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Hosseini Hooshiar M, Badkoobeh A, Kolahdouz S, Tadayonfard A, Mozaffari A, Nasiri K, Salari S, Safaralizadeh R, Yasamineh S. The potential use of nanozymes as an antibacterial agents in oral infection, periodontitis, and peri-implantitis. J Nanobiotechnology 2024; 22:207. [PMID: 38664778 PMCID: PMC11044492 DOI: 10.1186/s12951-024-02472-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 04/07/2024] [Indexed: 04/29/2024] Open
Abstract
Several studies suggest that oral pathogenic biofilms cause persistent oral infections. Among these is periodontitis, a prevalent condition brought on by plaque biofilm. It can even result in tooth loss. Furthermore, the accumulation of germs around a dental implant may lead to peri-implantitis, which damages the surrounding bone and gum tissue. Furthermore, bacterial biofilm contamination on the implant causes soft tissue irritation and adjacent bone resorption, severely compromising dental health. On decontaminated implant surfaces, however, re-osseointegration cannot be induced by standard biofilm removal techniques such as mechanical cleaning and antiseptic treatment. A family of nanoparticles known as nanozymes (NZs) comprise highly catalytically active multivalent metal components. The most often employed NZs with antibacterial activity are those that have peroxidase (POD) activity, among other types of NZs. Since NZs are less expensive, more easily produced, and more stable than natural enzymes, they hold great promise for use in various applications, including treating microbial infections. NZs have significantly contributed to studying implant success rates and periodontal health maintenance in periodontics and implantology. An extensive analysis of the research on various NZs and their applications in managing oral health conditions, including dental caries, dental pulp disorders, oral ulcers, peri-implantitis, and bacterial infections of the mouth. To combat bacteria, this review concentrates on NZs that imitate the activity of enzymes in implantology and periodontology. With a view to the future, there are several ways that NZs might be used to treat dental disorders antibacterially.
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Affiliation(s)
| | - Ashkan Badkoobeh
- Department of Oral and Maxillofacial Surgery, School of Dentistry, Qom University of Medical Sciences, Qom, Iran
| | - Shirin Kolahdouz
- School of Dentistry, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Azadeh Tadayonfard
- Postgraduate Department of Prosthodontics, Dental Faculty, Tehran University of Medical Sciences, Tehran, Iran
| | - Asieh Mozaffari
- Department of Periodontics, Faculty of Dentistry, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Kamyar Nasiri
- Department of Dentistry, Islamic Azad University of Medical Sciences, Tehran, Iran
| | - Sara Salari
- Islamic Azad University of Medical Sciences, Esfahan, Iran
| | - Reza Safaralizadeh
- Restarative Dentistry, Department of Dental, Faculty Tabriz Medical University, Tabriz, Iran.
| | - Saman Yasamineh
- Young Researchers and Elite Club, Tabriz Branch, Islamic Azad University, Tabriz, Iran.
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Gaur V, Kumar N, Vyas A, Chowdhury D, Singh J, Bera S. Identification of potential inhibitors against Escherichia coli Mur D enzyme to combat rising drug resistance: an in-silico approach. J Biomol Struct Dyn 2023:1-11. [PMID: 38149858 DOI: 10.1080/07391102.2023.2297007] [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: 05/02/2023] [Accepted: 12/13/2023] [Indexed: 12/28/2023]
Abstract
Indiscriminate use of anti-microbial agents has resulted in the inception, frequency, and spread of antibiotic resistance among targeted bacterial pathogens and the commensal flora. Mur enzymes, playing a crucial role in cell-wall synthesis, are one of the most appropriate targets for developing novel inhibitors against antibiotic-resistant bacterial pathogens. In the present study, in-silico high-throughput virtual (HTVS) and Standard-Precision (SP) screening was carried out with 0.3 million compounds from several small-molecule libraries against the E. coli Mur D enzyme (PDB ID 2UUP). The docked complexes were further subjected to extra-precision (XP) docking calculations, and highest Glide-score compound was further subjected to molecular simulation studies. The top six virtual hits (S1-S6) displayed a glide score (G-score) within the range of -9.013 to -7.126 kcal/mol and compound S1 was found to have the highest stable interactions with the Mur D enzyme (2UUP) of E. coli. The stability