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Wahyuni DK, Junairiah J, Rosyanti C, Kharisma VD, Syukriya AJ, Rahmawati CT, Purkan P, Subramaniam S, Prasongsuk S, Purnobasuki H. Computational and in vitro analyses of the antibacterial effect of the ethanolic extract of Pluchea indica L. leaves. Biomed Rep 2024; 21:137. [PMID: 39129835 PMCID: PMC11310492 DOI: 10.3892/br.2024.1825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 06/19/2024] [Indexed: 08/13/2024] Open
Abstract
The most common gram-negative, Escherichia coli, and gram-positive bacteria, Bacillus spp., have evolved different mechanisms that have caused the emergence of multi-drug resistance. As a result, drugs that block the bacterial growth cycle are needed. Here, in silico and in vitro studies were performed to assess compounds in the Pluchea indica leaf extract, a medicinal plant, that can inhibit bacterial proteins. Briefly, P. indica leaves were extracted using ethanol. The crude extract was then subjected to gas chromatography-mass spectrometry for metabolite screening. Molecular docking simulations with rhomboid protease (Rpro) (Protein data bank ID number: 3ZMI from E. coli and filamenting temperature-sensitive mutant Z (FtsZ) protein data bank ID number: 2VAM from Bacillus subtilis were performed. Moreover, the well diffusion method was used to confirm the antibacterial activity of P. indica leaf extract. A total of 10 compounds were identified in the P. indica extract and used for computational analysis. Based on drug-likeness prediction, P. indica compounds may be drug-like molecules. Binding affinity tests indicated that 10,10-Dimethyl-2,6-dimethylenebicyclo(7.2.0)undecan-5.β.-ol and 11,11-Dimethyl-4,8-dimethylenebicyclo(7.2.0)undecan-3-ol had the most negative values. Accordingly, these compounds may be potential ligands that bind to bacterial proteins. The root mean square fluctuation values was <2 Å, indicating stable fluctuation binding for the ligand-protein complex. According to in vitro antibacterial assays, a high concentration (50%) of the P. indica extract markedly inhibited E. coli and B. subtilis, with inhibitory zone diameters of 31.86±1.63 and 21.09±0.09 mm, respectively. Overall, the compounds in the P. indica leaf extract were identified as functional inhibitors of E. coli and B. subtilis proteins via in silico analysis. This may facilitate development of antibacterial agents.
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Affiliation(s)
- Dwi Kusuma Wahyuni
- Department of Biology, Faculty of Science and Technology, Universitas Airlangga, Surabaya, East Java 60115, Indonesia
- Center of Excellence in Plant Biodiversity and Biotechnology, Department of Biology, Faculty of Science and Technology, Universitas Airlangga, Surabaya, East Java 60115, Indonesia
| | - Junairiah Junairiah
- Department of Biology, Faculty of Science and Technology, Universitas Airlangga, Surabaya, East Java 60115, Indonesia
- Center of Excellence in Plant Biodiversity and Biotechnology, Department of Biology, Faculty of Science and Technology, Universitas Airlangga, Surabaya, East Java 60115, Indonesia
| | - Chery Rosyanti
- Department of Biology, Faculty of Science and Technology, Universitas Airlangga, Surabaya, East Java 60115, Indonesia
| | - Viol Dhea Kharisma
- Department of Biology, Faculty of Science and Technology, Universitas Airlangga, Surabaya, East Java 60115, Indonesia
| | - Alvi Jauharotus Syukriya
- Department of Biology, Faculty of Science and Technology, Universitas Airlangga, Surabaya, East Java 60115, Indonesia
| | - Cici Tya Rahmawati
- Department of Biology, Faculty of Science and Technology, Universitas Airlangga, Surabaya, East Java 60115, Indonesia
| | - Purkan Purkan
- Department of Chemistry, Faculty of Science and Technology, Universitas Airlangga, Surabaya, East Java 60115, Indonesia
| | - Sreeramanan Subramaniam
- Department of Biology, Faculty of Science and Technology, Universitas Airlangga, Surabaya, East Java 60115, Indonesia
- School of Biological Science, Universiti Sains Malaysia, Georgetown 11800, Malaysia
- Centre for Chemical Biology, Universiti Sains Malaysia (USM), Bayan Lepas, 11900, Penang, Malaysia
