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Sudhakar K, Dugar N, Jupudi S, Ashwin R, Gowthamarajan K. Unveiling molecular insights: in silico exploration of TLR4 antagonist for management of dry eye syndrome. BMJ Open Ophthalmol 2024; 9:e001610. [PMID: 38702178 PMCID: PMC11086362 DOI: 10.1136/bmjophth-2023-001610] [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: 12/08/2023] [Accepted: 04/17/2024] [Indexed: 05/06/2024] Open
Abstract
BACKGROUND Dry eye disease is the most commonplace multifractional ocular complication, which has already affected millions of people in the world. It is identified by the excessive buildup of reactive oxygen species, leading to substantial corneal epithelial cell demise and ocular surface inflammation attributed to TLR4. In this study, we aimed to identify potential compounds to treat of dry eye syndrome by exploring in silico methods. METHODS In this research, molecular docking and dynamics simulation tests were used to examine the effects of selected compounds on TLR4 receptor. Compounds were extracted from different databases and were prepared and docked against TLR4 receptor via Autodock Vina. Celastrol, lumacaftor and nilotinib were selected for further molecular dynamics studies for a deeper understanding of molecular systems consisting of protein and ligands by using the Desmond module of the Schrodinger Suite. RESULTS The docking results revealed that the compounds are having binding affinity in the range of -5.1 to -8.78 based on the binding affinity and three-dimensional interactions celastrol, lumacaftor and nilotinib were further studied for their activity by molecular dynamics. Among the three compounds, celastrol was the most stable based on molecular dynamics trajectory analysis from 100 ns in the catalytic pockets of 2Z63.pdb.pdb. Root mean square deviation of celastrol/2Z63 was in the range of 1.8-4.8 Å. CONCLUSION In particular, Glu376 of TLR4 receptor is crucial for the identification and binding of lipopolysaccharides (LPS), which are part of Gram-negative bacteria's outer membrane. In our investigation, celastrol binds to Glu376, suggesting that celastrol may prevent the dry eye syndrome by inhibiting LPS's binding to TLR4.
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Affiliation(s)
- Kothandan Sudhakar
- Department of Pharmaceutics, JSS College of Pharmacy, JSS Academy of Higher Education and Research, Ooty,The Nilgiris-643001, Tamil Nadu, India
| | - Neeru Dugar
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education and Research, Ooty, The Nilgiris-643001, Tamil Nadu, India
| | - Srikanth Jupudi
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education and Research, Ooty, The Nilgiris-643001, Tamil Nadu, India
| | - Ravichandran Ashwin
- Department of Pharmaceutics, JSS College of Pharmacy, JSS Academy of Higher Education and Research, Ooty,The Nilgiris-643001, Tamil Nadu, India
| | - Kuppusamy Gowthamarajan
- Department of Pharmaceutics, JSS College of Pharmacy, JSS Academy of Higher Education and Research, Ooty,The Nilgiris-643001, Tamil Nadu, India
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Li Y, Tang X, Yang Z, He J, Ma N, Huang A, Shi Y. BCp12/PLA combination: A novel antibacterial agent targeting Mur family, DNA gyrase and DHFR. Int J Food Microbiol 2023; 406:110370. [PMID: 37678070 DOI: 10.1016/j.ijfoodmicro.2023.110370] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 08/16/2023] [Accepted: 08/24/2023] [Indexed: 09/09/2023]
Abstract
The combination of natural antimicrobial peptide BCp12/phenyllatic acid (BCp12/PLA) presents a more efficient antibacterial effect, but its antibacterial mechanism remains unclear. This study studied the synergistic antibacterial mechanism of BCp12 and PLA against S. aureus. The results demonstrated that the BCp12/PLA combination presented a synergistic antibacterial effect against S. aureus, with a fractional inhibitory concentration of 0.05. Furthermore, flow cytometry and scanning electron microscope analysis revealed that BCp12 and PLA synergistically promoted cell membrane disruption compared with the group treated only with one compound, inducing structural cell damage and cytoplasmic leakage. In addition, fluorescence spectroscopy analysis suggested that BCp12 and PLA synergistically influenced genomic DNA. BCp12 and PLA targeted enzymes related to peptidoglycan and DNA synthesis and interacted by hydrogen bonding and hydrophobic interactions with mur enzymes (murC, murD, murE, murF, and murG), dihydrofolate reductase, and DNA gyrase. Additionally, the combined treatment successfully inhibited microbial reproduction in the storage of pasteurized milk, indicating that the combination of BCp12 and PLA can be used as a new preservative strategy in food systems. Overall, this study could provide potential strategies for preventing and controlling foodborne pathogens.
