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Czerkas K, Olchowik-Grabarek E, Łomanowska M, Abdulladjanova N, Sękowski S. Antibacterial Activity of Plant Polyphenols Belonging to the Tannins against Streptococcus mutans-Potential against Dental Caries. Molecules 2024; 29:879. [PMID: 38398630 PMCID: PMC10892310 DOI: 10.3390/molecules29040879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/01/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
Dental caries (DC) is the most common oral pathology. The main bacteria responsible for DC is Streptococcus mutans. One of the strategies that can decrease or eliminate the risk of DC development is using compounds that will inhibit both the growth and virulence factors of S. mutans. Tannins are plant polyphenols that have strong antibacterial activity. The purpose of this study was to assess the antibacterial activity of three tannins against S. mutans. In this investigation, microbiological tests (MIC and MBC) and physicochemical techniques like the fluorescence measurements of tannins' interaction with S. mutans cell membrane and membrane proteins, zeta potential, and thermodynamic analyses were used to obtain knowledge about the antibacterial potential of the investigated compounds against S. mutans as well as about the mechanisms associated with antibacterial activity. The obtained results demonstrate that the used compounds exhibit high antibacterial activity against S. mutans. The mechanisms of their antibacterial activity are linked to the strong change in the S. mutans membrane fluidity and potential, and to their interaction with membrane proteins that can result in great disturbance of bacterial physiology and ultimately the inhibition of bacterial growth, triggering their death. Therefore, it can be concluded that the investigated compounds can be potentially used as natural factors in the prevention of dental caries.
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Affiliation(s)
- Krzysztof Czerkas
- Doctoral School of Exact and Natural Sciences, University of Bialystok, 15-254 Bialystok, Poland
| | - Ewa Olchowik-Grabarek
- Laboratory of Molecular Biophysics, Department of Microbiology and Biotechnology, Faculty of Biology, University of Bialystok, 15-254 Bialystok, Poland; (M.Ł.); (S.S.)
| | - Magdalena Łomanowska
- Laboratory of Molecular Biophysics, Department of Microbiology and Biotechnology, Faculty of Biology, University of Bialystok, 15-254 Bialystok, Poland; (M.Ł.); (S.S.)
| | - Nodira Abdulladjanova
- Institute of Bioorganic Chemistry, Academy of Sciences of the Republic of Uzbekistan, Tashkent 100143, Uzbekistan;
| | - Szymon Sękowski
- Laboratory of Molecular Biophysics, Department of Microbiology and Biotechnology, Faculty of Biology, University of Bialystok, 15-254 Bialystok, Poland; (M.Ł.); (S.S.)
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Mangal P, Jha RK, Jain M, Singh AK, Muthukumaran J. Identification and prioritization of promising lead molecules from Syzygium aromaticum against Sortase C from Streptococcus pyogenes: an in silico investigation. J Biomol Struct Dyn 2022:1-18. [PMID: 35706070 DOI: 10.1080/07391102.2022.2086921] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Sortases are extracellular transpeptidases that play an essential role in the adhesion of secreted proteins to the peptidoglycan layer of the cell wall of Gram-negative bacteria. Sortases are an important drug target protein due to their involvement in synthesizing the peptidoglycan cell wall of Streptococcus pyogenes, and these are not found in Homo sapiens. In this study, initially, we have performed protein sequence analysis to understand the sequential properties of Sortase C. Next, a comparative protein modeling approach was used to predict the three-dimensional model of Sortase C based on the crystal structure of Sortase C from Streptococcus pneumoniae. Virtual screening with an in-house library of phytochemicals from Syzygium aromaticum and molecular docking studies were performed to identify the promising lead molecules. These compounds were also analyzed for their drug-like and pharmacokinetic properties. Subsequently, the protein-ligand complexes of the selected ligands were subjected to molecular dynamics (MD) simulations to investigate their dynamic behavior in physiological conditions. The global and essential dynamics analyses result implied that the Sortase C complexes of the proposed three lead candidates exhibited adequate stability during the MD simulations. Additionally, the three proposed molecules showed favorable MM/PBSA binding free energy values ranging from -13.8 +/- 9.41 to -56.6 +/- 8.82 kcal/mol. After an extensive computational investigation, we have identified three promising lead candidates (CID:13888122, CID:3694932 and CID:102445430) against Sortase C from S. pyogenes. The result obtained from these computational studies can be used to screen and develop the inhibitors against Sortase C from S. pyogenes. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Purti Mangal
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, India
| | - Rajat Kumar Jha
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, India
| | - Monika Jain
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, India
| | - Amit Kumar Singh
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, India
| | - Jayaraman Muthukumaran
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, India