| | - Sehanat Prasongsuk
- Plant Biomass Utilization Research Unit, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Hery Purnobasuki
- Department of Biology, Faculty of Science and Technology, Universitas Airlangga, Surabaya, East Java 60115, Indonesia
- Center of Excellence in Plant Biodiversity and Biotechnology, Department of Biology, Faculty of Science and Technology, Universitas Airlangga, Surabaya, East Java 60115, Indonesia
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Khurana D, Kumar B, Devi J, Antil N, Patil RB, Singh K, Singh Y. Unlocking the biological potential of transition metal complexes with Thiosemicarbazone ligands: Insights from computational studies. Heliyon 2024; 10:e33150. [PMID: 38994046 PMCID: PMC11238129 DOI: 10.1016/j.heliyon.2024.e33150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 06/12/2024] [Accepted: 06/14/2024] [Indexed: 07/13/2024] Open
Abstract
In the previous study, the synthesis and characterization of 4-(3-fluorophenyl)-3-thiosemicarbazide and benzaldehyde derivatives based thiosemicarbazone ligands and their Co(II), Ni(II), Cu(II), Zn(II) complexes were carried out to evaluate their malarial and oxidant and inflammatory inhibition abilities, demonstrating that these compounds have robust efficacy for these ailments. In the present research, to find out a combating agent against breast cancer, tuberculosis, bacterial and fungal ailments, the compounds were tested through MTT, microplate alamar blue and serial dilution protocols. ADMET and DFT investigation were analyzed against highly bioactive compounds (2, 7-10) to give a new insight about compound's reactivity, stability and drug likeness properties. Furthermore, activity results shows that the ligand (2) and its complexes demonstrate greater efficacy compared to ligand (1) and its complexes. The Cu(II) (9) and Zn(II) (10) complexes were observed as highly efficient for breast cancer (MCF-7 cell line), TB (H37Rv strain), bacterial and fungal ailments in comparison of standard drugs with 0.029 ± 0.001 μM IC50 value for (9) in anticancer activity and 0.0034 ± 0.0017 μmol/mL MIC value for (10) in anti-tuberculosis activity. In the molecular docking investigation, the various kind of binding interactions and lowest binding affinity of (9) (against 4RJ3 (-10.0 kcal/mol), 2VCJ (-7.9 kcal/mol)) and (10) (-7.8 and -8.3 kcal/mol for 5V3Y and 3PTY protein) support their bioactivity. This research highlights the pharmaceutical importance of transition metal complexes having thiosemicarbazones, presenting a significant approach for the discovery of potent anti-infectious agent.
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Affiliation(s)
- Daksh Khurana
- Department of Computer Science & Engineering, Symbiosis Institute of Technology, Pune, 412115, Maharashtra, India
| | - Binesh Kumar
- Department of Chemistry, Guru Jambheshwar University of Science and Technology, Hisar, 125001, Haryana, India
| | - Jai Devi
- Department of Chemistry, Guru Jambheshwar University of Science and Technology, Hisar, 125001, Haryana, India
| | - Nidhi Antil
- Department of Chemistry, Maharshi Dayanand University, Rohtak, 124001, Haryana, India
| | - Rajesh B Patil
- Sinhgad Technical Education Society's, Sinhgad College of Pharmacy, Off Sinhgad Road, Vadgaon (Bk), Pune, 411041, Maharashtra, India
| | - Khushwant Singh
- University Institute of Engineering and Technology, Maharshi Dayanand University, Rohtak, 124001, Haryana, India
| | - Yudhvir Singh
- University Institute of Engineering and Technology, Maharshi Dayanand University, Rohtak, 124001, Haryana, India
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Primo LMDG, Roque-Borda CA, Carnero Canales CS, Caruso IP, de Lourenço IO, Colturato VMM, Sábio RM, de Melo FA, Vicente EF, Chorilli M, da Silva Barud H, Barbugli PA, Franzyk H, Hansen PR, Pavan FR. Antimicrobial peptides grafted onto the surface of N-acetylcysteine-chitosan nanoparticles can revitalize drugs against clinical isolates of Mycobacterium tuberculosis. Carbohydr Polym 2024; 323:121449. [PMID: 37940311 DOI: 10.1016/j.carbpol.2023.121449] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 09/21/2023] [Accepted: 09/28/2023] [Indexed: 11/10/2023]
