Helix pomatia Lectin Induces Cell Death in Lymphoma Cells Negative for T/Tn Antigens. Cancers (Basel) 2021; 13:cancers13174356. [PMID: 34503166 PMCID: PMC8431231 DOI: 10.3390/cancers13174356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 08/23/2021] [Accepted: 08/25/2021] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Changes in glycosylation, such as incomplete synthesis and higher density of O-glycans on the cell surface, are frequently observed in cancer cells. Several types of truncated O-glycan structures, e.g., T/Tn antigens, are suspected to disrupt molecular interactions between tumor microenvironment and immune cells, for instance, facilitating cancer immune-escape. Therefore, numerous exogenous lectins targeting aberrant O-glycans are interesting tools for cancer diagnosis, prognosis, and therapy. However, the ability of exolectins to detect subtle alterations in the glycome of tumor cells and to interfere in tumor/healthy cell interactions remains largely unknown. The present article reports for the first time that the Helix pomatia (HPA) lectin, a well-known T/Tn-specific lectin, currently used as a tool in cancer diagnostics, kills Tn-positive leukemia cells and Tn-negative lymphoma cells but does not affect healthy lymphocytes. Thus, HPA could be used to discriminate between tumor and healthy cells, and detect subtle alterations in the glycosylation profile. Abstract Morniga G is a T/Tn-specific lectin, inducing cell death in Tn-positive leukemias but not in healthy lymphocytes. Helix pomatia lectin (HPA) is another T/Tn-specific lectin, currently used as tool for cancer diagnostics. The HPA-mediated tumor cell death was evaluated on human leukemia and mouse lymphoma cells, and compared to the effect of Morniga G. Both lectins induced an equivalent percentage of cell death in Tn-positive Jurkat human leukemia. In contrast, EL4 mouse lymphoma resisted Morniga G-mediated cytotoxicity but were killed by HPA at concentrations of 2.5 μg/mL (0.032 nM) and higher. In both malignant cells, HPA-mediated cell death showed features compatible with apoptosis (annexin-externalization, caspase-activation, mitochondrial membrane depolarization, and ROS production). Cytometry analysis indicated that EL4 cells are T/Tn-negative. Because previous results showed a high amount of N-acetylgalactosamine (GalNAc, sugar present in Tn antigen) on EL4 cell surface, this GalNAc could be involved in the formation of truncated O-glycans other than the T/Tn residues. When compared to Morniga G, bioinformatic analysis suggested that HPA benefits from an extended carbohydrate-binding site, better adapted than Morniga G to the accommodation of more complex branched and truncated O-glycans (such as core 2). Finally, HPA killed EL4 cells but not healthy lymphocytes in a mixture of lymphoma cells + lymphocytes, suggesting that HPA selectively triggers tumor cell death.
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Man-Specific Lectins from Plants, Fungi, Algae and Cyanobacteria, as Potential Blockers for SARS-CoV, MERS-CoV and SARS-CoV-2 (COVID-19) Coronaviruses: Biomedical Perspectives. Cells 2021; 10:cells10071619. [PMID: 34203435 PMCID: PMC8305077 DOI: 10.3390/cells10071619] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/06/2021] [Accepted: 06/25/2021] [Indexed: 12/18/2022] Open
Abstract
Betacoronaviruses, responsible for the “Severe Acute Respiratory Syndrome” (SARS) and the “Middle East Respiratory Syndrome” (MERS), use the spikes protruding from the virion envelope to attach and subsequently infect the host cells. The coronavirus spike (S) proteins contain receptor binding domains (RBD), allowing the specific recognition of either the dipeptidyl peptidase CD23 (MERS-CoV) or the angiotensin-converting enzyme ACE2 (SARS-Cov, SARS-CoV-2) host cell receptors. The heavily glycosylated S protein includes both complex and high-mannose type N-glycans that are well exposed at the surface of the spikes. A detailed analysis of the carbohydrate-binding specificity of mannose-binding lectins from plants, algae, fungi, and bacteria, revealed that, depending on their origin, they preferentially recognize either complex type N-glycans, or high-mannose type N-glycans. Since both complex and high-mannose glycans substantially decorate the S proteins, mannose-specific lectins are potentially useful glycan probes for targeting the SARS-CoV, MERS-CoV, and SARS-CoV-2 virions. Mannose-binding legume lectins, like pea lectin, and monocot mannose-binding lectins, like snowdrop lectin or the algal lectin griffithsin, which specifically recognize complex N-glycans and high-mannose glycans, respectively, are particularly adapted for targeting coronaviruses. The biomedical prospects of targeting coronaviruses with mannose-specific lectins are wide-ranging including detection, immobilization, prevention, and control of coronavirus infection.
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Borovsky D, Deckers K, Vanhove AC, Verstraete M, Rougé P, Shatters RG, Powell CA. Cloning and Characterization of Aedes aegypti Trypsin Modulating Oostatic Factor (TMOF) Gut Receptor. Biomolecules 2021; 11:biom11070934. [PMID: 34201823 PMCID: PMC8301768 DOI: 10.3390/biom11070934] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 06/18/2021] [Accepted: 06/20/2021] [Indexed: 12/17/2022] Open
Abstract
Trypsin Modulating Oostatic Factor (TMOF) receptor was solubilized from the guts of female Ae. Aegypti and cross linked to His6-TMOF and purified by Ni affinity chromatography. SDS PAGE identified two protein bands (45 and 61 kDa). The bands were cut digested and analyzed using MS/MS identifying a protein sequence (1306 amino acids) in the genome of Ae. aegypti. The mRNA of the receptor was extracted, the cDNA sequenced and cloned into pTAC-MAT-2. E. coli SbmA− was transformed with the recombinant plasmid and the receptor was expressed in the inner membrane of the bacterial cell. The binding kinetics of TMOF-FITC was then followed showing that the cloned receptor exhibits high affinity to TMOF (KD = 113.7 ± 18 nM ± SEM and Bmax = 28.7 ± 1.8 pmol ± SEM). Incubation of TMOF-FITC with E. coli cells that express the receptor show that the receptor binds TMOF and imports it into the bacterial cells, indicating that in mosquitoes the receptor imports TMOF into the gut epithelial cells. A 3D modeling of the receptor indicates that the receptor has ATP binding sites and TMOF transport into recombinant E. coli cells is inhibited with ATPase inhibitors Na Arsenate and Na Azide.
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Affiliation(s)
- Dov Borovsky
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz School of Medicine, Aurora, CO 80045, USA
- Correspondence:
| | - Kato Deckers
- Zoological Institute, Katholieke Universiteit Leuven, 3000 Leuven, Belgium; (K.D.); (A.C.V.); (M.V.)
| | - Anne Catherine Vanhove
- Zoological Institute, Katholieke Universiteit Leuven, 3000 Leuven, Belgium; (K.D.); (A.C.V.); (M.V.)
| | - Maud Verstraete
- Zoological Institute, Katholieke Universiteit Leuven, 3000 Leuven, Belgium; (K.D.); (A.C.V.); (M.V.)
