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Nguyen TL, Kim H. Discovering peptides and computational investigations of a multiepitope vaccine target Mycobacterium tuberculosis. Synth Syst Biotechnol 2024; 9:391-405. [PMID: 38585591 PMCID: PMC10997871 DOI: 10.1016/j.synbio.2024.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/09/2024] [Accepted: 03/12/2024] [Indexed: 04/09/2024] Open
Abstract
Mycobacterium tuberculosis (MTB) is the causative agent of tuberculosis (TB), a prevalent airborne infectious disease. Despite the availability of the Bacille Calmette-Guerin vaccine, its global efficacy remains modest, and tuberculosis persists as a significant global public health threat. Addressing this challenge and advancing towards the End MTB Strategy, we developed a multiepitope vaccine (MEV) based on immunoinformatics and computational approaches. Immunoinformatics screening of MBT protein identified immune-dominant epitopes based on Major Histocompatibility Complex (MHC) allele binding, immunogenicity, antigenicity, allergenicity, toxicity, and cytokine inducibility. Selected epitopes were integrated into an MEV construct with adjuvant and linkers, forming a fully immunogenic vaccine candidate. Comprehensive analyses encompassed the evaluation of immunological and physicochemical properties, determination of tertiary structure, molecular docking with Toll-Like Receptors (TLR), molecular dynamics (MD) simulations for all atoms, and immune simulations. Our MEV comprises 534 amino acids, featuring 6 cytotoxic T lymphocyte, 8 helper T lymphocyte, and 7 linear B lymphocyte epitopes, demonstrating high antigenicity and stability. Notably, molecular docking studies and triplicate MD simulations revealed enhanced interactions and stability of MEV with the TLR4 complex compared to TLR2. In addition, the immune simulation indicated the capacity to effectively induce elevated levels of antibodies and cytokines, emphasizing the vaccine's robust immunogenic response. This study presents a promising MEV against TB, exhibiting favorable immunological and physicochemical attributes. The findings provide theoretical support for TB vaccine development. Our study aligns with the global initiative of the End MTB Strategy, emphasizing its potential impact on addressing persistent challenges in TB control.
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Affiliation(s)
- Truc Ly Nguyen
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Heebal Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Republic of Korea
- eGnome, Inc., Seoul, 05836, Republic of Korea
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Abbaoui Z, Merzouki M, Oualdi I, Bitari A, Oussaid A, Challioui A, Touzani R, Hammouti B, Agerico Diño W. Alzheimer's disease: In silico study of rosemary diterpenes activities. Curr Res Toxicol 2024; 6:100159. [PMID: 38455759 PMCID: PMC10918482 DOI: 10.1016/j.crtox.2024.100159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 02/23/2024] [Accepted: 02/27/2024] [Indexed: 03/09/2024] Open
Abstract
The global surge in Alzheimer's disease poses a significant public health concern. In response, we study the efficacy of carnosic acid and related abietane-type diterpenes extracted from rosemary as acetylcholinesterase (AChE) inhibitors. Our analyses, using in silico techniques, encompassed all the compounds within this extract. Through molecular docking, we explored how these compounds interact with the active site of the AChE protein. The docking scores, ranging from -5.560 Kcal/mol to -7.270 Kcal/mol, indicate robust binding affinities. Assessment of the ADME/T (Adsorption, Distribution, Metabolism, Excretion, and Toxicity) properties and pharmacokinetics of these compounds reveal favorable profiles for all the tested substances. These encouraging results suggest the potential of these compounds as candidates for further development to prevent and/or treat Alzheimer's disease. Among these compounds, we find rosmanol as the most likely candidate for further research and clinical trials to validate their efficacy.
