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Alvarado Obando M, Rey-Varela D, Cava F, Dörr T. Genetic interaction mapping reveals functional relationships between peptidoglycan endopeptidases and carboxypeptidases. PLoS Genet 2024; 20:e1011234. [PMID: 38598601 PMCID: PMC11034669 DOI: 10.1371/journal.pgen.1011234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 04/22/2024] [Accepted: 03/25/2024] [Indexed: 04/12/2024] Open
Abstract
Peptidoglycan (PG) is the main component of the bacterial cell wall; it maintains cell shape while protecting the cell from internal osmotic pressure and external environmental challenges. PG synthesis is essential for bacterial growth and survival, and a series of PG modifications are required to allow expansion of the sacculus. Endopeptidases (EPs), for example, cleave the crosslinks between adjacent PG strands to allow the incorporation of newly synthesized PG. EPs are collectively essential for bacterial growth and must likely be carefully regulated to prevent sacculus degradation and cell death. However, EP regulation mechanisms are poorly understood. Here, we used TnSeq to uncover novel EP regulators in Vibrio cholerae. This screen revealed that the carboxypeptidase DacA1 (PBP5) alleviates EP toxicity. dacA1 is essential for viability on LB medium, and this essentiality was suppressed by EP overexpression, revealing that EP toxicity both mitigates, and is mitigated by, a defect in dacA1. A subsequent suppressor screen to restore viability of ΔdacA1 in LB medium identified hypomorphic mutants in the PG synthesis pathway, as well as mutations that promote EP activation. Our data thus reveal a more complex role of DacA1 in maintaining PG homeostasis than previously assumed.
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Affiliation(s)
- Manuela Alvarado Obando
- Department of Microbiology, Cornell University, Ithaca, New York, United States of America
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, United States of America
| | - Diego Rey-Varela
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Center for Microbial Research (UCMR), Science for Life Laboratory (SciLifeLab), Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Felipe Cava
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Center for Microbial Research (UCMR), Science for Life Laboratory (SciLifeLab), Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Tobias Dörr
- Department of Microbiology, Cornell University, Ithaca, New York, United States of America
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, United States of America
- Cornell Institute for Host-Microbe Interactions and Disease (CIHMID), Ithaca, New York, United States of America
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2
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Silva MC, Cunha G, Firmino P, Sallum LO, Menezes A, Dutra J, de Araujo-Neto J, Batista AA, Ellena J, Napolitano HB. Structural and Anticancer Studies of Methoxyflavone Derivative from Strychnos pseudoquina A.St.-Hil. (Loganiaceae) from Brazilian Cerrado. ACS OMEGA 2023; 8:40764-40774. [PMID: 37929093 PMCID: PMC10621014 DOI: 10.1021/acsomega.3c05841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 10/03/2023] [Indexed: 11/07/2023]
Abstract
The Cerrado biome is the world's largest and most diversified tropical savanna. Despite its diversity, there remains a paucity of scientific discussion and evidence about the medicinal use of Cerrado plants. One of the greatest challenges is the complexity of secondary metabolites, such as flavonoids, present in those plants and their extraction, purification, and characterization, which involves a wide range of approaches, tools, and techniques. Notwithstanding these difficulties, the search for accurately proven medicinal plants against cancer, a leading cause of death worldwide, has contributed to this growing area of research. This study set out to extract, purify, and characterize 3-O-methylquercetin isolated from the plant Strychnos pseudoquina A.St.-Hil. (Loganiaceae) and to test it for antiproliferative activity and selectivity against different tumor and nontumor human cell lines. A combined-method approach was employed using 1H and 13C nuclear magnetic resonance, thermogravimetric analysis, differential scanning calorimetry, single-crystal X-ray diffraction, Hirshfeld surface analysis, and theoretical calculations to extensively characterize this bioflavonoid. 3-O-methylquercetin melts around 275 °C and crystallizes in a nonplanar conformation with an angle of 18.02° between the pyran ring (C) and the phenyl ring (B), unlike quercetin and luteolin, which are planar. Finally, the in vitro cytotoxicity of 3-O-methylquercetin was compared with data from quercetin, luteolin, and cisplatin, showing that structural differences influenced the antiproliferative activity and the selectivity against different tumor cell lines.