| | - Pierre Rougé
- UMR 152 Pharma-Dev, Faculté des Sciences Pharmaceutiques, Institut de Recherche et Développement, Université Toulouse 3, F-31062 Toulouse, France;
| | - Robert G. Shatters
- USDA ARS, Subtropical Horticultural Laboratory, 2001 Rock Road, Ft. Pierce, FL 34945, USA;
| | - Charles A. Powell
- UF-IFAS Indian River Research and Education Center, Fort Pierce, FL 34945, USA;
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IgE-Binding Epitopes of Pis v 1, Pis v 2 and Pis v 3, the Pistachio (Pistacia vera) Seed Allergens. ALLERGIES 2021. [DOI: 10.3390/allergies1010006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Sequential IgE-binding epitopes were identified on the molecular surface of the Pis v 1 (2S albumin), Pis v 2 (11S globulin/legumin) and Pis v 3 (7S globulin/vicilin)—major allergens from pistachio (Pistacia vera) seeds—using the Spot technique. They essentially consist of hydrophilic and electropositively charged residues well exposed on the surface of the allergens. Most of the epitopic regions identified on Pis v 1 and Pis v 3 do not coincide with the putative N-glycosylation sites and thus are not considered as glycotopes. Surface analysis of these epitopic regions indicates a high degree of conformational similarity with the previously identified epitopic regions of the corresponding allergens Ana o 1 (vicilin), Ana o 2 (legumin) and Ana o 3 (2S albumin) from the cashew (Anacardium occidentale) nut. These results offer a molecular basis for the IgE-binding cross-reactivity often observed between pistachio and cashew nut. They support the recommendation for prescribing pistachio avoidance in cashew allergic patients. Other conformational similarities were identified with the corresponding allergens Ses i 1 (2S albumin), Ses i 3 (vicilin) and Ses i 6 (legumin) from sesame (Sesamum indicum), and Jug r 1 (2S albumin), Jug r 2 (vicilin) and Jug r 4 (legumin) from walnut (Juglans regia). Conversely, conformation of most of the epitopic regions of the pistachio allergens often differs from that of epitopes occurring on the molecular surface of the corresponding Ara h 1 (vicilin), Ara h 2 (2S albumin) and Ara h 3 (legumin) allergens from peanut (Arachis hypogaea).
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Rational protein engineering of α-L-arabinofuranosidase from Aspergillus niger for improved catalytic hydrolysis efficiency on kenaf hemicellulose. Process Biochem 2021. [DOI: 10.1016/j.procbio.2020.12.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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26
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Cerqueira APM, Santana IB, Araújo JSC, Lima HG, Batatinha MJM, Branco A, Santos Junior MCD, Botura MB. Homology modeling, docking, molecular dynamics and in vitro studies to identify Rhipicephalus microplus acetylcholinesterase inhibitors. J Biomol Struct Dyn 2021; 40:6787-6797. [PMID: 33645442 DOI: 10.1080/07391102.2021.1889666] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Rhipicephalus microplus is an important ectoparasite of cattle, causing considerable economical losses. Resistance to chemical acaricides has stimulated the search for new antiparasitic drugs, including natural products as an eco-friendly alternative of control. Flavonoids represent a class of natural compounds with many biological activities, such as enzyme inhibitors. Acetylcholinesterase is an essential enzyme for tick survival that stands out as an important target for the development of acaricides. This work aimed to predict this 3D structure by homology modeling and use the model to identify compound with inhibitory activity. The model of R. microplus AChE1 (RmAChE1) was constructed using MODELLER program. The optimization and molecular dynamic investigation were performed in GROMACS program. The model developed was used, by molecular docking, to evaluate the anticholinesterase activity of flavonoids (quercetin, rutin, diosmin, naringin and hesperidin) and an acaricide synthetic (eserine). Additionally, in vitro inhibition of AChE and larval immersion tests were performed. The model of RmAChE1 showed to be sterically and energetically acceptable. In molecular dynamics simulations, the 3D structure remains stable with Root Mean Square Deviation = 3.58 Å and Root Mean Square Fluctuation = 1.43 Å. In molecular docking analyses, only eserine and quercetin show affinity energy to the RmAChE (Gridscore: -52.17 and -39.44 kcal/mol, respectively). Among the flavonoids, quercetin exhibited the best in vitro inhibition of AChE activity (15.8%) and mortality of larvae tick (30.2%). The use of in silico and in vitro techniques has shown that quercetin showed promising anti-tick activity and structural requirements to interact with RmAChE1. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Amanda Ponce Morais Cerqueira
- Departamento de Biologia, Programa de Pós-Graduação em Biotecnologia, Universidade Estadual de Feira de Santana, Feira de Santana, BA, Brazil
| | - Isis Bugia Santana
- Departamento de Biologia, Programa de Pós-Graduação em Biotecnologia, Universidade Estadual de Feira de Santana, Feira de Santana, BA, Brazil
| | - Janay Stefany Carneiro Araújo
- Departamento de Biologia, Programa de Pós-Graduação em Biotecnologia, Universidade Estadual de Feira de Santana, Feira de Santana, BA, Brazil
| | - Hélimar Gonçalves Lima
- Laboratório de Toxicologia, Hospital de Medicina Veterinária, Universidade Federal da Bahia, Ondina, Salvador, BA, Brazil
| | - Maria José Moreira Batatinha
- Laboratório de Toxicologia, Hospital de Medicina Veterinária, Universidade Federal da Bahia, Ondina, Salvador, BA, Brazil
| | - Alexsandro Branco
- Departamento de Saúde, Universidade Estadual de Feira de Santana, Feira de Santana, BA, Brazil
| | | | - Mariana Borges Botura
- Departamento de Saúde, Universidade Estadual de Feira de Santana, Feira de Santana, BA, Brazil
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Barre A, Pichereaux C, Simplicien M, Burlet-Schiltz O, Benoist H, Rougé P. A Proteomic- and Bioinformatic-Based Identification of Specific Allergens from Edible Insects: Probes for Future Detection as Food Ingredients. Foods 2021; 10:foods10020280. [PMID: 33573235 PMCID: PMC7911787 DOI: 10.3390/foods10020280] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/25/2021] [Accepted: 01/27/2021] [Indexed: 12/12/2022] Open
Abstract
The increasing development of edible insect flours as alternative sources of proteins added to food and feed products for improving their nutritional value, necessitates an accurate evaluation of their possible adverse side-effects, especially for individuals suffering from food allergies. Using a proteomic- and bioinformatic-based approach, the diversity of proteins occurring in currently consumed edible insects such as silkworm (Bombyx mori), cricket (Acheta domesticus), African migratory locust (Locusta migratoria), yellow mealworm (Tenebrio molitor), red palm weevil (Rhynchophorus ferrugineus), and giant milworm beetle (Zophobas atratus), was investigated. Most of them consist of phylogenetically-related protein allergens widely distributed in the different groups of arthropods (mites, insects, crustaceans) and mollusks. However, a few proteins belonging to discrete protein families including the chemosensory protein, hexamerin, and the odorant-binding protein, emerged as proteins highly specific for edible insects. To a lesser extent, other proteins such as apolipophorin III, the larval cuticle protein, and the receptor for activated protein kinase, also exhibited a rather good specificity for edible insects. These proteins, that are apparently missing or much less represented in other groups of arthropods, mollusks and nematods, share well conserved amino acid sequences and very similar three-dimensional structures. Owing to their ability to trigger allergic responses in sensitized people, they should be used as probes for the specific detection of insect proteins as food ingredients in various food products and thus, to assess their food safety, especially for people allergic to edible insects.
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Affiliation(s)
- Annick Barre
- UMR 152 PharmaDev, Institut de Recherche et Développement, Faculté de Pharmacie, Université Paul Sabatier, 35 Chemin des Maraîchers, 31062 Toulouse, France; (A.B.); (M.S.); (H.B.)
| | - Carole Pichereaux
- Fédération de Recherche (FR3450), Agrobiosciences, Interactions et Biodiversité (AIB), CNRS, 31326 Toulouse, France;
- Institut de Pharmacologie et Biologie Structurale (IPBS), Université de Toulouse UPS, CNRS, 31077 Toulouse, France;
| | - Mathias Simplicien
- UMR 152 PharmaDev, Institut de Recherche et Développement, Faculté de Pharmacie, Université Paul Sabatier, 35 Chemin des Maraîchers, 31062 Toulouse, France; (A.B.); (M.S.); (H.B.)
| | - Odile Burlet-Schiltz
- Institut de Pharmacologie et Biologie Structurale (IPBS), Université de Toulouse UPS, CNRS, 31077 Toulouse, France;
| | - Hervé Benoist
- UMR 152 PharmaDev, Institut de Recherche et Développement, Faculté de Pharmacie, Université Paul Sabatier, 35 Chemin des Maraîchers, 31062 Toulouse, France; (A.B.); (M.S.); (H.B.)
| | - Pierre Rougé
- UMR 152 PharmaDev, Institut de Recherche et Développement, Faculté de Pharmacie, Université Paul Sabatier, 35 Chemin des Maraîchers, 31062 Toulouse, France; (A.B.); (M.S.); (H.B.)