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Affiliation(s)
- Zakariae Abbaoui
- University Mohammed Premier, Faculty of Science, Laboratory of Applied Chemistry and Environment (LCAE), Oujda, Morocco
| | - Mohammed Merzouki
- University Mohammed Premier, Faculty of Science, Laboratory of Applied Chemistry and Environment (LCAE), Oujda, Morocco
| | - Imane Oualdi
- University Mohammed Premier, Faculty of Science, Laboratory of Applied Chemistry and Environment (LCAE), Oujda, Morocco
| | - Abdelhamid Bitari
- University Mohammed Premier, Faculty of Science, Laboratory of Bioresources, Biotechnology, Ethnopharmacology and Health (LBBES), Oujda, Morocco
| | - Abdelouhed Oussaid
- University Mohammed Premier, Multidisciplinary Faculty of Nador, Laboratory of Molecular Chemistry, Materials and Environment (LCM2E), Oujda, Morocco
| | - Allal Challioui
- University Mohammed Premier, Faculty of Science, Laboratory of Applied Chemistry and Environment (LCAE), Oujda, Morocco
| | - Rachid Touzani
- University Mohammed Premier, Faculty of Science, Laboratory of Applied Chemistry and Environment (LCAE), Oujda, Morocco
| | | | - Wilson Agerico Diño
- Osaka University, Department of Applied Physics, Suita, Osaka 565-0871, Japan
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Manzi A, De-Carli BP, Roggero A, Ferreira De Moraes LL, Annunciato I, Novo Belchor M, Lima Neto DFD, Antonio De Oliveira M, Hikari Toyama M. Theoretical evaluation of the malathion and its chemical derivatives interaction with cytosolic phospholipase A2 from zebrafish. Chemosphere 2023; 311:136984. [PMID: 36306964 DOI: 10.1016/j.chemosphere.2022.136984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 10/11/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
Cytosolic phospholipase A2 (cPLA2) belongs to a large family of proteins and plays a crucial role in the regulation of arachidonic acid metabolism and inflammation cascade in zebrafish (Danio rerio). This enzyme with a molecular weight of 85 kDa, has two distinct domains. One is the regulatory and calcium-dependent (Ca2+) domain called C2, the other is the catalytic α/β hydrolase Ca2+-independent domain, where serine and aspartic acid catalytic dyad residues are present. We investigated the interaction of malathion and their organophosphate metabolites in the cPLA2 using in silico tools. Molecular docking results showed hydrophobic interactions with the paraoxon and catalytic site residue (Ser 223). Malathion increases intracellular Ca2+ due to endoplasmic reticulum influx which in turn activities phospholipase A2 and arachidonic acid release. Molecular docking and homology modelling of proteins and ligands could be a complementary tool for ecotoxicology and environment pollution assessment.
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Affiliation(s)
- Agatha Manzi
- Instituto de Biociências, Universidade Estadual Paulista (UNESP), São Vicente, SP, Brazil; BIOMOLPEP, Instituto de Biociências, Universidade Estadual Paulista (UNESP), São Vicente, 11330-900, São Paulo, Brazil.
| | - Bruno Paes De-Carli
- BIOMOLPEP, Instituto de Biociências, Universidade Estadual Paulista (UNESP), São Vicente, 11330-900, São Paulo, Brazil; Universidade Paulista UNIP, Santos, SP, Brazil
| | - Airam Roggero
- Instituto de Biociências, Universidade Estadual Paulista (UNESP), São Vicente, SP, Brazil; BIOMOLPEP, Instituto de Biociências, Universidade Estadual Paulista (UNESP), São Vicente, 11330-900, São Paulo, Brazil
| | - Laila Lucyane Ferreira De Moraes
- Instituto de Biociências, Universidade Estadual Paulista (UNESP), São Vicente, SP, Brazil; BIOMOLPEP, Instituto de Biociências, Universidade Estadual Paulista (UNESP), São Vicente, 11330-900, São Paulo, Brazil
| | - Isabelly Annunciato
- Instituto de Biociências, Universidade Estadual Paulista (UNESP), São Vicente, SP, Brazil; BIOMOLPEP, Instituto de Biociências, Universidade Estadual Paulista (UNESP), São Vicente, 11330-900, São Paulo, Brazil
| | - Mariana Novo Belchor
- BIOMOLPEP, Instituto de Biociências, Universidade Estadual Paulista (UNESP), São Vicente, 11330-900, São Paulo, Brazil
| | | | | | - Marcos Hikari Toyama
- Instituto de Biociências, Universidade Estadual Paulista (UNESP), São Vicente, SP, Brazil; BIOMOLPEP, Instituto de Biociências, Universidade Estadual Paulista (UNESP), São Vicente, 11330-900, São Paulo, Brazil