of compound S1 with the Mur D (2UUP) complex was validated by a 100-ns molecular dynamics simulation. Binding free energy calculation by the MM-GBSA strategy of the S1-2UUP (Mur D) complex established van der Waals, hydrogen bonding, lipophilic, and Coulomb energy terms as significant favorable contributors for ligand binding. The final lead molecules were subjected to ADMET predictions to study their pharmacokinetic properties and displayed promising results, except for certain modifications required to improve QPlogHERG values. So, the compounds screened against the Mur D enzyme can be further studied as preparatory points for in-vivo studies to develop potential drugs. HIGHLIGHTSE.coli is a common cause of urinary tract infections.E.coli MurD enzyme is a suitable target for drug development.Novel inhibitors against E.coli MurD enzyme were identified.Molecular dynamics studies identified in-silico potential of identified compound.ADMET predictions and Lipinski's rule of five studies showed promising results.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Vinita Gaur
- Department of Microbiology, School of Bioengineering and Biosciences, Lovely Professional University, Punjab, India
| | - Neeraj Kumar
- Department of Pharmaceutical Chemistry, Bhupal Nobles' University, Udaipur, Rajasthan, India
| | - Ashish Vyas
- Department of Microbiology, School of Bioengineering and Biosciences, Lovely Professional University, Punjab, India
| | - Debabrata Chowdhury
- School of Medicine - Infectious Diseases, Stanford University, Stanford, CA, USA
| | - Joginder Singh
- Department of Microbiology, School of Bioengineering and Biosciences, Lovely Professional University, Punjab, India
| | - Surojit Bera
- Department of Microbiology, School of Bioengineering and Biosciences, Lovely Professional University, Punjab, India
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Siswina T, Rustama MM, Sumiarsa D, Apriyanti E, Dohi H, Kurnia D. Antifungal Constituents of Piper crocatum and Their Activities as Ergosterol Biosynthesis Inhibitors Discovered via In Silico Study Using ADMET and Drug-Likeness Analysis. Molecules 2023; 28:7705. [PMID: 38067436 PMCID: PMC10708292 DOI: 10.3390/molecules28237705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 11/14/2023] [Accepted: 11/16/2023] [Indexed: 12/18/2023] Open
Abstract
Along with the increasing resistance of Candida spp. to some antibiotics, it is necessary to find new antifungal drugs, one of which is from the medicinal plant Red Betel (Piper crocatum). The purpose of this research is to isolate antifungal constituents from P. crocatum and evaluate their activities as ergosterol biosynthesis inhibitors via an in silico study of ADMET and drug-likeness analysis. Two new active compounds 1 and 2 and a known compound 3 were isolated, and their structures were determined using spectroscopic methods, while their bioactivities were evaluated via in vitro and in silico studies, respectively. Antifungal compound 3 was the most active compared to 1 and 2 with zone inhibition values of 14.5, 11.9, and 13.0 mm, respectively, at a concentration of 10% w/v, together with MIC/MFC at 0.31/1.2% w/v. Further in silico study demonstrated that compound 3 had a stronger ΔG than the positive control and compounds 1 and 2 with -11.14, -12.78, -12.00, and -6.89 Kcal/mol against ERG1, ERG2, ERG11, and ERG24, respectively, and also that 3 had the best Ki with 6.8 × 10-3, 4 × 10-4, 1.6 × 10-3, and 8.88 μM. On the other hand, an ADMET analysis of 1-3 met five parameters, while 1 had one violation of Ro5. Based on the research data, the promising antifungal constituents of P. crocatum allow P. crocatum to be proposed as a new antifungal candidate to treat and cure infections due to C. albicans.
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Affiliation(s)
- Tessa Siswina
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Sumedang 45363, Indonesia; (T.S.); (D.S.); (E.A.)
- Department of Midwifery, Poltekkes Kemenkes Pontianak, Pontianak 78124, Indonesia
| | - Mia Miranti Rustama
- Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Sumedang 45363, Indonesia;
| | - Dadan Sumiarsa
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Sumedang 45363, Indonesia; (T.S.); (D.S.); (E.A.)
| | - Eti Apriyanti
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Sumedang 45363, Indonesia; (T.S.); (D.S.); (E.A.)
| | - Hirofumi Dohi
- Graduate School of Horticulture, Chiba University, 1-33 Yayoi, Inage-ku, Chiba 263-8522, Japan;
| | - Dikdik Kurnia
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Sumedang 45363, Indonesia; (T.S.); (D.S.); (E.A.)