- Correspondence: ; Tel.: +33-6955-20851
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28
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Silva RCDO, da Silva Júnior AHP, Gurgel APAD, Barros Junior MR, Santos DL, de Lima RDCP, Batista MVA, Pena LJ, Chagas BS, Freitas AC. Structural and functional impacts of E5 genetic variants of human papillomavirus type 31. Virus Res 2020; 290:198143. [PMID: 32871208 DOI: 10.1016/j.virusres.2020.198143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 08/19/2020] [Accepted: 08/21/2020] [Indexed: 11/29/2022]
Abstract
Persistent infections caused by high-risk human papillomavirus (HR-HPV) are important, for the development of cervical lesions, but environmental and genetic factors are also related in the process of carcinogenesis. Among the genetic factors, the genetic variants of HR-HPV appear to be related to the risk of persistent infections. Therefore, the present study investigates variants of HPV31 E5 oncogene in cervical scraping samples from Brazilian women to assess their functional and structural effects, in order to identify possible repercussions of these variants on the infectious and carcinogenic process. Our results detected nucleotide changes previously described in the HPV31 E5 oncogene, which may play a critical role in the development of cancer due to its ability to promote cell proliferation and signal transmission. In our study, the interaction percentage of the 31E5 sequence generated by the Immune Epitope Server database and the Analysis Resource (IEDB) allowed us to include possible immunogenic epitopes with the MHC-I and MHC-II molecules, which may represent a possible relationship between protein suppression of the immune system. In the structural analysis of the HPV31 E5 oncoprotein, the N5D, I48 V, P56A, F80I and V64I polymorphisms can be found inserted within transmembrane regions. The P56A mutation has been predicted to be highly stabilizing and, therefore, can cause a change in protein function. Regarding the interaction of the E5 protein from HPV31 with the signaling of NF-kB pathway, we observed that in all variants of the E5 gene from HPV-31, the activity of the NF-kB pathway was increased compared to the prototype. Our study contributes to a more refined design of studies with the E5 gene from HPV31 and provides important data for a better understanding of how variants can be distinguished under their clinical consequences.
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Affiliation(s)
- Ruany C de O Silva
- Laboratory of Molecular Studies and Experimental Therapy (LEMTE), Department of Genetics, Federal University of Pernambuco, Pernambuco, Brazil
| | | | - Ana P A D Gurgel
- Department of Engineering and Environment, Federal University of Paraiba, Paraiba, Brazil
| | - Marconi R Barros Junior
- Laboratory of Molecular Studies and Experimental Therapy (LEMTE), Department of Genetics, Federal University of Pernambuco, Pernambuco, Brazil
| | - Daffany L Santos
- Laboratory of Molecular Studies and Experimental Therapy (LEMTE), Department of Genetics, Federal University of Pernambuco, Pernambuco, Brazil
| | - Rita de C P de Lima
- Laboratory of Molecular Studies and Experimental Therapy (LEMTE), Department of Genetics, Federal University of Pernambuco, Pernambuco, Brazil
| | - Marcus V A Batista
- Laboratory of Molecular Genetics and Biotechnology (GMBio), Department of Biology, Federal University of Sergipe, Sergipe, Brazil
| | - Lindomar J Pena
- Department of Virology and Experimental Therapy, Research Center Aggeu Magalhães, Oswaldo Cruz Foundation, Pernambuco, Brazil
| | - Bárbara S Chagas
- Laboratory of Molecular Studies and Experimental Therapy (LEMTE), Department of Genetics, Federal University of Pernambuco, Pernambuco, Brazil
| | - Antonio C Freitas
- Laboratory of Molecular Studies and Experimental Therapy (LEMTE), Department of Genetics, Federal University of Pernambuco, Pernambuco, Brazil.
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Martins Alves AM, Pereira Menezes Reis S, Peres Gramacho K, Micheli F. The glutathione peroxidase family of Theobroma cacao: Involvement in the oxidative stress during witches' broom disease. Int J Biol Macromol 2020; 164:3698-3708. [PMID: 32882281 DOI: 10.1016/j.ijbiomac.2020.08.222] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 05/26/2020] [Accepted: 08/28/2020] [Indexed: 11/27/2022]
Abstract
The glutathione peroxidases (GPXs) are enzymes which are part of the cell antioxidant system inhibiting the ROS-induced damages of membranes and proteins. In cacao (Theobroma cacao L.) genome, five GPX genes were identified. Cysteine insertion codons (UGU) were found in TcPHGPX, TcGPX2, TcGPX4, TcGPX6 and tryptophan insertion codon (UGG) in TcGPX8. Multiple alignments revealed conserved domains between TcGPXs and other plants and human GPXs. Homology modeling was performed using the Populus trichocarpa GPX5 structure as template, and the molecular modeling showed that TcGPXs have affinity with selenometionine in their active site. In silico analysis of the TcGPXs promoter region revealed the presence of conserved cis-elements related to biotic stresses and hormone responsiveness. The expression analysis of TcGPXs in cacao plantlet meristems infected by M. perniciosa showed that TcGPXs are most expressed in susceptible variety than in resistant one, mainly in disease stages in which oxidative stress and programmed cell death occurred. This data, associated with phylogenetic and location analysis suggested that TcGPXs may play a role in protecting cells from oxidative stress as a try of disease progression reduction. To our knowledge, this is the first study of the overall GPX family from T. cacao.
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Affiliation(s)
- Akyla Maria Martins Alves
- Universidade Estadual de Santa Cruz (UESC), Departamento de Ciências Biológicas (DCB), Centro de Biotecnologia e Genética (CBG), Rodovia Ilhéus-Itabuna, km 16, 45662-900 Ilhéus, BA, Brazil
| | - Sara Pereira Menezes Reis
- Universidade Estadual de Santa Cruz (UESC), Departamento de Ciências Biológicas (DCB), Centro de Biotecnologia e Genética (CBG), Rodovia Ilhéus-Itabuna, km 16, 45662-900 Ilhéus, BA, Brazil
| | | | - Fabienne Micheli
- Universidade Estadual de Santa Cruz (UESC), Departamento de Ciências Biológicas (DCB), Centro de Biotecnologia e Genética (CBG), Rodovia Ilhéus-Itabuna, km 16, 45662-900 Ilhéus, BA, Brazil; CIRAD, UMR AGAP, F-34398 Montpellier, France.
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30
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Barre A, Damme EJV, Simplicien M, Benoist H, Rougé P. Are Dietary Lectins Relevant Allergens in Plant Food Allergy? Foods 2020; 9:foods9121724. [PMID: 33255208 PMCID: PMC7760050 DOI: 10.3390/foods9121724] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 11/18/2020] [Accepted: 11/21/2020] [Indexed: 01/17/2023] Open
Abstract
Lectins or carbohydrate-binding proteins are widely distributed in seeds and vegetative parts of edible plant species. A few lectins from different fruits and vegetables have been identified as potential food allergens, including wheat agglutinin, hevein (Hev b 6.02) from the rubber tree and chitinases containing a hevein domain from different fruits and vegetables. However, other well-known lectins from legumes have been demonstrated to behave as potential food allergens taking into account their ability to specifically bind IgE from allergic patients, trigger the degranulation of sensitized basophils, and to elicit interleukin secretion in sensitized people. These allergens include members from the different families of higher plant lectins, including legume lectins, type II ribosome-inactivating proteins (RIP-II), wheat germ agglutinin (WGA), jacalin-related lectins, GNA (Galanthus nivalis agglutinin)-like lectins, and Nictaba-related lectins. Most of these potentially active lectin allergens belong to the group of seed storage proteins (legume lectins), pathogenesis-related protein family PR-3 comprising hevein and class I, II, IV, V, VI, and VII chitinases containing a hevein domain, and type II ribosome-inactivating proteins containing a ricin B-chain domain (RIP-II). In the present review, we present an exhaustive survey of both the structural organization and structural features responsible for the allergenic potency of lectins, with special reference to lectins from dietary plant species/tissues consumed in Western countries.