Abstract
Tuberculosis is caused by Mycobacterium tuberculosis (MTB) and is the leading cause of death from infectious diseases in the World. The search for new antituberculosis drugs is a high priority, since several drug-resistant TB-strains have emerged. Many nanotechnology strategies are being explored to repurpose or revive drugs. An interesting approach is to graft antimicrobial peptides (AMPs) to antibiotic-loaded nanoparticles. The objective of the present work was to determine the anti-MTB activity of rifampicin-loaded N-acetylcysteine-chitosan-based nanoparticles (NPs), conjugated with the AMP Ctx(Ile21)-Ha; against clinical isolates (multi- and extensively-drug resistant) and the H37Rv strain. The modified chitosan and drug-loaded NPs were characterized with respect to their physicochemical stability and their antimycobacterial profile, which showed potent inhibition (MIC values <0.977 μg/mL) by the latter. Furthermore, their accumulation within macrophages and cytotoxicity were determined. To understand the possible mechanisms of action, an in silico study of the peptide against MTB membrane receptors was performed. The results presented herein demonstrate that antibiotic-loaded NPs grafted with an AMP can be a powerful tool for revitalizing drugs against multidrug-resistant M. tuberculosis strains, by launching multiple attacks against MTB. This approach could potentially serve as a novel treatment strategy for various long-term diseases requiring extended treatment periods.
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Affiliation(s)
- Laura Maria Duran Gleriani Primo
- São Paulo State University (UNESP), Tuberculosis Research Laboratory, School of Pharmaceutical Sciences, Araraquara, São Paulo, Brazil
| | - Cesar Augusto Roque-Borda
- São Paulo State University (UNESP), Tuberculosis Research Laboratory, School of Pharmaceutical Sciences, Araraquara, São Paulo, Brazil; Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Christian Shleider Carnero Canales
- Vicerrectorado de Investigación, Facultad de Ciencias Farmacéuticas bioquímicas y biotecnológicas, Universidad Católica de Santa María, Arequipa, Peru
| | - Icaro Putinhon Caruso
- Department of Physics - Institute of Biosciences, Humanities and Exact Sciences (IBILCE), São Paulo State University (UNESP), 15054-000 São José do Rio Preto, São Paulo, Brazil
| | - Isabella Ottenio de Lourenço
- Department of Physics - Institute of Biosciences, Humanities and Exact Sciences (IBILCE), São Paulo State University (UNESP), 15054-000 São José do Rio Preto, São Paulo, Brazil
| | - Vitória Maria Medalha Colturato
- Department of Biotechnology, Laboratory of Polymers and Biomaterials, University of Araraquara (UNIARA), Araraquara, São Paulo, Brazil
| | - Rafael Miguel Sábio
- São Paulo State University (UNESP), Department of Drug and Medicines, School of Pharmaceutical Sciences, Araraquara, São Paulo, Brazil
| | - Fernando Alves de Melo
- Department of Physics - Institute of Biosciences, Humanities and Exact Sciences (IBILCE), São Paulo State University (UNESP), 15054-000 São José do Rio Preto, São Paulo, Brazil
| | - Eduardo Festozo Vicente
- School of Sciences and Engineering, São Paulo State University (UNESP), Tupã, São Paulo, Brazil
| | - Marlus Chorilli
- São Paulo State University (UNESP), Department of Drug and Medicines, School of Pharmaceutical Sciences, Araraquara, São Paulo, Brazil
| | - Hernane da Silva Barud
- Department of Biotechnology, Laboratory of Polymers and Biomaterials, University of Araraquara (UNIARA), Araraquara, São Paulo, Brazil
| | - Paula Aboud Barbugli
- Department of Dental Materials and Prosthodontics, School of Dentistry, Sao Paulo State University (UNESP), Araraquara, São Paulo, Brazil
| | - Henrik Franzyk
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Paul Robert Hansen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Fernando Rogério Pavan
- São Paulo State University (UNESP), Tuberculosis Research Laboratory, School of Pharmaceutical Sciences, Araraquara, São Paulo, Brazil.