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Madadi Mahani N, Mostaghni F, Shafiekhani H. Cuspareine as alkaloid against COVID-19 designed with ionic liquids: DFT and docking molecular approaches. J Photochem Photobiol B 2022; 231:112447. [PMID: 35483276 PMCID: PMC9020645 DOI: 10.1016/j.jphotobiol.2022.112447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 04/08/2022] [Accepted: 04/18/2022] [Indexed: 06/14/2023]
Abstract
Cuspareine as an antiviral alkaloid can be used in the treatment of COVID-19. In this study, we introduced the ionic liquids (ILs) concluded cuspareinium as a cation with CH3COO-, CF3COO-, and PF6 as anions. The optimized geometry, thermodynamic parameters, and reactivity descriptors were calculated with density functional theory (DFT) approach and time-dependent density functional theory (TD-DFT) using B3LYP/6-311G. In addition, the UV and IR spectra of the introduced ILs were investigated. Based on DFT calculation, the designed IL CH3COO- can be to the most suitable anions due to most solubility in the water. DFT studies displayed that all the introduced ILs have more polarity than pristine cuspareine and CH3COO--cuspareine is the most polarity due to high dipole moment. Also, the thermo- chemical data of the designed ionic liquids revealed that PF6-cuspareine is distinguished to be stable. A molecular docking study of the designed ILs with 6 LU7 protease was performed to display interactions and binding energy. Results of molecular docking displayed that CH3COO- ion liquid has the highest binding energy (- 7.20 kcal/mol) and Ala7, and Lys 5 residues are involved in an interaction. DFT and molecular docking studies of cuspareine as alkaloid based on ionic liquids can be helpful to for more pharmaceutical and biological researches of cuspareine as an antiviral agent against COVID-19.
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Affiliation(s)
| | - Fatemeh Mostaghni
- Department of Chemistry, Payame Noor University, 19395-4697 Tehran, Iran
| | - Homa Shafiekhani
- Department of Chemistry, Payame Noor University, 19395-4697 Tehran, Iran
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Andrade-Pavón D, Gómez-García O. Etoposide and Camptothecin Reduce Growth, Viability, the Generation of Petite Mutants, and Recognize the Active Site of DNA Topoisomerase I and II Enzymes in Candida glabrata. Indian J Microbiol 2021; 61:306-314. [PMID: 34294997 DOI: 10.1007/s12088-021-00942-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 04/18/2021] [Indexed: 11/30/2022] Open
Abstract
Candidemia, one of the most common invasive fungal infections in hospitalized patients, can lead to death and huge financial losses. Candida albicans is the main causative agent of this disorder and Candida glabrata occupies the second or third place, for which new therapeutic alternatives must be found. The objective of the present study was to evaluate the inhibitory effect of etoposide and camptothecin (inhibitors of deoxyribonucleic acid (DNA) topoisomerase) on the C. glabrata CBS138 strain. Etoposide and camptothecin showed better or similar MIC (minimum inhibitory concentration) (5 and 2.5 μg/mL, respectively), with respect to fluconazole (8 μg/mL) and itraconazole (4 μg/mL). They also suppressed colony formation during the 12-h test. On the other hand, petite colonies were less formed by exposing C. glabrata to etoposide or camptothecin (indicating low toxicity), with respect fluconazole and itraconazole. Such colonies are phenotypically observed as limited growth in medium containing a non-fermentable carbon source, and are genotypically characterized by a partial or total loss of mitochondrial DNA (mtDNA) fragments. Using PCR techniques and cell staining with 4',6-diamidino-2-phenylindole (DAPI), loss of mtDNA was detected only in yeast cells treated with fluconazole. Additionally, molecular docking studies with etoposide and camptothecin showed recognition in the active site of the Topo I and II enzymes from C. glabrata. Since etoposide and camptothecin showed good inhibitory activity and low toxicity on C. glabrata; they should certainly be of interest for the treatment of C. glabrata infections and the design and development of new antifungal compounds derived from these drugs. Supplementary Information The online version contains supplementary material available at 10.1007/s12088-021-00942-6.