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Affiliation(s)
- Annick Barre
- UMR 152 PharmaDev, Institut de Recherche et Développement, Université Paul Sabatier, Faculté de Pharmacie, 35 Chemin des Maraîchers, 31062 Toulouse, France; (A.B.); (M.S.); (H.B.)
| | - Els J.M. Van Damme
- Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, B-9000 Ghent, Belgium;
| | - Mathias Simplicien
- UMR 152 PharmaDev, Institut de Recherche et Développement, Université Paul Sabatier, Faculté de Pharmacie, 35 Chemin des Maraîchers, 31062 Toulouse, France; (A.B.); (M.S.); (H.B.)
| | - Hervé Benoist
- UMR 152 PharmaDev, Institut de Recherche et Développement, Université Paul Sabatier, Faculté de Pharmacie, 35 Chemin des Maraîchers, 31062 Toulouse, France; (A.B.); (M.S.); (H.B.)
| | - Pierre Rougé
- UMR 152 PharmaDev, Institut de Recherche et Développement, Université Paul Sabatier, Faculté de Pharmacie, 35 Chemin des Maraîchers, 31062 Toulouse, France; (A.B.); (M.S.); (H.B.)
- Correspondence: ; Tel.: +33-069-552-0851
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31
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Barre A, Damme EJV, Simplicien M, Benoist H, Rougé P. Man-Specific, GalNAc/T/Tn-Specific and Neu5Ac-Specific Seaweed Lectins as Glycan Probes for the SARS-CoV-2 (COVID-19) Coronavirus. Mar Drugs 2020; 18:E543. [PMID: 33138151 PMCID: PMC7693892 DOI: 10.3390/md18110543] [Citation(s) in RCA: 10] [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: 10/10/2020] [Revised: 10/25/2020] [Accepted: 10/26/2020] [Indexed: 12/12/2022] Open
Abstract
Seaweed lectins, especially high-mannose-specific lectins from red algae, have been identified as potential antiviral agents that are capable of blocking the replication of various enveloped viruses like influenza virus, herpes virus, and HIV-1 in vitro. Their antiviral activity depends on the recognition of glycoprotein receptors on the surface of sensitive host cells-in particular, hemagglutinin for influenza virus or gp120 for HIV-1, which in turn triggers fusion events, allowing the entry of the viral genome into the cells and its subsequent replication. The diversity of glycans present on the S-glycoproteins forming the spikes covering the SARS-CoV-2 envelope, essentially complex type N-glycans and high-mannose type N-glycans, suggests that high-mannose-specific seaweed lectins are particularly well adapted as glycan probes for coronaviruses. This review presents a detailed study of the carbohydrate-binding specificity of high-mannose-specific seaweed lectins, demonstrating their potential to be used as specific glycan probes for coronaviruses, as well as the biomedical interest for both the detection and immobilization of SARS-CoV-2 to avoid shedding of the virus into the environment. The use of these seaweed lectins as replication blockers for SARS-CoV-2 is also discussed.
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Affiliation(s)
- Annick Barre
- Institut de Recherche et Développement, Faculté de Pharmacie, UMR 152 PharmaDev, Université Paul Sabatier, 35 Chemin des Maraîchers, 31062 Toulouse, France; (A.B.); (M.S.); (H.B.)
| | - Els J.M. Van Damme
- Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, B-9000 Ghent, Belgium;
| | - Mathias Simplicien
- Institut de Recherche et Développement, Faculté de Pharmacie, UMR 152 PharmaDev, Université Paul Sabatier, 35 Chemin des Maraîchers, 31062 Toulouse, France; (A.B.); (M.S.); (H.B.)
| | - Hervé Benoist
- Institut de Recherche et Développement, Faculté de Pharmacie, UMR 152 PharmaDev, Université Paul Sabatier, 35 Chemin des Maraîchers, 31062 Toulouse, France; (A.B.); (M.S.); (H.B.)
| | - Pierre Rougé
- Institut de Recherche et Développement, Faculté de Pharmacie, UMR 152 PharmaDev, Université Paul Sabatier, 35 Chemin des Maraîchers, 31062 Toulouse, France; (A.B.); (M.S.); (H.B.)
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32
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Karpov PA, Rayevsky AV, Sheremet YA, Yemets AI, Blume YB. Structural Biological Characteristics of CK1-Like Protein Kinase Isotypes Associated with Regulation of Plant Microtubules. CYTOL GENET+ 2020. [DOI: 10.3103/s0095452720040052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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33
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Liu T, Wang Z. MASS: predict the global qualities of individual protein models using random forests and novel statistical potentials. BMC Bioinformatics 2020; 21:246. [PMID: 32631256 PMCID: PMC7336608 DOI: 10.1186/s12859-020-3383-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 01/22/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Protein model quality assessment (QA) is an essential procedure in protein structure prediction. QA methods can predict the qualities of protein models and identify good models from decoys. Clustering-based methods need a certain number of models as input. However, if a pool of models are not available, methods that only need a single model as input are indispensable. RESULTS We developed MASS, a QA method to predict the global qualities of individual protein models using random forests and various novel energy functions. We designed six novel energy functions or statistical potentials that can capture the structural characteristics of a protein model, which can also be used in other protein-related bioinformatics research. MASS potentials demonstrated higher importance than the energy functions of RWplus, GOAP, DFIRE and Rosetta when the scores they generated are used as machine learning features. MASS outperforms almost all of the four CASP11 top-performing single-model methods for global quality assessment in terms of all of the four evaluation criteria officially used by CASP, which measure the abilities to assign relative and absolute scores, identify the best model from decoys, and distinguish between good and bad models. MASS has also achieved comparable performances with the leading QA methods in CASP12 and CASP13. CONCLUSIONS MASS and the source code for all MASS potentials are publicly available at http://dna.cs.miami.edu/MASS/ .
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Affiliation(s)
- Tong Liu
- Department of Computer Science, University of Miami, 1365 Memorial Drive, P.O. Box 248154, Coral Gables, FL, 33124, USA
| | - Zheng Wang
- Department of Computer Science, University of Miami, 1365 Memorial Drive, P.O. Box 248154, Coral Gables, FL, 33124, USA.
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Sheik Amamuddy O, Veldman W, Manyumwa C, Khairallah A, Agajanian S, Oluyemi O, Verkhivker GM, Tastan Bishop Ö. Integrated Computational Approaches and Tools forAllosteric Drug Discovery. Int J Mol Sci 2020; 21:E847. [PMID: 32013012 PMCID: PMC7036869 DOI: 10.3390/ijms21030847] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Revised: 01/20/2020] [Accepted: 01/21/2020] [Indexed: 12/16/2022] Open
Abstract
Understanding molecular mechanisms underlying the complexity of allosteric regulationin proteins has attracted considerable attention in drug discovery due to the benefits and versatilityof allosteric modulators in providing desirable selectivity against protein targets while minimizingtoxicity and other side effects. The proliferation of novel computational approaches for predictingligand-protein interactions and binding using dynamic and network-centric perspectives has ledto new insights into allosteric mechanisms and facilitated computer-based discovery of allostericdrugs. Although no absolute method of experimental and in silico allosteric drug/site discoveryexists, current methods are still being improved. As such, the critical analysis and integration ofestablished approaches into robust, reproducible, and customizable computational pipelines withexperimental feedback could make allosteric drug discovery more efficient and reliable. In this article,we review computational approaches for allosteric drug discovery and discuss how these tools can beutilized to develop consensus workflows for in silico identification of allosteric sites and modulatorswith some applications to pathogen resistance and precision medicine. The emerging realization thatallosteric modulators can exploit distinct regulatory mechanisms and can provide access to targetedmodulation of protein activities could open opportunities for probing biological processes and insilico design of drug combinations with improved therapeutic indices and a broad range of activities.