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Windaryanti D, Gabriel CS, Hidayat IW, Zainuddin A, Dharsono HDA, Satari MH, Kurnia D. The Potential of 24-Propylcholestrol as Antibacterial Oral Bacteria of Enterococcus faecalis ATCC 29212 and Inhibitor Biofilms Formation: in vitro and in silico Study. Adv Appl Bioinform Chem 2022; 15:99-111. [PMID: 36578792 PMCID: PMC9792223 DOI: 10.2147/aabc.s372337] [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: 06/22/2022] [Accepted: 11/22/2022] [Indexed: 12/24/2022] Open
Abstract
Introduction Uncontrolled biofilm can cause several diseases such as dental caries, gingivitis, and periodontitis. Dental caries is a disease caused by the accumulation of plaque-containing pathogenic bacteria, including Enterococcus faecalis. These bacteria infect the root canals of teeth and colonize to form biofilms. Biofilm inhibition is carried out by interfering with cell wall formation metabolism. MurA enzyme has a role in peptidoglycan biosynthesis of cell walls. Enterococcal surface protein (Esp) is the main contributor of E. faecalis to form biofilms. In addition, inhibition of biofilms by interfering with the quorum sensing (QS) system, suppressing gelatinase virulence factors by blocking autoinducers gelatinase biosynthesis-activating pheromone (GBAP). Purpose Knowing the potential of Piper betel Linn. compounds as antibacterial in vitro and antibiofilm agents against E. faecalis in silico. Patients and Methods The compounds were purified by a bioactivity-guided chromatographic method. Antibacterial activity was tested by disc diffusion method, in vitro studies. In silico study, compound P. betel L. was used as the test ligand and compared with positive control fosfomycin, ambuic acid, quercetin, and taxifolin. The proteins used MurA, Esp, GBAP, and gelatinase were docking with the Autodock Vina PyRx 0.8 followed by the PYMOL program and visualized with the Discovery Studio 2020 program. Results An antibacterial compound was identified 24-propylcholesterol which can inhibit the activity of E. faecalis ATCC 29212 with MIC value of 78.1 µg/mL and MBC value of 156.3 µg/mL. Molecular docking results showed the binding affinity of 24-propylcholesterol with MurA, ESP, GBAP, and gelatinase enzymes was -7.6, -8.7, -5.3, and -7.9 kcal/mol. Conclusion 24-propylcholesterol has potential as an antibacterial against E. faecalis and as an antibiofilm through in silico inhibition of QS. However, further research is needed in vitro and in vivo to determine the effectiveness of these compounds as antibacterial and antibiofilm.
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Affiliation(s)
- Devi Windaryanti
- Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Padjadjaran, Sumedang, Indonesia
| | - Christine Sondang Gabriel
- Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Padjadjaran, Sumedang, Indonesia
| | - Ika Wiani Hidayat
- Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Padjadjaran, Sumedang, Indonesia
| | - Achmad Zainuddin
- Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Padjadjaran, Sumedang, Indonesia
| | - Hendra Dian Adhita Dharsono
- Department of Conservative Dentistry, Faculty of Dentistry, Universitas Padjadjaran, Bandung, Jawa Barat, Indonesia
| | - Mieke Hemiawati Satari
- Department of Oral Biology, Faculty of Dentistry, Universitas Padjadjaran, Bandung, Jawa Barat, Indonesia
| | - Dikdik Kurnia
- Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Padjadjaran, Sumedang, Indonesia,Correspondence: Dikdik Kurnia, Jl. Raya Bandung Sumedang km.21, Hegarmanah, Jatinangor, Kabupaten Sumedang, Sumedang, Jawa Barat, 45363, Indonesia, Tel/Fax +022 7794391, Email
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Zhou J, Cai Y, Liu Y, An H, Deng K, Ashraf MA, Zou L, Wang J. Breaking down the cell wall: Still an attractive antibacterial strategy. Front Microbiol 2022; 13:952633. [PMID: 36212892 PMCID: PMC9544107 DOI: 10.3389/fmicb.2022.952633] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/18/2022] [Indexed: 11/17/2022] Open
Abstract
Since the advent of penicillin, humans have known about and explored the phenomenon of bacterial inhibition via antibiotics. However, with changes in the global environment and the abuse of antibiotics, resistance mechanisms have been selected in bacteria, presenting huge threats and challenges to the global medical and health system. Thus, the study and development of new antimicrobials is of unprecedented urgency and difficulty. Bacteria surround themselves with a cell wall to maintain cell rigidity and protect against environmental insults. Humans have taken advantage of antibiotics to target the bacterial cell wall, yielding some of the most widely used antibiotics to date. The cell wall is essential for bacterial growth and virulence but is absent from humans, remaining a high-priority target for antibiotic screening throughout the antibiotic era. Here, we review the extensively studied targets, i.e., MurA, MurB, MurC, MurD, MurE, MurF, Alr, Ddl, MurI, MurG, lipid A, and BamA in the cell wall, starting from the very beginning to the latest developments to elucidate antimicrobial screening. Furthermore, recent advances, including MraY and MsbA in peptidoglycan and lipopolysaccharide, and tagO, LtaS, LspA, Lgt, Lnt, Tol-Pal, MntC, and OspA in teichoic acid and lipoprotein, have also been profoundly discussed. The review further highlights that the application of new methods such as macromolecular labeling, compound libraries construction, and structure-based drug design will inspire researchers to screen ideal antibiotics.