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Affiliation(s)
- Dulce Andrade-Pavón
- Laboratorio de Biología Molecular de Bacterias Y Levaduras, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prol. de Carpio Y Plan de Ayala. Col. Sto. Tomás, 11340 México City, México.,Departamento de Fisiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Av. Wilfrido Massieu S/N Unidad Profesional "Adolfo López Mateos", Zacatenco. Col. Lindavista, Del, 07700 Venustiano Carranza, D.F México
| | - Omar Gómez-García
- Departamento de Química Orgánica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prol. de Carpio Y Plan de Ayala. Col. Sto. Tomás, 11340 México City, México
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Tomiotto-Pellissier F, Alves DR, Morais SMD, Bortoleti BTDS, Gonçalves MD, Silva TF, Tavares ER, Yamauchi LM, Costa IN, Marinho ES, Marinho MM, Conchon-Costa I, Miranda-Sapla MM, Pavanelli WR. Caryocar coriaceum Wittm. fruit extracts as Leishmania inhibitors: in-vitro and in-silico approaches. J Biomol Struct Dyn 2021; 40:8040-8055. [PMID: 33769210 DOI: 10.1080/07391102.2021.1905557] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Leishmaniasis is a group of neglected diseases caused by parasites of the Leishmania genus. The treatment of Leishmaniasis represents a great challenge, because the available drugs present high toxicity and none of them is fully effective. Caryocar is a botanical genus rich in phenolic compounds, which leaves extracts have already been described by its antileishmanial action. Thus, we investigated the effect of pulp and peel extracts of the Caryocar coriaceum fruit on promastigote and amastigote forms of Leishmania amazonensis. Both extracts had antipromastigote effect after 24, 48, and 72 h, and this effect was by apoptosis-like process induction, with reactive oxygen species (ROS) production, damage to the mitochondria and plasma membrane, and phosphatidylserine exposure. Knowing that the fruit extracts did not alter the viability of macrophages, we observed that the treatment reduced the infection of these cells. Thereafter, in the in vitro infection context, the extracts showed antioxidant proprieties, by reducing NO, ROS, and MDA levels. Besides, both peel and pulp extracts up-regulated Nrf2/HO-1/Ferritin expression and increase the total iron-bound in infected macrophages, which culminates in a depletion of available iron for L. amazonensis replication. In silico, the molecular modeling experiments showed that the three flavonoids presented in the C. coriaceum extracts can act as synergistic inhibitors of Leishmania proteins, and compete for the active site. Also, there is a preference for rutin at the active site due to its greater interaction binding strength.
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Affiliation(s)
- Fernanda Tomiotto-Pellissier
- Biosciences and Biotechnology Graduate Program, Carlos Chagas Institute (ICC), Fiocruz, Curitiba, Paraná, Brazil.,Department of Pathology Science, Center of Biological Sciences, State University of Londrina, Londrina, Paraná, Brazil
| | - Daniela Ribeiro Alves
- Department of Natural Sciences, Ceará State University, Fortaleza, Ceará, Brazil.,Theoretical and Electrochemical Chemistry Group, Faculty of Philosophy Dom Aureliano Matos, State University of Ceará, Limoeiro do Norte, Ceará, Brazil
| | | | - Bruna Taciane da Silva Bortoleti
- Biosciences and Biotechnology Graduate Program, Carlos Chagas Institute (ICC), Fiocruz, Curitiba, Paraná, Brazil.,Department of Pathology Science, Center of Biological Sciences, State University of Londrina, Londrina, Paraná, Brazil
| | - Manoela Daiele Gonçalves
- Department of Chemistry, Center of Exact Sciences, State University of Londrina, Londrina, Paraná, Brazil
| | - Taylon Felipe Silva
- Department of Pathology Science, Center of Biological Sciences, State University of Londrina, Londrina, Paraná, Brazil
| | - Eliandro Reis Tavares