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Affiliation(s)
- Marianna C. Silva
- Laboratório
de Novos Materiais, Universidade Evangélica
de Goiás, 75083-515 Anápolis, GO, Brazil
| | - Gracielle Cunha
- Laboratório
de Produtos Naturais, Universidade Estadual
de Goiás, 75132-903 Anápolis, GO, Brazil
| | - Pollyana Firmino
- Laboratório
Multiusuário de Cristalografia Estrutural, Instituto de Física
de São Carlos, Universidade de São
Paulo, 13566-590 São Carlos, SP, Brazil
| | - Loide O. Sallum
- Laboratório
de Novos Materiais, Universidade Evangélica
de Goiás, 75083-515 Anápolis, GO, Brazil
| | - Antônio Menezes
- Laboratório
de Produtos Naturais, Universidade Estadual
de Goiás, 75132-903 Anápolis, GO, Brazil
| | - Jocely Dutra
- Laboratório
de Estrutura e Reatividade de Compostos Inorgânicos, Departamento
de Química, Universidade Federal
de São Carlos, 13565-905 São Carlos, SP, Brazil
| | - João de Araujo-Neto
- Laboratório
de Bioinorgânica, Catálise e Farmacologia, Instituto
de Química, Universidade de São
Paulo, 05508-000 São Paulo, SP, Brazil
| | - Alzir A. Batista
- Laboratório
de Estrutura e Reatividade de Compostos Inorgânicos, Departamento
de Química, Universidade Federal
de São Carlos, 13565-905 São Carlos, SP, Brazil
| | - Javier Ellena
- Laboratório
Multiusuário de Cristalografia Estrutural, Instituto de Física
de São Carlos, Universidade de São
Paulo, 13566-590 São Carlos, SP, Brazil
| | - Hamilton B. Napolitano
- Grupo
de Química Teórica e Estrutural de Anápolis, Universidade Estadual de Goiás, 75132-903 Anápolis, GO, Brazil
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Frlan R, Hrast M, Gobec S. Inhibition of MurA Enzyme from Escherichia coli by Flavonoids and Their Synthetic Analogues. ACS OMEGA 2023; 8:33006-33016. [PMID: 37720776 PMCID: PMC10500568 DOI: 10.1021/acsomega.3c04813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 08/10/2023] [Indexed: 09/19/2023]
Abstract
MurA catalyzes the first step of peptidoglycan (PG) biosynthesis and is a validated target for the development of new antimicrobial agents. In this study, a library of 49 plant flavonoids and their synthetic derivatives were evaluated for their inhibitory properties against MurA fromEscherichia coli. The compounds were tested with and without preincubation and with the addition of DTT to understand the mechanism of inhibition. Thirteen compounds were identified as reversible, time-dependent inhibitors, with inhibition levels ranging from 480 nM to 57 μM, and ampelopsin as the most potent compound. To investigate the major pharmacophore elements responsible for the activity, 2D-QSAR and docking analyzes were performed. The results showed that the catechol moiety and an additional aromatic system were the most important features contributing to the activity of the compounds. However, most of the compounds did not show antibacterial activity againstE. coli andStaphylococcus aureusstrains, suggesting that their inhibitory activity against MurA may not be strong enough to induce antibacterial effects. Nevertheless, our results suggest that flavonoids are a promising starting point to develop new inhibitors of MurA and show great potential for further steps in drug development.
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Affiliation(s)
- Rok Frlan
- The Department of Pharmaceutical
Chemistry, University of Ljubljana, Faculty
of Pharmacy, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Martina Hrast
- The Department of Pharmaceutical
Chemistry, University of Ljubljana, Faculty
of Pharmacy, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Stanislav Gobec
- The Department of Pharmaceutical
Chemistry, University of Ljubljana, Faculty
of Pharmacy, Aškerčeva 7, 1000 Ljubljana, Slovenia
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4
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Obando MA, Dörr T. Novel role for peptidoglycan carboxypeptidases in maintaining the balance between bacterial cell wall synthesis and degradation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.12.548665. [PMID: 37503280 PMCID: PMC10369974 DOI: 10.1101/2023.07.12.548665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Peptidoglycan (PG) is the main component of the bacterial cell wall; it maintains cell shape while protecting the cell from internal osmotic pressure and external environmental challenges. PG synthesis is essential for bacterial growth and survival, and a series of PG modifications are required to allow expansion of the sacculus. Endopeptidases (EPs), for example, cleave the crosslinks between adjacent PG strands to allow the incorporation of newly synthesized PG. EPs are collectively essential for bacterial growth and must likely be carefully regulated to prevent sacculus degradation and cell death. However, EP regulation mechanisms are poorly understood. Here, we used TnSeq to uncover novel EP regulation factors in Vibrio cholerae. This screen revealed that the carboxypeptidase DacA1 (PBP5) alleviates EP toxicity. dacA1 is essential for viability on LB medium, and this essentiality was suppressed by EP overexpression, revealing that EP toxicity both mitigates, and is mitigated by, a defect in dacA1. A subsequent suppressor screen to restore viability of ΔdacA1 in LB medium was answered by hypomorphic mutants in the PG synthesis pathway, as well as mutations that promote PG degradation. Our data thus reveal a key role of DacA1 in maintaining the balance between PG synthesis and degradation.