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Affiliation(s)
- Jingxuan Zhou
- The People’s Hospital of China Three Gorges University, Yichang, Hubei, China
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
- The Institute of Infection and Inflammation, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
| | - Yi Cai
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
- The Institute of Infection and Inflammation, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
| | - Ying Liu
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
- The Institute of Infection and Inflammation, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
| | - Haoyue An
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
- The Institute of Infection and Inflammation, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
| | - Kaihong Deng
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
- The Institute of Infection and Inflammation, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
| | - Muhammad Awais Ashraf
- Department of Microbiology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Lili Zou
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
- The Institute of Infection and Inflammation, College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
| | - Jun Wang
- The People’s Hospital of China Three Gorges University, Yichang, Hubei, China
- *Correspondence: Jun Wang,
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Heliawati L, Lestari S, Hasanah U, Ajiati D, Kurnia D. Phytochemical Profile of Antibacterial Agents from Red Betel Leaf (Piper crocatum Ruiz and Pav) against Bacteria in Dental Caries. Molecules 2022; 27:molecules27092861. [PMID: 35566225 PMCID: PMC9101570 DOI: 10.3390/molecules27092861] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 04/22/2022] [Accepted: 04/27/2022] [Indexed: 12/23/2022] Open
Abstract
Based on data from The Global Burden of Disease Study in 2016, dental and oral health problems, especially dental caries, are a disease experienced by almost half of the world’s population (3.58 billion people). One of the main causes of dental caries is the pathogenesis of Streptococcus mutans. Prevention can be achieved by controlling S. mutans using an antibacterial agent. The most commonly used antibacterial for the treatment of dental caries is chlorhexidine. However, long-term use of chlorhexidine has been reported to cause resistance and some side effects. Therefore, the discovery of a natural antibacterial agent is an urgent need. A natural antibacterial agent that can be used are herbal medicines derived from medicinal plants. Piper crocatum Ruiz and Pav has the potential to be used as a natural antibacterial agent for treating dental and oral health problems. Several studies reported that the leaves of P. crocatum Ruiz and Pav contain secondary metabolites such as essential oils, flavonoids, alkaloids, terpenoids, tannins, and phenolic compounds that are active against S. mutans. This review summarizes some information about P. crocatum Ruiz and Pav, various isolation methods, bioactivity, S. mutans bacteria that cause dental caries, biofilm formation mechanism, antibacterial properties, and the antibacterial mechanism of secondary metabolites in P. crocatum Ruiz and Pav.
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Affiliation(s)
- Leny Heliawati
- Study Program of Chemistry, Faculty of Mathematics and Natural Science, Universitas Pakuan, Bogor 16143, Indonesia; (S.L.); (U.H.)
- Correspondence: ; Tel.: +62-8521-615-0330
| | - Seftiana Lestari
- Study Program of Chemistry, Faculty of Mathematics and Natural Science, Universitas Pakuan, Bogor 16143, Indonesia; (S.L.); (U.H.)
| | - Uswatun Hasanah
- Study Program of Chemistry, Faculty of Mathematics and Natural Science, Universitas Pakuan, Bogor 16143, Indonesia; (S.L.); (U.H.)
| | - Dwipa Ajiati
- Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Padjadjaran, Sumedang 45363, Indonesia; (D.A.); (D.K.)
| | - Dikdik Kurnia
- Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Padjadjaran, Sumedang 45363, Indonesia; (D.A.); (D.K.)