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Affiliation(s)
- Olivier Sheik Amamuddy
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa; (O.S.A.); (W.V.); (C.M.); (A.K.)
| | - Wayde Veldman
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa; (O.S.A.); (W.V.); (C.M.); (A.K.)
| | - Colleen Manyumwa
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa; (O.S.A.); (W.V.); (C.M.); (A.K.)
| | - Afrah Khairallah
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa; (O.S.A.); (W.V.); (C.M.); (A.K.)
| | - Steve Agajanian
- Graduate Program in Computational and Data Sciences, Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, One University Drive, Orange, CA 92866, USA; (S.A.); (O.O.)
| | - Odeyemi Oluyemi
- Graduate Program in Computational and Data Sciences, Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, One University Drive, Orange, CA 92866, USA; (S.A.); (O.O.)
| | - Gennady M. Verkhivker
- Graduate Program in Computational and Data Sciences, Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, One University Drive, Orange, CA 92866, USA; (S.A.); (O.O.)
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA 92618, USA
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa; (O.S.A.); (W.V.); (C.M.); (A.K.)
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Structural-functional analyses of textile dye degrading azoreductase, laccase and peroxidase: A comparative in silico study. ELECTRON J BIOTECHN 2020. [DOI: 10.1016/j.ejbt.2019.12.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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The Novel Serine/Threonine Protein Kinase LmjF.22.0810 from Leishmania major may be Involved in the Resistance to Drugs such as Paromomycin. Biomolecules 2019; 9:biom9110723. [PMID: 31718000 PMCID: PMC6920834 DOI: 10.3390/biom9110723] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 11/01/2019] [Accepted: 11/05/2019] [Indexed: 12/13/2022] Open
Abstract
The identification and clarification of the mechanisms of action of drugs used against leishmaniasis may improve their administration regimens and prevent the development of resistant strains. Herein, for the first time, we describe the structure of the putatively essential Ser/Thr kinase LmjF.22.0810 from Leishmania major. Molecular dynamics simulations were performed to assess the stability of the kinase model. The analysis of its sequence and structure revealed two druggable sites on the protein. Furthermore, in silico docking of small molecules showed that aminoglycosides preferentially bind to the phosphorylation site of the protein. Given that transgenic LmjF.22.0810-overexpressing parasites displayed less sensitivity to aminoglycosides such as paromomycin, our predicted models support the idea that the mechanism of drug resistance observed in those transgenic parasites is the tight binding of such compounds to LmjF.22.0810 associated with its overexpression. These results may be helpful to understand the complex machinery of drug response in Leishmania.
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Hilu KW, Friend SA, Vallanadu V, Brown AM, Hollingsworth LR, Bevan DR. Molecular evolution of genes encoding allergen proteins in the peanuts genus Arachis: Structural and functional implications. PLoS One 2019; 14:e0222440. [PMID: 31675366 PMCID: PMC6824556 DOI: 10.1371/journal.pone.0222440] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 08/29/2019] [Indexed: 12/14/2022] Open
Abstract
Food allergies are severe immune responses to plant and animal products mediated by immunoglobulin E (IgE). Peanuts (Arachis hypogaea L.) are among the top 15 crops that feed the world. However, peanuts is among the "big eight food allergens", and allergies induced by peanuts are a significant public health problem and a life-threatening concern. Targeted mutation studies in peanuts demonstrate that single residue alterations in these allergen proteins could result in substantial reduction in allergenicity. Knowledge of peanut allergen proteins is confined to the allotetraploid crop and its two progenitors. We explored frequencies and positions of natural mutations in the hyperallergenic homologues Ara h 2 and Ara h 6 in newly generated sequences for 24 Arachis wild species and the crop species, assessed potential mutational impact on allergenicity using immunoblots and structural modeling, and evaluated whether these mutations follow evolutionary trends. We uncovered a wealth of natural mutations, both substitutions and gaps, including the elimination of immunodominant epitopes in some species. These molecular alterations appear to be associated with substantial reductions in allergenicity. The study demonstrated that Ara h 2 and Ara h 6 follow contrasting modes of natural selection and opposing mutational patterns, particularly in epitope regions. Phylogenetic analysis revealed a progressive trend towards immunodominant epitope evolution in Ara h 2. The findings provide valuable insight into the interactions among mutations, protein structure and immune system response, thus presenting a valuable platform for future manipulation of allergens to minimize, treat or eliminate allergenicity. The study strongly encourages exploration of genepools of economically important plants in allergenicity research.
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Affiliation(s)
- Khidir W. Hilu
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, United States of America
| | - Sheena A. Friend
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, United States of America
| | - Viruthika Vallanadu
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, United States of America
| | - Anne M. Brown
- Research and Informatics, Virginia Tech, Blacksburg, VA, United States of America
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, United States of America
| | | | - David R. Bevan
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, United States of America
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Barre A, Pichereaux C, Velazquez E, Maudouit A, Simplicien M, Garnier L, Bienvenu F, Bienvenu J, Burlet-Schiltz O, Auriol C, Benoist H, Rougé P. Insights into the Allergenic Potential of the Edible Yellow Mealworm ( Tenebrio molitor). Foods 2019; 8:E515. [PMID: 31635354 PMCID: PMC6836238 DOI: 10.3390/foods8100515] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 09/07/2019] [Accepted: 09/25/2019] [Indexed: 12/04/2022] Open
Abstract
The edible yellow mealworm (Tenebrio molitor), contains an extremely diverse panel of soluble proteins, including proteins with structural functions such as muscle proteins, as well as proteins involved in metabolic functions such as enzymes. Most of these proteins display a more or less pronounced allergenic character toward previously sensitized people, especially people allergic to shrimps and other shellfish. A mass spectrometry approach following the separation of a mealworm protein, extracted by sodiumdodecyl sulfate-polyacrylamide gel electrophoresis, allowed us to identify up to 106 distinct protein fractions including molecules with structural and functional functions, susceptible to developing an allergenic potential due to the possibility of immunoglobulin E-binding cross-reactions with their counterparts occurring in shellfish. In this respect, most of the sera from people allergic to shrimps reacted with the mealworm protein extract in Western blot experiments. Moreover, the potential mealworm allergens triggered the in vitro degranulation of rat leukemic basophils transfected with the human high-affinity IgE receptor (FcεRI), upon sensitization by the IgE-containing sera from people allergic to shrimps and other shellfish foods. Owing to the large repertoire of IgE-binding cross-reacting allergens the yellow mealworm shares with other phylogenetically-related groups of arthropods, it would seem prudent to inform the consumers, especially those allergic to shellfish, by appropriate labeling on edible mealworm packages about the potential risk of developing an allergic reaction.