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Affiliation(s)
- Manuela Alvarado Obando
- Department of Microbiology, Cornell University, Ithaca, NY
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY
| | - Tobias Dörr
- Department of Microbiology, Cornell University, Ithaca, NY
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY
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Siswina T, Miranti Rustama M, Sumiarsa D, Kurnia D. Phytochemical profiling of Piper crocatum and its antifungal mechanism action as Lanosterol 14 alpha demethylase CYP51 inhibitor: a review. F1000Res 2023; 11:1115. [PMID: 37151610 PMCID: PMC10157293.2 DOI: 10.12688/f1000research.125645.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/17/2023] [Indexed: 03/29/2023] Open
Abstract
Mycoses or fungal infections are general health problem that often occurs in healthy and immunocompromised people in the community. The development of resistant strains in Fungi and the incidence of azole antibiotic resistance in the Asia Pacific which reached 83% become a critical problem nowadays. To control fungal infections, substances and extracts isolated from natural resources, especially in the form of plants as the main sources of drug molecules today, are needed. Especially from Piperaceae, which have long been used in India, China, and Korea to treat human ailments in traditional medicine. The purpose of this review is to describe the antifungal mechanism action from Piper crocatum and its phytochemical profiling against lanosterol 14a demethylase CYP51. The methods used to search databases from Google Scholar to find the appropriate databases using Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) Flow Diagram as a clinical information retrieval method. From 1.150.000 results searched by database, there is 73 final results article to review. The review shows that P. crocatum contains flavonoids, tannins, terpenes, saponins, polyphenols, eugenol, alkaloids, quinones, chavibetol acetate, glycosides, triterpenoids or steroids, hydroxychavikol, phenolics, glucosides, isoprenoids, and non-protein amino acids. Its antifungal mechanisms in fungal cells occur due to ergosterol especially lanosterol 14a demethylase (CYP51) inhibition, which is one of the main target sites for antifungal activity because it functions to maintain the integrity and function of cell membranes in Candida. P. crocatum has an antifungal activity through its phytochemical profiling against fungal by inhibiting the lanosterol 14a demethylase, make damaging cell membranes, fungal growth inhibition, and fungal cell lysis.
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Siswina T, Miranti Rustama M, Sumiarsa D, Kurnia D. Phytochemical profiling of Piper crocatum and its antifungal mechanism action as Lanosterol 14 alpha demethylase CYP51 inhibitor: a review. F1000Res 2022; 11:1115. [PMID: 37151610 PMCID: PMC10157293 DOI: 10.12688/f1000research.125645.3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/26/2023] [Indexed: 07/20/2023] Open
Abstract
Mycoses or fungal infections are a general health problem that often occurs in healthy and immunocompromised people in the community. The development of resistant strains in Fungi and the incidence of azole antibiotic resistance in the Asia Pacific which reached 83% become a critical problem nowadays. To control fungal infections, substances and extracts isolated from natural resources, especially in the form of plants as the main sources of drug molecules today, are needed. Especially from Piperaceae, which have long been used in India, China, and Korea to treat human ailments in traditional medicine. The purpose of this review is to describe the antifungal mechanism action from Piper crocatum and its phytochemical profiling against lanosterol 14a demethylase CYP51. The methods used to search databases from Google Scholar to find the appropriate databases using Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) Flow Diagram as a clinical information retrieval method. From 1.150.000 results searched by database, there is 73 final results article to review. The review shows that P. crocatum contains flavonoids, tannins, terpenes, saponins, polyphenols, eugenol, alkaloids, quinones, chavibetol acetate, glycosides, triterpenoids or steroids, hydroxychavikol, phenolics, glucosides, isoprenoids, and non-protein amino acids. Its antifungal mechanisms in fungal cells occur due to ergosterol, especially lanosterol 14a demethylase (CYP51) inhibition, which is one of the main target sites for antifungal activity because it functions to maintain the integrity and function of cell membranes in Candida. P. crocatum has an antifungal activity through its phytochemical profiling against fungal by inhibiting the lanosterol 14a demethylase, make damaging cell membranes, fungal growth inhibition, and fungal cell lysis.