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AlEraky DM, Madi M, El Tantawi M, AlHumaid J, Fita S, AbdulAzeez S, Borgio JF, Al-Harbi FA, Alagl AS. Predominance of non- Streptococcus mutans bacteria in dental biofilm and its relation to caries progression. Saudi J Biol Sci 2021; 28:7390-7395. [PMID: 34867042 PMCID: PMC8626303 DOI: 10.1016/j.sjbs.2021.08.052] [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: 04/25/2021] [Revised: 08/13/2021] [Accepted: 08/15/2021] [Indexed: 12/26/2022] Open
Abstract
This study aims to assess differences in biofilm bacterial composition between patients with low and high caries. Patients without a medical problem and with no history of antibiotic use, mouth wash or fluoride application in the previous 3 months were recruited. Caries was recorded at cavitation level; score was calculated by a national mean (dmft of 4.8 and DMFT of 2.7). Pooled biofilm samples were collected from mesial, distal, buccal, lingual, and occlusal surfaces. Based on caries experience, individuals were classified into low and high caries and both groups were compared regarding bacteria identified using 16S rRNA gene sequencing, and molecular phylogenetic analysis of the isolates was performed. A total of twenty seven randomly selected samples with low (n = 13) and high (n = 14) caries. Identification of oral bacteria was performed using 16S rRNA sequence, Rothia mucilaginosa and R. aeria were identified in low caries individuals, while R. dentocariosa was detected in high caries individuals. Two Streptococcus spp. were identified only in low caries S. salivarius and S. gordonii whereas S. sanguinis, S. mitis, S. sinensis, S. rubneri, S. vestibularis, S. cristatus and S. massiliensis were identified only in individuals with high caries. This study revealed the absence of R. mucilaginosa in the high caries subjects and its coexistence with the low caries subjects. Streptococcus mutans was insignificant contributor of caries among samples, while, Streptococcus sanguinis was the main constituent of high caries Saudi patients.
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Affiliation(s)
- Doaa M AlEraky
- Department of Biomedical Dental Sciences, College of Dentistry, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Marwa Madi
- Department of Preventive Dental Sciences, College of Dentistry, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Maha El Tantawi
- Department of Pediatric Dentistry and Dental Public Health, Faculty of Dentistry, Alexandria University, Alexandria, Egypt
| | - Jehan AlHumaid
- Department of Preventive Dental Sciences, College of Dentistry, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Sarah Fita
- Department of Preventive Dental Sciences, College of Dentistry, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Sayed AbdulAzeez
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - J Francis Borgio
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia.,Department of Epidemic Diseases Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Fahad A Al-Harbi
- Department of Substitutive Dental Science, College of Dentistry, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Adel S Alagl
- Department of Preventive Dental Sciences, College of Dentistry, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
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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: 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: 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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Shadrina AAN, Herdiyati Y, Wiani I, Satari MH, Kurnia D. Prediction Mechanism of Nevadensin as Antibacterial Agent against S. sanguinis: In vitro and In silico Studies. Comb Chem High Throughput Screen 2021; 25:1488-1497. [PMID: 34238151 DOI: 10.2174/1386207324666210707104440] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 05/16/2021] [Accepted: 05/21/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Streptococcus sanguinis can contribute to tooth demineralization, which can lead to dental caries. Antibiotics used indefinitely to treat dental caries can lead to bacterial resistance. Discovering new antibacterial agents from natural products like Ocimum basilicum will help combat antibiotic resistance. In silico analysis (molecular docking) can help determine the lead compound by studying the molecular interaction between the drug and the target receptor (MurA enzyme and DNA gyrase). It is a potential candidate for antibacterial drug development. OBJECTIVE The research objective is to isolate the secondary metabolite of O. basilicum extract that has activity against S. sanguinis through in vitro and in silico analysis. METHODS n-Hexane extract of O. basilicum was purified by combining column chromatography with bioactivity-guided. The in vitro antibacterial activity against S. sanguinis was determined using the disc diffusion and microdilution method, while molecular docking simulation of nevadensin (1) with MurA enzyme and DNA gyrase was performed used PyRx 0.8 program. RESULTS Nevadensin from O. basilicum was successfully isolated and characterized by spectroscopic methods. This compound showed antibacterial activity against S. sanguinis with MIC and MBC values of 3750 and 15000 μg/mL, respectively. In silico analysis showed that the binding affinity to MurA was -8.5 Kcal/mol, and the binding affinity to DNA gyrase was -6.7 Kcal/mol. The binding of nevadensin-MurA is greater than fosfomycin-MurA. Otherwise, Nevadensin-DNA gyrase has a weaker binding affinity than fluoroquinolone-DNA gyrase and chlorhexidine-DNA gyrase. CONCLUSION Nevadensin showed potential as a new natural antibacterial agent by inhibiting the MurA enzyme rather than DNA gyrase.