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Affiliation(s)
- Annick Barre
- UMR 152 Pharmacochimie et Biologie pour le Développement, Université Paul Sabatier, Institut de Recherche et Développement, Faculté de Pharmacie, 35 Chemin des Maraîchers, 31062 Toulouse, France.
| | - Carole Pichereaux
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, 31077 Toulouse, France.
| | - Esmeralda Velazquez
- UMR 152 Pharmacochimie et Biologie pour le Développement, Université Paul Sabatier, Institut de Recherche et Développement, Faculté de Pharmacie, 35 Chemin des Maraîchers, 31062 Toulouse, France.
| | - Agathe Maudouit
- UMR 152 Pharmacochimie et Biologie pour le Développement, Université Paul Sabatier, Institut de Recherche et Développement, Faculté de Pharmacie, 35 Chemin des Maraîchers, 31062 Toulouse, France.
| | - Mathias Simplicien
- UMR 152 Pharmacochimie et Biologie pour le Développement, Université Paul Sabatier, Institut de Recherche et Développement, Faculté de Pharmacie, 35 Chemin des Maraîchers, 31062 Toulouse, France.
| | - Lorna Garnier
- Laboratoire d'Immunologie, Hospices Civils de Lyon, Centre Hospitalier Lyon Sud, 165 Chemin du Grand Revoyet, 69495 Pierre-Bénite, France.
| | - Françoise Bienvenu
- Laboratoire d'Immunologie, Hospices Civils de Lyon, Centre Hospitalier Lyon Sud, 165 Chemin du Grand Revoyet, 69495 Pierre-Bénite, France.
| | - Jacques Bienvenu
- Laboratoire d'Immunologie, Hospices Civils de Lyon, Centre Hospitalier Lyon Sud, 165 Chemin du Grand Revoyet, 69495 Pierre-Bénite, France.
| | - Odile Burlet-Schiltz
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, 31077 Toulouse, France.
| | - Cédric Auriol
- Micronutris, 6 Rue de Partanaïs, 31650 Saint-Orens-de-Gameville, France.
| | - Hervé Benoist
- UMR 152 Pharmacochimie et Biologie pour le Développement, Université Paul Sabatier, Institut de Recherche et Développement, Faculté de Pharmacie, 35 Chemin des Maraîchers, 31062 Toulouse, France.
| | - Pierre Rougé
- UMR 152 Pharmacochimie et Biologie pour le Développement, Université Paul Sabatier, Institut de Recherche et Développement, Faculté de Pharmacie, 35 Chemin des Maraîchers, 31062 Toulouse, France.
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Martins Alves AM, Pereira Menezes S, Matos Lima E, Peres Gramacho K, Silva Andrade B, Macêdo Ferreira M, Pirovani CP, Micheli F. The selenium-binding protein of Theobroma cacao: A thermostable protein involved in the witches' broom disease resistance. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 142:472-481. [PMID: 31430675 DOI: 10.1016/j.plaphy.2019.08.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 06/23/2019] [Accepted: 08/08/2019] [Indexed: 06/10/2023]
Abstract
The selenium-binding proteins are known to be inducers of apoptosis in human and animals, and have been studied as target for the treatment of various types of cancer. In plants, SBP expression has been related to abiotic and biotic stress resistance. The SBP from Theobroma cacao (TcSBP) was first identified from a cocoa-Moniliophthora perniciosa cDNA library. The present study provides details on the TcSBP gene and protein structure. Multiple alignments revealed conserved domains between SBP from plants, human and archea. Homology modeling and molecular docking were performed and showed that the TcSBP has affinity to selenite in the active CSSC site. This result was confirmed by circular dichroism of the recombinant TcSBP, which also presented thermostable behavior. RT-qPCR analysis showed that TcSBP was differentially expressed in resistant vs susceptible cacao varieties inoculated by M. perniciosa and its expression was probably due to hormone induction via cis-regulating elements present in its promotor. The presence of the CSSC domain suggested that TcSBP acted by altering oxidation/reduction of proteins during H2O2 production and programmed cell death in the final stages of the witches' broom disease. To our knowledge, this is the first in silico and in vitro analysis of the SBP from cacao.
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Affiliation(s)
- Akyla Maria Martins Alves
- Universidade Estadual de Santa Cruz (UESC), Departamento de Ciências Biológicas (DCB), Centro de Biotecnologia e Genética (CBG), Rodovia Ilhéus-Itabuna, km 16, 45662-900, Ilhéus-BA, Brazil
| | - Sara Pereira Menezes
- Universidade Estadual de Santa Cruz (UESC), Departamento de Ciências Biológicas (DCB), Centro de Biotecnologia e Genética (CBG), Rodovia Ilhéus-Itabuna, km 16, 45662-900, Ilhéus-BA, Brazil
| | - Eline Matos Lima
- Universidade Estadual de Santa Cruz (UESC), Departamento de Ciências Biológicas (DCB), Centro de Biotecnologia e Genética (CBG), Rodovia Ilhéus-Itabuna, km 16, 45662-900, Ilhéus-BA, Brazil
| | | | - Bruno Silva Andrade
- Universidade Estadual do Sudoeste da Bahia (UESB), Av. José Moreira Sobrinho, Jequié, Bahia, 45206-190, Brazil
| | - Monaliza Macêdo Ferreira
- Universidade Estadual de Santa Cruz (UESC), Departamento de Ciências Biológicas (DCB), Centro de Biotecnologia e Genética (CBG), Rodovia Ilhéus-Itabuna, km 16, 45662-900, Ilhéus-BA, Brazil
| | - Carlos Priminho Pirovani
- Universidade Estadual de Santa Cruz (UESC), Departamento de Ciências Biológicas (DCB), Centro de Biotecnologia e Genética (CBG), Rodovia Ilhéus-Itabuna, km 16, 45662-900, Ilhéus-BA, Brazil
| | - Fabienne Micheli
- Universidade Estadual de Santa Cruz (UESC), Departamento de Ciências Biológicas (DCB), Centro de Biotecnologia e Genética (CBG), Rodovia Ilhéus-Itabuna, km 16, 45662-900, Ilhéus-BA, Brazil; CIRAD, UMR AGAP, F-34398, Montpellier, France.
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Vashishtha S, Barwal TS, Bansal S. Structure and Sequence Based Analysis of Pullulanases: Understanding Dual Catalytic Mechanism. Protein Pept Lett 2019; 26:893-903. [PMID: 31429684 DOI: 10.2174/0929866526666190820160611] [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: 06/29/2018] [Revised: 04/25/2019] [Accepted: 05/26/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Starch processing requires a combination of enzymes with other chemical and physical processes, which increases cost and time. Enzymes used in these processes have a characteristic (α/β)8 barrel domain architecture, although, show variable activity. Pullulanase type 1 and isoamylase act on α-1-6 linkage, amylase on α-1-4 linkage whereas pullulanase type 2 acts on both α-1-6, and α-1-4 linkages of starch. OBJECTIVE This article focusses on elucidating the importance of sequence and structural-based differences in pullulanase, that may lead to its dual catalytic nature. METHODS Initially, sequences and structures of pullulanase type 1, pullulanase type 2, amylase and isoamylase were retrieved from the database (NCBI and PDB). Homology modelling using SWISS-MODEL and PHYRE2 was carried out for predicting the structure of the enzymes with unavailable structures. Further, the modelled structures were validated using ANOLEA, Verify 3D and PROCHECK, structures with high confidence value were selected and used for analysis. Finally, the selected structures were compared by using PDBefold, and their domain alignment and analysis was performed manually using Pymol. RESULTS Modelled structures of pullulanase and isoamylase were validated and selected based on the confidence score. Comparative analysis of complete structures low similarity between the enzymes, although, domain analysis showed good similarity. Moreover, alignment of catalytic site residues showed high similarities with the change in orientation of critical site residues (HIS 242, ASP 347 and GLN 375). CONCLUSION The change in orientation of active site residues along with the absence or presence of few residues might play a crucial role in imparting dual functionality.