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Kaushik S, Yadav J, Das S, Karthikeyan D, Chug R, Jyoti A, Srivastava VK, Jain A, Kumar S, Sharma V. Identification of Protein Drug Targets of Biofilm Formation and Quorum
Sensing in Multidrug Resistant Enterococcus faecalis. Curr Protein Pept Sci 2022; 23:248-263. [DOI: 10.2174/1389203723666220526155644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 03/16/2022] [Accepted: 04/06/2022] [Indexed: 11/22/2022]
Abstract
Abstract:
Enterococcus faecalis (E. faecalis) is an opportunistic multidrug-resistant (MDR) pathogen
found in the guts of humans and farmed animals. Due to the occurrence of (MDR) strain there is an
urgent need to look for an alternative treatment approach. E. faecalis is a Gram-positive bacterium,
which is among the most prevalent multidrug resistant hospital pathogens. Its ability to develop quorum
sensing (QS) mediated biofilm formation further exacerbates the pathogenicity and triggers lifethreatening
infections. Therefore, developing a suitable remedy for curing E. faecalis mediated enterococcal
infections is an arduous task. Several putative virulence factors and proteins are involved in the
development of biofilms in E. faecalis. Such proteins often play important roles in virulence, disease,
and colonization by pathogens. The elucidation of the structure-function relationship of such protein
drug targets and the interacting compounds could provide an attractive paradigm towards developing
structure-based drugs against E. faecalis. This review provides a comprehensive overview of the current
status, enigmas that warrant further studies, and the prospects toward alleviating the antibiotic resistance
in E. faecalis. Specifically, the role of biofilm and quorum sensing (QS) in the emergence of
MDR strains had been elaborated along with the importance of the protein drug targets involved in both
the processes.
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Affiliation(s)
- Sanket Kaushik
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Jyoti Yadav
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Satyajeet Das
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
- Structural Biology Lab, CSIR-Institute of Microbial Technology, Chandigarh, India
| | | | - Ravneet Chug
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Anupam Jyoti
- Department of Biotechnology, University Institute of Biotechnology,
Chandigarh University, Chandigarh, India
| | | | - Ajay Jain
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Sanjit Kumar
- Centre for Bioseparation Technology, VIT
University, Vellore-632014, Tamil Nadu, India
| | - Vinay Sharma
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
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Kaushik S, Singh H, Das S, Gupta P, Batra S, Prakash R, Srivastava V, Jyoti A, Gupta V, Kothari SL. Binding of metronidazole to Enterococcus faecalis homoserine kinase: Binding studies, docking studies, and molecular dynamics simulation studies. Pharmacogn Mag 2020. [DOI: 10.4103/pm.pm_99_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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Das S, Batra S, Gupta PP, Kumar M, Srivastava VK, Jyoti A, Singh N, Kaushik S. Identification and evaluation of quercetin as a potential inhibitor of naphthoate synthase from Enterococcus faecalis. J Mol Recognit 2019; 32:e2802. [PMID: 31353747 DOI: 10.1002/jmr.2802] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 05/29/2019] [Accepted: 06/07/2019] [Indexed: 12/31/2022]
Abstract
Enterococcus faecalis is a gram-positive, rod-shape bacteria responsible for around 65% to 80% of all enterococcal nosocomial infections. It is multidrug resistant (MDR) bacterium resistant to most of the first-line antibiotics. Due to the emergence of MDR strains, there is an urgent need to find novel targets to develop new antibacterial drugs against E. faecalis. In this regard, we have identified naphthoate synthase (1,4-dihydroxy-2-naphthoyl-CoA synthase, EC: 4.1.3.36; DHNS) as an anti-E. faecalis target, as it is an essential enzyme for menaquinone (vitamin K2 ) synthetic pathway in the bacterium. Thus, inhibiting naphtholate synthase may consequently inhibit the bacteria's growth. In this regard, we report here cloning, expression, purification, and preliminary structural studies of naphthoate synthase along with in silico modeling, molecular dynamic simulation of the model and docking studies of naphthoate synthase with quercetin, a plant alkaloid. Biochemical studies have indicated quercetin, a plant flavonoid as the potential lead compound to inhibit catalytic activity of EfDHNS. Quercetin binding has also been validated by spectrofluorimetric studies in order to confirm the bindings of the ligand compound with EfDHNS at ultralow concentrations. Reported studies may provide a base for structure-based drug development of antimicrobial compounds against E. faecalis.
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Affiliation(s)
- Satyajeet Das
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Sagar Batra
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Pramodkumar P Gupta
- School of Biotechnology and Bioinformatics, DY Patil Deemed to be University, Navi Mumbai, India
| | - Mukesh Kumar
- School of Medicine, Case Western reserve University, Cleveland, Ohio
| | | | - Anupam Jyoti
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Nagendra Singh
- School of Biotechnology, Gautam Buddha University, Greater Noida, India
| | - Sanket Kaushik
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
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