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Affiliation(s)
- Aldina Amalia Nur Shadrina
- 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
| | - 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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Nayaka NMDMW, Sasadara MMV, Sanjaya DA, Yuda PESK, Dewi NLKAA, Cahyaningsih E, Hartati R. Piper betle (L): Recent Review of Antibacterial and Antifungal Properties, Safety Profiles, and Commercial Applications. Molecules 2021; 26:molecules26082321. [PMID: 33923576 PMCID: PMC8073370 DOI: 10.3390/molecules26082321] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 04/06/2021] [Accepted: 04/07/2021] [Indexed: 02/06/2023] Open
Abstract
Piper betle (L) is a popular medicinal plant in Asia. Plant leaves have been used as a traditional medicine to treat various health conditions. It is highly abundant and inexpensive, therefore promoting further research and industrialization development, including in the food and pharmaceutical industries. Articles published from 2010 to 2020 were reviewed in detail to show recent updates on the antibacterial and antifungal properties of betel leaves. This current review showed that betel leaves extract, essential oil, preparations, and isolates could inhibit microbial growth and kill various Gram-negative and Gram-positive bacteria as well as fungal species, including those that are multidrug-resistant and cause serious infectious diseases. P. betle leaves displayed high efficiency on Gram-negative bacteria such as Escherichia coli and Pseudomonas aeruginosa, Gram-positive bacteria such as Staphylococcus aureus, and Candida albicans. The ratio of MBC/MIC indicated bactericidal and bacteriostatic effects of P. betle leaves, while MFC/MIC values showed fungicidal and fungistatic effects. This review also provides a list of phytochemical compounds in betel leaves extracts and essential oils, safety profiles, and value-added products of betel leaves. Some studies also showed that the combination of betel leaves extract and essential oil with antibiotics (streptomycin, chloramphenicol and gentamicin) could provide potentiating antibacterial properties. Moreover, this review delivers a scientific resume for researchers in respected areas and manufacturers who want to develop betel leaves-based products.
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Affiliation(s)
- Ni Made Dwi Mara Widyani Nayaka
- Department of Natural Medicine, Mahasaraswati University of Denpasar, Denpasar 80233, Indonesia; (M.M.V.S.); or (D.A.S.); (P.E.S.K.Y.); (N.L.K.A.A.D.); or (E.C.)
- Correspondence: or
| | - Maria Malida Vernandes Sasadara
- Department of Natural Medicine, Mahasaraswati University of Denpasar, Denpasar 80233, Indonesia; (M.M.V.S.); or (D.A.S.); (P.E.S.K.Y.); (N.L.K.A.A.D.); or (E.C.)
| | - Dwi Arymbhi Sanjaya
- Department of Natural Medicine, Mahasaraswati University of Denpasar, Denpasar 80233, Indonesia; (M.M.V.S.); or (D.A.S.); (P.E.S.K.Y.); (N.L.K.A.A.D.); or (E.C.)
| | - Putu Era Sandhi Kusuma Yuda
- Department of Natural Medicine, Mahasaraswati University of Denpasar, Denpasar 80233, Indonesia; (M.M.V.S.); or (D.A.S.); (P.E.S.K.Y.); (N.L.K.A.A.D.); or (E.C.)
| | - Ni Luh Kade Arman Anita Dewi
- Department of Natural Medicine, Mahasaraswati University of Denpasar, Denpasar 80233, Indonesia; (M.M.V.S.); or (D.A.S.); (P.E.S.K.Y.); (N.L.K.A.A.D.); or (E.C.)
| | - Erna Cahyaningsih
- Department of Natural Medicine, Mahasaraswati University of Denpasar, Denpasar 80233, Indonesia; (M.M.V.S.); or (D.A.S.); (P.E.S.K.Y.); (N.L.K.A.A.D.); or (E.C.)
| | - Rika Hartati
- Pharmaceutical Biology Department, Bandung Institute of Technology, Bandung 40132, Indonesia;
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