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Affiliation(s)
- Tessa Siswina
- Midwifery, Poltekkes Kemenkes Pontianak, Pontianak, Kalimantan Barat, 78124, Indonesia
- Chemistry, Padjadjaran University, Sumedang, Jawa Barat, 45363, Indonesia
| | | | - Dadan Sumiarsa
- Chemistry, Padjadjaran University, Sumedang, Jawa Barat, 45363, Indonesia
| | - Dikdik Kurnia
- Chemistry, Padjadjaran University, Sumedang, Jawa Barat, 45363, Indonesia
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Siswina T, Miranti Rustama M, Sumiarsa D, Kurnia D. Phytochemical profiling of Piper crocatum and its antifungal activity as Lanosterol 14 alpha demethylase CYP51 inhibitor: a review. F1000Res 2022; 11:1115. [PMID: 37151610 PMCID: PMC10157293 DOI: 10.12688/f1000research.125645.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/20/2022] [Indexed: 11/20/2022] Open
Abstract
Mycoses or fungal infections are a general health problem that often occurs in healthy and immunocompromised people in the community. The development of resistant strains in Fungi and the incidence of azole antibiotic resistance in the Asia Pacific which reached 83% become a critical problem nowadays. To control fungal infections, substances and extracts isolated from natural resources, especially in the form of plants as the main sources of drug molecules today, are needed. Especially from Piperaceae, which have long been used in India, China, and Korea to treat human ailments in traditional medicine. The purpose of this review was to describe antifungal activity from Piper crocatum and its phytochemical profiling against lanosterol 14 alpha demethylase CYP51. The methods used search databases from Google Scholar to find the appropriate databases using Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) flow diagram as a clinical information retrieval method. From 1,150,000 results search by database, there were 73 selected articles to review. The review shows that P. crocatum contains flavonoids, tannins, terpenes, saponins, polyphenols, eugenol, alkaloids, quinones, chavibetol acetate, glycosides, triterpenoids or steroids, hydroxychavikol, phenolics, glucosides, isoprenoids, and non-protein amino acids. Its antifungal mechanisms in fungal cells occur due to ergosterol especially lanosterol 14 alpha demethylase CYP51 inhibition as a result of 5,6 desaturase (ERG3) downregulation. P. crocatum has an antifungal activity by its phytochemical profiling that act against fungi by inhibiting the fungal cytochrome P 450 pathway, make damaging cell membranes, fungal growth inhibition, morphological changes, and fungal cell lysis.
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Primasari A, Apriyanti E, Ambardhani N, Satari MH, Herdiyati Y, Kurnia D. Formulation and Antibacterial Potential of Sarang Semut (Myrmecodia pendans) against Oral Pathogenic Bacteria: An In Vitro Study. Open Dent J 2022. [DOI: 10.2174/18742106-v16-e2112140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Background:
Dental diseases are generally caused by oral bacteria such as Enterococcus faecalis, Streptococcus mutans, and Streptococcus sanguinis. These bacteria have resistance to synthetic drugs; thus, it is required to discover new antibacterial agents. Sarang Semut (Myrmecodia pendans) has been empirically used as a medicinal plant to treat various conditions, including those caused by pathogenic bacteria.
Objective:
The present study was aimed to investigate the antibacterial activity of Sarang Semut extracts against E. faecalis, S. mutans, and S. sanguinis.
Materials and Methods:
Sarang Semut was extracted with several solvents to yield n-hexane, ethyl acetate, methanol, and water extracts. Each extract and combination were adjusted for assay with chlorhexidine, fosfomycin, and quercetin and used as positive controls.
Results:
The n-hexane extract showed activity with inhibition zone values of 7.15 and 10.45 ppm against E. faecalis and S. mutans at 1%, respectively. All combination extracts could inhibit the growth of E. faecalis and S. sanguinis. The synergistic effects resulting from the combination of extract-fosfomycin were also presented in this evaluation, with the strongest shown by water-fosfomycin against S. mutans, with inhibition zones of 28.5 mm at 1%.
Conclusion:
Sarang Semut extracts demonstrated antibacterial activity against oral pathogenic bacteria. These results offer alternative natural sources for the new antibacterial drug candidate.