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Rao KU, Godaly G. Isolation and Purification of Mycobacterial Extracellular Vesicles (EVs). Methods Mol Biol 2023; 2674:55-60. [PMID: 37258959 DOI: 10.1007/978-1-0716-3243-7_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Bacterial extracellular vesicles (EVs) contain numerous active substances that mediate bacterial interactions with their host and with other microbes. Best defined are the EVs from Gram-negative bacteria that have been shown to deliver virulence factors, modulate the immune responses, mediate antibiotic resistance, and also inhibit competitive microbes. Due to the complex cell wall structures of Gram-positive bacteria and mycobacteria, EVs from these bacteria were only recently reported. This protocol describes the isolation of EVs from mycobacteria.
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Affiliation(s)
- Komal Umashankar Rao
- Department of Microbiology, Immunology and Glycobiology, Institution of Laboratory Medicine, Lund University, Lund, Sweden
| | - Gabriela Godaly
- Department of Microbiology, Immunology and Glycobiology, Institution of Laboratory Medicine, Lund University, Lund, Sweden.
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Novel In Silico Insights into Rv1417 and Rv2617c as Potential Protein Targets: The Importance of the Medium on the Structural Interactions with Exported Repetitive Protein (Erp) of Mycobacterium tuberculosis. Polymers (Basel) 2022; 14:polym14132577. [PMID: 35808623 PMCID: PMC9269478 DOI: 10.3390/polym14132577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 11/17/2022] Open
Abstract
Nowadays, tuberculosis is the second leading cause of death from a monopathogenic transmitted disease, only ahead of COVID-19. The role of exported repetitive protein (Erp) in the virulence of Mycobacterium tuberculosis has been extensively demonstrated. In vitro and in vivo assays have identified that Erp interacts with Rv1417 and Rv2617c proteins, forming putative transient molecular complexes prior to localization to the cell envelope. Although new insights into the interactions and functions of Erp have emerged over the years, knowledge about its structure and protein–protein interactions at the atomistic level has not been sufficiently explored. In this work, we have combined several in silico methodologies to gain new insights into the structural relationship between these proteins. Two system conditions were evaluated by MD simulations: Rv1417 and Rv2617c embedded in a lipid membrane and another with a semi-polar solvent to mimic the electrostatic conditions on the membrane surface. The Erp protein was simulated as an unanchored structure. Stabilized structures were docked, and complexes were evaluated to recognize the main residues involved in protein–protein interactions. Our results show the influence of the medium on the structural conformation of proteins. Globular conformations were favored under high polarity conditions and showed a higher energetic affinity in complex formation. Meanwhile, disordered conformations were favored under semi-polar conditions and an increase in the number of contacts between residues was observed. In addition, the electrostatic potential analysis showed remarkable changes in protein interactions due to the polarity of the medium, demonstrating the relevance of Erp protein in heterodimer formation. On the other hand, contact analysis showed that several C-terminal residues of Erp were involved in the protein interactions, which seems to contradict experimental observations; however, these complexes could be transient forms. The findings presented in this work are intended to open new perspectives in the studies of Erp protein molecular interactions and to improve the knowledge about its function and role in the virulence of Mycobacterium tuberculosis.
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Algal Metabolites Can Be an Immune Booster against COVID-19 Pandemic. Antioxidants (Basel) 2022; 11:antiox11030452. [PMID: 35326102 PMCID: PMC8944855 DOI: 10.3390/antiox11030452] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 02/22/2022] [Accepted: 02/23/2022] [Indexed: 02/05/2023] Open
Abstract
The world has faced the challenges of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) for the last two years, first diagnosed at the end of 2019 in Wuhan and widely distributed worldwide. As a result, the WHO has proclaimed the illness brought on by this virus to be a global pandemic. To combat COVID-19, researcher communities continuously develop and implement rapid diagnoses, safe and effective vaccinations and other alternative therapeutic procedures. However, synthetic drug-related side effects and high costs have piqued scientists’ interest in natural product-based therapies and medicines. In this regard, antiviral substances derived from natural resources and some medicines have seen a boom in popularity. For instance, algae are a rich source of compounds such as lectins and sulfated polysaccharides, which have potent antiviral and immunity-boosting properties. Moreover, Algae-derived compounds or metabolites can be used as antibodies and vaccine raw materials against COVID-19. Furthermore, some algal species can boost immunity, reduce viral activity in humans and be recommended for usage as a COVID-19 preventative measure. However, this field of study is still in its early stages of development. Therefore, this review addresses critical characteristics of algal metabolites, their antioxidant potential and therapeutic potential in COVID-19.
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