- Department of Microbiology, Center of Biological Sciences, State University of Londrina, Londrina, Paraná, Brazil
| | - Lucy Megumi Yamauchi
- Department of Microbiology, Center of Biological Sciences, State University of Londrina, Londrina, Paraná, Brazil
| | - Idessania Nazareth Costa
- Department of Pathology Science, Center of Biological Sciences, State University of Londrina, Londrina, Paraná, Brazil
| | - Emmanuel Silva Marinho
- Theoretical and Electrochemical Chemistry Group, Faculty of Philosophy Dom Aureliano Matos, State University of Ceará, Limoeiro do Norte, Ceará, Brazil
| | - Marcia Machado Marinho
- Iguatu Faculty of Education, Science and Letters, State University of Ceará, Iguatu, Ceará, Brazil
| | - Ivete Conchon-Costa
- Department of Pathology Science, Center of Biological Sciences, State University of Londrina, Londrina, Paraná, Brazil
| | | | - Wander Rogério Pavanelli
- Biosciences and Biotechnology Graduate Program, Carlos Chagas Institute (ICC), Fiocruz, Curitiba, Paraná, Brazil.,Department of Pathology Science, Center of Biological Sciences, State University of Londrina, Londrina, Paraná, Brazil
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Vasconcelos MA, Orsolin PC, Oliveira VC, Lima PMAP, Naves MPC, de Morais CR, Nicolau-Júnior N, Bonetti AM, Spanó MA. Modulating effect of vitamin D3 on the mutagenicity and carcinogenicity of doxorubicin in Drosophila melanogaster and in silico studies. Food Chem Toxicol 2020; 143:111549. [PMID: 32640329 PMCID: PMC7335493 DOI: 10.1016/j.fct.2020.111549] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/18/2020] [Accepted: 06/21/2020] [Indexed: 02/07/2023]
Abstract
Vitamin D3 (VD3) deficiency increases DNA damage, while supplementation may exert a pro-oxidant activity, prevent viral infections and formation of tumors. The aim of this study was to investigate the mutagenicity and carcinogenicity of VD3 alone or in combination with doxorubicin (DXR) using the Somatic Mutation and Recombination Test and the Epithelial Tumor Test, both in Drosophila melanogaster. For better understanding of the molecular interactions of VD3 and receptors, in silico analysis were performed with molecular docking associated with molecular dynamics. Findings revealed that VD3 alone did not increase the frequency of mutant spots, but reduced the frequency of mutant spots when co-administered with DXR. In addition, VD3 did not alter the recombinogenic effect of DXR in both ST and HB crosses. VD3 alone did not increase the total frequency of tumor, but significantly reduced the total frequency of tumor when co-administered with DXR. Molecular modeling and molecular dynamics between calcitriol and Ecdysone Receptor (EcR) showed a stable interaction, indicating the possibility of signal transduction between VD3 and EcR. In conclusion, under these experimental conditions, VD3 has modulatory effects on the mutagenicity and carcinogenicity induced by DXR in somatic cells of D. melanogaster and exhibited satisfactory interactions with the EcR.
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Affiliation(s)
- Mirley Alves Vasconcelos
- Institute of Biotechnology, Federal University of Uberlândia, Campus Umuarama, Uberlândia, MG, Brazil.
| | - Priscila Capelari Orsolin
- Laboratory of Cytogenetic and Mutagenesis, University Center of Patos de Minas, Patos de Minas, MG, Brazil.
| | - Victor Constante Oliveira
- Institute of Biotechnology, Federal University of Uberlândia, Campus Umuarama, Uberlândia, MG, Brazil.
| | | | | | | | - Nilson Nicolau-Júnior
- Institute of Biotechnology, Federal University of Uberlândia, Campus Umuarama, Uberlândia, MG, Brazil.
| | - Ana Maria Bonetti
- Institute of Biotechnology, Federal University of Uberlândia, Campus Umuarama, Uberlândia, MG, Brazil.
| | - Mário Antônio Spanó
- Institute of Biotechnology, Federal University of Uberlândia, Campus Umuarama, Uberlândia, MG, Brazil.
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