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Bio-Mechanism of Catechin as Pheromone Signal Inhibitor: Prediction of Antibacterial Agent Action Mode by In Vitro and In Silico Study. Molecules 2021; 26:molecules26216381. [PMID: 34770790 PMCID: PMC8587927 DOI: 10.3390/molecules26216381] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/13/2021] [Accepted: 10/19/2021] [Indexed: 11/24/2022] Open
Abstract
The utilization of medicinal plants has long been explored for the discovery of antibacterial agents and the most effective mechanisms or new targets that can prevent and control the spread of antibiotic resistance. One kind of bacterial cell wall inhibition is the inactivation of the MurA enzyme that contributes to the formation of peptidoglycan. Another approach is to interfere with the cell–cell communication of bacteria called the Quorum sensing (QS) system. The blocking of auto-inducer such as gelatinase biosynthesis-activating pheromone (GBAP) can also suppress the virulence factors of gelatinase and serine protease. This research, in particular, aims to analyze lead compounds as antibacterial and anti-QS agents from Gambir (Uncaria gambir Roxburgh) through protein inhibition by in silico study. Antibacterial agents were isolated by bioactivity-guided isolation using a combination of chromatographic methods, and their chemical structures were determined by spectroscopic analysis methods. The in vitro antibacterial activity was evaluated by disc diffusion methods to determine inhibitory values. Meanwhile, in the in silico analysis, the compound of Uncaria gambir was used as ligand and compared with fosfomycin, ambuic acid, quercetin, and taxifolin as the standard ligand. These ligands were attached to MurA, GBAP, gelatinase, and serine proteases using Autodock Vina in PyRx 0.8 followed by PYMOL for combining the ligand conformation and proteins. plus programs to explore the complex, and visualized by Discovery Studio 2020 Client program. The antibacterial agent was identified as catechin that showed inhibitory activity against Enterococcus faecalis ATCC 29212 with inhibition zones of 11.70 mm at 10%, together with MIC and MBC values of 0.63 and 1.25 μg/mL, respectively. In the in silico study, the molecular interaction of catechin with MurA, GBAP, and gelatinase proteins showed good binding energy compared with two positive controls, namely fosfomycin and ambuic acid. It is better to use catechin–MurA (−8.5 Kcal/mol) and catechin–gelatinase (−7.8 Kcal/mol), as they have binding energies which are not marginally different from quercetin and taxifolin. On the other hand, the binding energy of serine protease is lower than quercetin, taxifolin, and ambuic acid. Based on the data, catechin has potency as an antibacterial through the inhibition of GBAP proteins, gelatinase, and serine protease that play a role in the QS system. This is the first discovery of the potential of catechin as an alternative antibacterial agent with an effective mechanism to prevent and control oral disease affected by antibiotic resistance.
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Apriyanti E, Satari MH, Kurnia D. Potential of MurA Enzyme and GBAP in Fsr Quorum Sensing System as Antibacterial Drugs Target: In vitro and In silico Study of Antibacterial Compounds from Myrmecodia pendans. Comb Chem High Throughput Screen 2021; 24:109-118. [PMID: 32598250 PMCID: PMC8778655 DOI: 10.2174/1386207323666200628111348] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 02/29/2020] [Accepted: 04/02/2020] [Indexed: 11/29/2022]
Abstract
Background Increasing the resistance issue has become the reason for the development of new antibacterial in crucial condition. Many ways are tracked to determine the most effective antibacterial agent. Some proteins that are a key role in bacteria metabolism are targeted, including MurA in cell wall biosynthesis and gelatinase biosynthesis-activating pheromone (GBAP) in Fsr Quorum Sensing (QS) system. Objective The objective of this research is the analysis of compounds 1-4 from M. pendans as antibacterial and anti-QS activity trough protein inhibition by in silico study; focus on the structure-activity relationships, to appraise their role as an antibacterial and anti-QS agent in the molecular level. Methods Both activities of M. pendans compounds (1-4) were analyzed by in silico, compared to Fosfomycin, Ambuic acid, Quercetin, and Taxifolin as a standard. Chemical structures of M. pendans compounds were converted using an online program molview. The compounds were docked to MurA, GBAP, gelatinase and serine protease using Autodock Vina in Pyrx 0.8 followed PYMOL to visualization and proteis.plus program to analyze of the complex. Results All compounds from M. pendans bound on MurA, GBAP, gelatinase and serine protease except compound 2. This biflavonoid did not attach to MurA and serine protease yet is the favorable ligand for GBAP and gelatinase with the binding affinity of -6.9 and -9.4 Kcal/mol respectively. Meanwhile, for MurA and serine protease, compound 4 is the highest of bonding energy with values of -8.7 and -6.4 Kcal/mol before quercetin (MurA, -8.9 Kcal/mol) and taxifolin (serine protease, -6.6 Kcal/mol). Conclusion Based on the data, biflavonoid acts better as anti-QS than an inhibitor of MurA enzyme while the others can be acted into both of them either the therapeutic agent of anti-QS or antibacterial agent of MurA inhibitor.