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Affiliation(s)
- Shubham Vashishtha
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, Himachal Pradesh, India
| | - Tushar S Barwal
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, Himachal Pradesh, India
| | - Saurabh Bansal
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, Himachal Pradesh, India
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Barre A, Simplicien M, Benoist H, Van Damme EJM, Rougé P. Mannose-Specific Lectins from Marine Algae: Diverse Structural Scaffolds Associated to Common Virucidal and Anti-Cancer Properties. Mar Drugs 2019; 17:E440. [PMID: 31357490 PMCID: PMC6723950 DOI: 10.3390/md17080440] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 07/23/2019] [Accepted: 07/24/2019] [Indexed: 02/06/2023] Open
Abstract
To date, a number of mannose-specific lectins have been isolated and characterized from seaweeds, especially from red algae. In fact, man-specific seaweed lectins consist of different structural scaffolds harboring a single or a few carbohydrate-binding sites which specifically recognize mannose-containing glycans. Depending on the structural scaffold, man-specific seaweed lectins belong to five distinct structurally-related lectin families, namely (1) the griffithsin lectin family (β-prism I scaffold); (2) the Oscillatoria agardhii agglutinin homolog (OAAH) lectin family (β-barrel scaffold); (3) the legume lectin-like lectin family (β-sandwich scaffold); (4) the Galanthus nivalis agglutinin (GNA)-like lectin family (β-prism II scaffold); and, (5) the MFP2-like lectin family (MFP2-like scaffold). Another algal lectin from Ulva pertusa, has been inferred to the methanol dehydrogenase related lectin family, because it displays a rather different GlcNAc-specificity. In spite of these structural discrepancies, all members from the five lectin families share a common ability to specifically recognize man-containing glycans and, especially, high-mannose type glycans. Because of their mannose-binding specificity, these lectins have been used as valuable tools for deciphering and characterizing the complex mannose-containing glycans from the glycocalyx covering both normal and transformed cells, and as diagnostic tools and therapeutic drugs that specifically recognize the altered high-mannose N-glycans occurring at the surface of various cancer cells. In addition to these anti-cancer properties, man-specific seaweed lectins have been widely used as potent human immunodeficiency virus (HIV-1)-inactivating proteins, due to their capacity to specifically interact with the envelope glycoprotein gp120 and prevent the virion infectivity of HIV-1 towards the host CD4+ T-lymphocyte cells in vitro.
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Affiliation(s)
- Annick Barre
- Institut de Recherche et Développement, Faculté de Pharmacie, UMR 152 PharmaDev, Université Paul Sabatier, 35 Chemin des Maraîchers, 31062 Toulouse, France
| | - Mathias Simplicien
- Institut de Recherche et Développement, Faculté de Pharmacie, UMR 152 PharmaDev, Université Paul Sabatier, 35 Chemin des Maraîchers, 31062 Toulouse, France
| | - Hervé Benoist
- Institut de Recherche et Développement, Faculté de Pharmacie, UMR 152 PharmaDev, Université Paul Sabatier, 35 Chemin des Maraîchers, 31062 Toulouse, France
| | - Els J M Van Damme
- Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, B-9000 Ghent, Belgium
| | - Pierre Rougé
- Institut de Recherche et Développement, Faculté de Pharmacie, UMR 152 PharmaDev, Université Paul Sabatier, 35 Chemin des Maraîchers, 31062 Toulouse, France.
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Dulcey CE, López de Los Santos Y, Létourneau M, Déziel E, Doucet N. Semi-rational evolution of the 3-(3-hydroxyalkanoyloxy)alkanoate (HAA) synthase RhlA to improve rhamnolipid production in Pseudomonas aeruginosa and Burkholderia glumae. FEBS J 2019; 286:4036-4059. [PMID: 31177633 DOI: 10.1111/febs.14954] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 04/12/2019] [Accepted: 06/06/2019] [Indexed: 12/15/2022]
Abstract
The 3-(3-hydroxyalkanoyloxy)alkanoate (HAA) synthase RhlA is an essential enzyme involved in the biosynthesis of HAAs in Pseudomonas and Burkholderia species. RhlA modulates the aliphatic chain length in rhamnolipids, conferring distinct physicochemical properties to these biosurfactants exhibiting promising industrial and pharmaceutical value. A detailed molecular understanding of substrate specificity and catalytic performance in RhlA could offer protein engineering tools to develop designer variants involved in the synthesis of novel rhamnolipid mixtures for tailored eco-friendly products. However, current directed evolution progress remains limited due to the absence of high-throughput screening methodologies and lack of an experimentally resolved RhlA structure. In the present work, we used comparative modeling and chimeric-based approaches to perform a comprehensive semi-rational mutagenesis of RhlA from Pseudomonas aeruginosa. Our extensive RhlA mutational variants and chimeric hybrids between the Pseudomonas and Burkholderia homologs illustrate selective modulation of rhamnolipid alkyl chain length in both Pseudomonas aeruginosa and Burkholderia glumae. Our results also demonstrate the implication of a putative cap-domain motif that covers the catalytic site of the enzyme and provides substrate specificity to RhlA. This semi-rational mutant-based survey reveals promising 'hot-spots' for the modulation of RL congener patterns and potential control of enzyme activity, in addition to uncovering residue positions that modulate substrate selectivity between the Pseudomonas and Burkholderia functional homologs. DATABASE: Model data are available in the PMDB database under the accession number PM0081867.
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Affiliation(s)
- Carlos Eduardo Dulcey
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Université du Québec, Laval, Canada
| | - Yossef López de Los Santos
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Université du Québec, Laval, Canada
| | - Myriam Létourneau
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Université du Québec, Laval, Canada
| | - Eric Déziel
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Université du Québec, Laval, Canada
| | - Nicolas Doucet
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Université du Québec, Laval, Canada.,PROTEO, the Québec Network for Research on Protein Function, Engineering, and Applications, Université Laval, Canada
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Structure and Activity of a Cytosolic Ribosome-Inactivating Protein from Rice. Toxins (Basel) 2019; 11:toxins11060325. [PMID: 31174339 PMCID: PMC6628440 DOI: 10.3390/toxins11060325] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 05/30/2019] [Accepted: 06/04/2019] [Indexed: 02/07/2023] Open
Abstract
Ribosome-inactivating proteins (RIPs) are cytotoxic enzymes that inhibit protein translation by depurinating ribosomal RNA. Although most plant RIPs are synthesized with leader sequences that sequester them away from the host ribosomes, several RIPs from cereals lack these signal peptides and therefore probably reside in the cytosol near the plant ribosomes. More than 30 RIP genes have been identified in the rice (Oryza sativa spp. japonica) genome, many of them lacking a signal peptide. This paper focuses on a presumed cytosolic type-1 RIP from rice, referred to as OsRIP1. Using 3D modeling it is shown that OsRIP1 structurally resembles other cereal RIPs and has an active site that meets the requirements for activity. Furthermore, localization studies indicate that OsRIP1-eGFP fusion proteins reside in the nucleocytoplasmic space when expressed in epidermal cells of Nicotiana benthamiana or Arabidopsis thaliana suspension cells. Finally, OsRIP1 was recombinantly produced in Escherichia coli and was demonstrated to possess catalytic activity. Interestingly, this recombinant RIP inactivates wheat ribosomes far less efficiently than rabbit ribosomes in an in vitro system. These findings raise some interesting questions concerning the mode of action and physiological role of OsRIP1. This is the first time a RIP from rice is investigated at protein level and is shown to possess biological activity.
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The preliminary efficacy evaluation of the CTLA-4-Ig treatment against Lupus nephritis through in-silico analyses. J Theor Biol 2019; 471:74-81. [DOI: 10.1016/j.jtbi.2019.03.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 03/22/2019] [Indexed: 01/04/2023]
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Neves Cruz J, da Costa KS, de Carvalho TAA, de Alencar NAN. Measuring the structural impact of mutations on cytochrome P450 21A2, the major steroid 21-hydroxylase related to congenital adrenal hyperplasia. J Biomol Struct Dyn 2019; 38:1425-1434. [PMID: 30982438 DOI: 10.1080/07391102.2019.1607560] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Congenital adrenal hyperplasia is an inherited autosomal recessive disorder related to deficient cortisol synthesis. The deficiency of steroid 21-hydroxylase (cytochrome P450 21A2), an enzyme involved in cortisol synthesis, is responsible for ∼95% of cases of congenital adrenal hyperplasia. This metabolic disease exhibits three clinical forms: salt-wasting, simple virilizing, and non-classical form, which are divided according to the degree of severity. In the present study, structural and mutational analyses were performed in order to identify the structural impact of mutations on cytochrome P450 21A2 and correlate them with patient clinical severity. The following mutations were selected: arginine-356 to tryptophan (R356W), proline-30 to leucine (P30L), isoleucine-172 to asparagine (I172N), valine-281 to leucine (V281L), and the null mutation glutamine-318 (Q318X). Our computational approach mapped the location of residues on P450 and identified their implications on enzyme electrostatic potential mapping to progesterone and heme binding pockets. Using molecular dynamics simulations, we analyzed the structural stability of ligand binding and protein structure, as well as possible conformational changes at the catalytic pocket that leads to impairment of enzymatic activity. Our study sheds light on the impact structural mutations have over steroid 21-hydroxylase structure-function in the cell.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jorddy Neves Cruz
- Faculty of Pharmaceutical Sciences, University of the Amazon, Belém, Brazil.,Institute of Natural Sciences, Federal University of Pará, Belém, Brazil
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Battisti A, Zamuner S, Sarti E, Laio A. Toward a unified scoring function for native state discrimination and drug-binding pocket recognition. Phys Chem Chem Phys 2019; 20:17148-17155. [PMID: 29900428 DOI: 10.1039/c7cp08170g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Protein folding and receptor-ligand recognition are fundamental processes for any living organism. Although folding and ligand recognition are based on the same chemistry, the existing empirical scoring functions target just one problem: predicting the correct fold or the correct binding pose. We here introduce a statistical potential which considers moieties as fundamental units. The scoring function is able to deal with both folding and ligand pocket recognition problems with a performance comparable to the scoring functions specifically tailored for one of the two tasks. We foresee that the capability of the new scoring function to tackle both problems in a unified framework will be a key to deal with the induced fit phenomena, in which a target protein changes significantly its conformation upon binding. Moreover, the new scoring function might be useful in docking protocols towards intrinsically disordered proteins, whose flexibility cannot be handled with the available docking software.