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Affiliation(s)
- Eti Apriyanti
- Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Padjadjaran, Sumedang, Indonesia
| | - Mieke H Satari
- Department of Oral Biology, Faculty of Dentistry, Universitas Padjadjaran, Sumedang, Indonesia
| | - Dikdik Kurnia
- Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Padjadjaran, Sumedang, Indonesia
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Effectiveness of Bioactive Compound as Antibacterial and Anti-Quorum Sensing Agent from Myrmecodia pendans: An In Silico Study. Molecules 2021; 26:molecules26092465. [PMID: 33922641 PMCID: PMC8122932 DOI: 10.3390/molecules26092465] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 04/16/2021] [Accepted: 04/19/2021] [Indexed: 11/20/2022] Open
Abstract
Background: antibiotic resistance encourages the development of new therapies, or the discovery of novel antibacterial agents. Previous research revealed that Myrmecodia pendans (Sarang Semut) contain potential antibacterial agents. However, specific proteins inhibited by them have not yet been identified as either proteins targeted by antibiotics or proteins that have a role in the quorum-sensing system. This study aims to investigate and predict the action mode of antibacterial compounds with specific proteins by following the molecular docking approach. Methods: butein (1), biflavonoid (2), 3″-methoxyepicatechin-3-O-epicatechin (3), 2-dodecyl-4-hydroxylbenzaldehyde (4), 2-dodecyl-4-hydroxylbenzaldehyde (5), pomolic acid (6), betulin (7), and sitosterol-(6′-O-tridecanoil)-3-O-β-D-glucopyranoside (8) from M. pendans act as the ligand. Antibiotics or substrates in each protein were used as a positive control. To screen the bioactivity of compounds, ligands were analyzed by Prediction of Activity Spectra for Substances (PASS) program. They were docked with 12 proteins by AutoDock Vina in the PyRx 0.8 software application. Those proteins are penicillin-binding protein (PBP), MurB, Sortase A (SrtA), deoxyribonucleic acid (DNA) gyrase, ribonucleic acid (RNA) polymerase, ribosomal protein, Cytolysin M (ClyM), FsrB, gelatinase binding-activating pheromone (GBAP), and PgrX retrieved from UniProt. The docking results were analyzed by the ProteinsPlus and Discovery Studio software applications. Results: most compounds have Pa value over 0.5 against proteins in the cell wall. In nearly all proteins, biflavonoid (2) has the strongest binding affinity. However, compound 2 binds only three residues, so that 2 is the non-competitive inhibitor. Conclusion: compound 2 can be a lead compound for an antibacterial agent in each pathway.
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12
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Jiang L, Xie N, Chen M, Liu Y, Wang S, Mao J, Li J, Huang X. Synergistic Combination of Linezolid and Fosfomycin Closing Each Other's Mutant Selection Window to Prevent Enterococcal Resistance. Front Microbiol 2021; 11:605962. [PMID: 33633692 PMCID: PMC7899970 DOI: 10.3389/fmicb.2020.605962] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 12/30/2020] [Indexed: 12/21/2022] Open
Abstract
Enterococci, the main pathogens associated with nosocomial infections, are resistant to many common antibacterial drugs including β-lactams, aminoglycosides, etc. Combination therapy is considered an effective way to prevent bacterial resistance. Preliminary studies in our group have shown that linezolid combined with fosfomycin has synergistic or additive antibacterial activity against enterococci, while the ability of the combination to prevent resistance remains unknown. In this study, we determined mutant prevention concentration (MPC) and mutant selection window (MSW) of linezolid, fosfomycin alone and in combination including different proportions for five clinical isolates of Enterococcus and characterized the resistance mechanism for resistant mutants. The results indicated that different proportions of linezolid combined with fosfomycin had presented different MPCs and MSWs. Compared with linezolid or fosfomycin alone, the combination can restrict the enrichment of resistant mutants at a lower concentration. A rough positive correlation between the selection index (SI) of the two agents in combination and the fractional inhibitory concentration index (FICI) of the combination displayed that the smaller FICI of linezolid and fosfomycin, the more probable their MSWs were to close each other. Mutations in ribosomal proteins (L3 and L4) were the mechanisms for linezolid resistant mutants. Among the fosfomycin-resistant mutants, only two strains have detected the MurA gene mutation related to fosfomycin resistance. In conclusion, the synergistic combination of linezolid and fosfomycin closing each other’s MSW could effectively suppress the selection of enterococcus resistant mutants, suggesting that the combination may be an alternative for preventing enterococcal resistance. In this study, the resistance mechanism of fosfomycin remains to be further studied.
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Affiliation(s)
- Lifang Jiang
- Department of Basic and Clinical Pharmacology, School of Pharmacy, Anhui Medical University, Hefei, China.,Anhui Province Key Laboratory of Major Autoimmune Diseases, School of Pharmacy, Anhui Institute of Innovative Drugs, Anhui Medical University, Hefei, China
| | - Na Xie
- Department of Basic and Clinical Pharmacology, School of Pharmacy, Anhui Medical University, Hefei, China.,Anhui Province Key Laboratory of Major Autoimmune Diseases, School of Pharmacy, Anhui Institute of Innovative Drugs, Anhui Medical University, Hefei, China
| | - Mingtao Chen
- Department of Basic and Clinical Pharmacology, School of Pharmacy, Anhui Medical University, Hefei, China.,Anhui Province Key Laboratory of Major Autoimmune Diseases, School of Pharmacy, Anhui Institute of Innovative Drugs, Anhui Medical University, Hefei, China
| | - Yanyan Liu
- Department of Infectious Diseases, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Shuaishuai Wang
- Department of Basic and Clinical Pharmacology, School of Pharmacy, Anhui Medical University, Hefei, China.,Anhui Province Key Laboratory of Major Autoimmune Diseases, School of Pharmacy, Anhui Institute of Innovative Drugs, Anhui Medical University, Hefei, China
| | - Jun Mao
- Department of Basic and Clinical Pharmacology, School of Pharmacy, Anhui Medical University, Hefei, China.,Anhui Province Key Laboratory of Major Autoimmune Diseases, School of Pharmacy, Anhui Institute of Innovative Drugs, Anhui Medical University, Hefei, China
| | - Jiabin Li
- Department of Infectious Diseases, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Xiaohui Huang
- Department of Basic and Clinical Pharmacology, School of Pharmacy, Anhui Medical University, Hefei, China.,Anhui Province Key Laboratory of Major Autoimmune Diseases, School of Pharmacy, Anhui Institute of Innovative Drugs, Anhui Medical University, Hefei, China
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Herdiyati Y, Astrid Y, Shadrina AAN, Wiani I, Satari MH, Kurnia D. Potential Fatty Acid as Antibacterial Agent Against Oral Bacteria of Streptococcus mutans and Streptococcus sanguinis from Basil (Ocimum americanum): In vitro and In silico Studies. Curr Drug Discov Technol 2021; 18:532-541. [PMID: 32652913 DOI: 10.2174/1570163817666200712171652] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 05/11/2020] [Accepted: 05/12/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Streptococcus mutans and Streptococcus sanguinis are Gram-positive bacteria that cause dental caries. MurA enzyme acts as a catalyst in the formation of peptidoglycan in bacterial cell walls, making it ideal as an antibacterial target. Basil (Ocimum americanum) is an edible plant that is diverse and has been used as a herbal medicine for a long time. It has been reported that basil has a pharmacological effect as well as antibacterial activity. The purpose of this study was to identify antibacterial compounds in O. americanum and analyze their inhibition activity on MurA enzyme. METHODS Fresh leaves from O. americanum were extracted with n-hexane and purified by a combination of column chromatography on normal and reverse phases together with in vitro bioactivity assay against S. mutans ATCC 25175 and S. sanguinis ATCC 10556, respectively, while in silico molecular docking simulation of lauric acid (1) was conducted using PyRx 0.8. RESULTS The structure determination of antibacterial compound by spectroscopic methods resulted in an active compound lauric acid (1). The in vitro evaluation of antibacterial activity in compound 1 showed Minimum Inhibitory Concentration (MIC) and Minimum Bactericidal Concentration (MBC) values of 78.13 and 156.3 ppm and 1250 and 2500 ppm against S. sanguinis and S. mutans, respectively. Further analysis and in silico evaluation determined lauric acid (1) as MurA Enzyme inhibitor. Lauric acid (1) showed a binding affinity of -5.2 Kcal/mol, which was higher than fosfomycin. CONCLUSION Lauric acid showed the potential as a new natural antibacterial agent through MurA inhibition in bacterial cell wall biosynthesis.
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Affiliation(s)
- Yetty Herdiyati
- Department of Pediatric Dentistry, Faculty of Dentistry, Universitas Padjadjaran - Bandung, Indonesia
| | - Yonada Astrid
- Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Padjadjaran, Sumedang, Indonesia
| | - Aldina Amalia Nur Shadrina
- Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Padjadjaran, Sumedang, Indonesia
| | - Ika Wiani
- Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Padjadjaran, Sumedang, Indonesia
| | - Mieke Hemiawati Satari
- Department of Oral Biology, Faculty of Dentistry, Universitas Padjadjaran, Bandung, Indonesia
| | - Dikdik Kurnia
- Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Padjadjaran, Sumedang, Indonesia
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Herdiyati Y, Atmaja HE, Satari MH, Kurnia D. Potential Antibacterial Flavonoid from Buah Merah (Pandanus conodieus Lam.) Against Pathogenic Oral Bacteria of Enterococcus faecalis ATCC 29212. Open Dent J 2020. [DOI: 10.2174/1874210602014010433] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Background:
Dental caries is an oral disease generated by pathogenic bacteria, Enterococcus faecalis, which is most frequently found in teeth with pulp necrosis. On the other hand, the use of the medicinal plant to treat pathogenic disease, including caries is an alternative option, which consumes synthetic drug having a side effect.