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Affiliation(s)
- Anna Battisti
- International School for Advanced Studies (SISSA), Via Bonomea 265, I-34136 Trieste, Italy.
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Yusof NA, Kamaruddin S, Abu Bakar FD, Mahadi NM, Abdul Murad AM. Structural and functional insights into TRiC chaperonin from a psychrophilic yeast, Glaciozyma antarctica. Cell Stress Chaperones 2019; 24:351-368. [PMID: 30649671 PMCID: PMC6439030 DOI: 10.1007/s12192-019-00969-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 01/04/2019] [Accepted: 01/08/2019] [Indexed: 12/29/2022] Open
Abstract
Studies on TCP1-1 ring complex (TRiC) chaperonin have shown its indispensable role in folding cytosolic proteins in eukaryotes. In a psychrophilic organism, extreme cold temperature creates a low-energy environment that potentially causes protein denaturation with loss of activity. We hypothesized that TRiC may undergo evolution in terms of its structural molecular adaptation in order to facilitate protein folding in low-energy environment. To test this hypothesis, we isolated G. antarctica TRiC (GaTRiC) and found that the expression of GaTRiC mRNA in G. antarctica was consistently expressed at all temperatures indicating their importance in cell regulation. Moreover, we showed GaTRiC has the ability of a chaperonin whereby denatured luciferase can be folded to the functional stage in its presence. Structurally, three categories of residue substitutions were found in α, β, and δ subunits: (i) bulky/polar side chains to alanine or valine, (ii) charged residues to alanine, and (iii) isoleucine to valine that would be expected to increase intramolecular flexibility within the GaTRiC. The residue substitutions observed in the built structures possibly affect the hydrophobic, hydrogen bonds, and ionic and aromatic interactions which lead to an increase in structural flexibility. Our structural and functional analysis explains some possible structural features which may contribute to cold adaptation of the psychrophilic TRiC folding chamber.
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Affiliation(s)
- Nur Athirah Yusof
- Biotechnology Research Institute, Universiti Malaysia Sabah, 88400, Kota Kinabalu, Sabah, Malaysia.
| | - Shazilah Kamaruddin
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Farah Diba Abu Bakar
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Nor Muhammad Mahadi
- Malaysia Genome Institute, Jalan Bangi, 43000, Kajang, Selangor Darul Ehsan, Malaysia
| | - Abdul Munir Abdul Murad
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
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Pourtaghi-Anvarian S, Mohammadi S, Hamzeh-Mivehroud M, Alizadeh AA, Dastmalchi S. Characterization of the novel anti-TNF-α single-chain fragment antibodies using experimental and computational approaches. Prep Biochem Biotechnol 2019; 49:38-47. [DOI: 10.1080/10826068.2018.1487855] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Samira Pourtaghi-Anvarian
- School of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Samin Mohammadi
- School of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Maryam Hamzeh-Mivehroud
- School of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ali Akbar Alizadeh
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Siavoush Dastmalchi
- School of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Faculty of Pharmacy, Near East University, North Cyprus, Turkey
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Jangra MR, Batra R, Passricha N, Sikka VK. Cloning, Sequencing and In Silico Analysis of phbC Gene from Pseudomonas spp. Indian J Microbiol 2019; 59:58-63. [PMID: 30728631 DOI: 10.1007/s12088-018-0767-4] [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: 10/20/2018] [Accepted: 10/31/2018] [Indexed: 10/27/2022] Open
Abstract
We report here isolation and analysis of PCR amplified phbC gene from Pseudomonas spp. strain phbmbb15-B3. This strain was previously developed from mutations of landfill isolates and found to be an efficient Poly Hydroxy butyrate (PHB) producer. The fragment was cloned into pTZ57R/T cloning vector and then the gene has been sequenced and submitted to GenBank (Accession Number KT933807). The sequence results confirmed the clone to be phbC homologue and the ORF was 910 base pairs long and coded for 303 amino acids, which shared 92-99% amino acid sequence identity with the available bacterial sequences in Gene Bank. We could also predict the primary and secondary structural features of the expected phbC protein. Phylogenetic analysis also revealed its similarity with several pseudomonads. The results of the present study shall provide a stable foundation for further research on modeling studies of PHB synthase and developing PHB a commercial technology.
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Affiliation(s)
- Mukesh R Jangra
- 1Department of Molecular Biology, Biotechnology and Bioinformatics, CCS Haryana Agricultural University, Hisar, India
| | - Ritu Batra
- Bioinformatics Infrastructure Facility, Department of Genetics and Plant Breeding, CCSU, Meerut, India
| | - Nishat Passricha
- 3International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Virendra K Sikka
- 1Department of Molecular Biology, Biotechnology and Bioinformatics, CCS Haryana Agricultural University, Hisar, India
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Costa CHS, Oliveira ARS, Dos Santos AM, da Costa KS, Lima AHLE, Alves CN, Lameira J. Computational study of conformational changes in human 3-hydroxy-3-methylglutaryl coenzyme reductase induced by substrate binding. J Biomol Struct Dyn 2019; 37:4374-4383. [PMID: 30470158 DOI: 10.1080/07391102.2018.1549508] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The enzyme 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGR) is mainly involved in the regulation of cholesterol biosynthesis. HMGR catalyses the reduction of 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) to mevalonate at the expense of two NADPH molecules in a two-step reversible reaction. In the present study, we constructed a model of human HMGR (hHMGR) to explore the conformational changes of HMGR in complex with HMG-CoA and NADPH. In addition, we analysed the complete sequence of the Flap domain using molecular dynamics (MD) simulations and principal component analysis (PCA). The simulations revealed that the Flap domain plays an important role in catalytic site activation and substrate binding. The apo form of hHMGR remained in an open state, while a substrate-induced closure of the Flap domain was observed for holo hHMGR. Our study also demonstrated that the phosphorylation of Ser872 induces significant conformational changes in the Flap domain that lead to a complete closure of the active site, suggesting three principal conformations for the first stage of hHMGR catalysis. Our results were consistent with previous proposed models for the catalytic mechanism of hHMGR. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | | | - Alberto M Dos Santos
- Institute of Biological Sciences, Federal University of Pará , Belém , Pará , Brazil
| | - Kauê Santana da Costa
- Institute of Biodiversity, Federal University of West of Pará , Santarém , Pará , Brazil
| | | | - Cláudio N Alves
- Institute of Natural Sciences, Federal University of Pará , Belém , Pará , Brazil
| | - Jerônimo Lameira
- Institute of Biological Sciences, Federal University of Pará , Belém , Pará , Brazil
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