Objective:
The purpose of this study is to isolate antibacterial agents from Buah Merah (Pandanus conoideus Lam) and to test the antibacterial activity of those compounds against Enterococcus faecalis ATCC 29212.
Methods:
Isolation of the antibacterial constituents from Buah Merah used a combinational column chromatography technique which include a normal and reversed-phase. The chosen fraction of each separation is based on the most active fraction. The compounds at various concentrations, 1000 - 20000 μg/mL, were assessed against E. faecalis ATCC 29212 by agar disc diffusion method, and chlorhexidine 2000 μg/mL was used as a positive control.
Results:
Four compounds isolated from Buah Merah were determined as flavonoid 1, diterpenoid 2, and two fatty acid derivatives 3 and 4. The compounds were then tested against E. faecalis cultured to find inhibition zones, and the study found that only compound 1 identified as Quercetin-3-O-glucose showed an inhibited zone 88 mm at 20000 ppm.
Conclusion:
This study demonstrated that ethyl acetate fraction of Buah Merah contains an antibacterial flavonoid active against E. faecalis. This research gives information for the use of this plant in herbal medicine and contributes to the necessity of a new antibacterial agent for oral infectious disease. Moreover, this data can be based on information to find the substituted antiseptic applied in the dentistry field.
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Kurnia D, Hutabarat GS, Windaryanti D, Herlina T, Herdiyati Y, Satari MH. Potential Allylpyrocatechol Derivatives as Antibacterial Agent Against Oral Pathogen of S. sanguinis ATCC 10,556 and as Inhibitor of MurA Enzymes: in vitro and in silico Study. Drug Des Devel Ther 2020; 14:2977-2985. [PMID: 32801638 PMCID: PMC7396738 DOI: 10.2147/dddt.s255269] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 07/07/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Streptococcus sanguinis is Gram-positive bacteria that contribute to caries. Many antibacterial agents are resistant against bacteria so that the discovery of new antibacterial agents is a crucial issue. Mechanism of antibacterial agents by disrupting cell wall bacteria is a promising target to be developed. One of the enzymes contributing to the cell wall is MurA enzyme. MurA is an enzyme catalyzing the first step of peptidoglycan biosynthesis in the cell wall formation. Inhibiting MurA is an effective and efficient way to kill the bacteria. Source of bioactive compounds including the antibacterial agent can be found in natural product such as herbal plant. Piper betle L. was reported to contain active antibacterial compounds. However, there is no more information on the antibacterial activity and molecular mechanism of P. betle's compound against S. sanguinis. PURPOSE The study aims to identify antibacterial constituents of P. betle L. and evaluate their activities through two different methods including in vitro and in silico analysis. MATERIALS AND METHODS The antibacterial agent was purified by bioactivity-guided isolation with combination chromatography methods and the chemical structure was determined by spectroscopic methods. The in vitro antibacterial activity was evaluated by disc diffusion and dilution methods while the in silico study of a compound binds on the MurA was determined using PyRx program. RESULTS The antibacterial compound identified as allylpyrocatechol showed inhibitory activity against S. sanguinis with an inhibition zone of 11.85 mm at 1%, together with MIC and MBC values of 39.1 and 78.1 μg/mL, respectively. Prediction for molecular inhibition mechanism of allylpyrocatechols against the MurA presented two allylpyrocatechol derivatives showing binding activity of -5.4, stronger than fosfomycin as a reference with the binding activity of -4.6. CONCLUSION Two allylpyrocatechol derivatives were predicted to have a good potency as a novel natural antibacterial agent against S. sanguinis through blocking MurA activity that causes disruption of bacterial cell wall.
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Affiliation(s)
- Dikdik Kurnia
- Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Padjadjaran, Sumedang, Indonesia
| | - Geofanny Sarah Hutabarat
- Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Padjadjaran, Sumedang, Indonesia
| | - Devi Windaryanti
- Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Padjadjaran, Sumedang, Indonesia
| | - Tati Herlina
- Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Padjadjaran, Sumedang, Indonesia
| | - Yetty Herdiyati
- Department of Pediatric Dentistry, Faculty of Dentistry, Universitas Padjadjaran, Bandung, Indonesia
| | - Mieke Hemiawati Satari
- Department of Oral Biology, Faculty of Dentistry, Universitas Padjadjaran, Bandung, Indonesia
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