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Affiliation(s)
- Yufang Li
- College of Food Science and Technology, Yunnan Agricultural University, Kunming 650201, Yunnan, China
| | - Xiaozhao Tang
- Yunnan Center for Disease Control and Prevention, Kunming 650022, Yunnan, China
| | - Zushun Yang
- Yunnan Center for Disease Control and Prevention, Kunming 650022, Yunnan, China
| | - Jinze He
- College of Food Science and Technology, Yunnan Agricultural University, Kunming 650201, Yunnan, China
| | - Ni Ma
- Yunnan Center for Disease Control and Prevention, Kunming 650022, Yunnan, China
| | - Aixiang Huang
- College of Food Science and Technology, Yunnan Agricultural University, Kunming 650201, Yunnan, China.
| | - Yanan Shi
- College of Food Science and Technology, Yunnan Agricultural University, Kunming 650201, Yunnan, China.
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Ali S, Alam M, Hasan GM, Hassan MI. Potential therapeutic targets of Klebsiella pneumoniae: a multi-omics review perspective. Brief Funct Genomics 2021; 21:63-77. [PMID: 34448478 DOI: 10.1093/bfgp/elab038] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/03/2021] [Accepted: 08/04/2021] [Indexed: 11/15/2022] Open
Abstract
The multidrug resistance developed in many organisms due to the prolonged use of antibiotics has been an increasing global health crisis. Klebsiella pneumoniae is a causal organism for various infections, including respiratory, urinary tract and biliary diseases. Initially, immunocompromised individuals are primarily affected by K. pneumoniae. Due to the emergence of hypervirulent strains recently, both healthy and immunocompetent individuals are equally susceptible to K. pneumoniae infections. The infections caused by multidrug-resistant and hypervirulent K. pneumoniae strains are complicated to treat, illustrating an urgent need to develop novel and more practical approaches to combat the pathogen. We focused on the previously performed high-throughput analyses by other groups to discover several novel enzymes that may be considered attractive drug targets of K. pneumoniae. These targets qualify most of the selection criteria for drug targeting, including an absence of its homolog's gene in the host. The capsule, lipopolysaccharide, fimbriae, siderophores and essential virulence factors facilitate the pathogen entry, infection and survival inside the host. This review discusses K. pneumoniae pathophysiology, including its virulence determinants and further the potential drug targets that might facilitate the discovery of novel drugs and effective treatment regimens shortly.
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Affiliation(s)
- Sabeeha Ali
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar New Delhi 110025, India
| | - Manzar Alam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar New Delhi 110025, India
| | - Gulam Mustafa Hasan
- Department of Biochemistry, College of Medicine, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar New Delhi 110025, India
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Losada-Barreiro S, Sova M, Mravljak J, Saso L, Bravo-Díaz C. Synthesis, In Vitro Antioxidant Properties and Distribution of a New Cyanothiophene-Based Phenolic Compound in Olive Oil-In-Water Emulsions. Antioxidants (Basel) 2020; 9:antiox9070623. [PMID: 32708549 PMCID: PMC7402159 DOI: 10.3390/antiox9070623] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/06/2020] [Accepted: 07/13/2020] [Indexed: 01/13/2023] Open
Abstract
We synthesized and determined the antioxidant activity and distribution of a new cyanothiophene-based compound, N-(3-cyano-4,5,6,7-tetrahydrobenzo[b]thiophen-2-yl)-3,5-dihydroxybenzamide (SIM-53B), in intact stripped olive oil-in-water emulsion. The in vitro antioxidant properties of SIM-53B were evaluated and compared to those for Trolox and resveratrol. Addition of an emulsifier (Tween 20) creates a narrow region, the aqueous-oil interface, and the distribution of SIM-53B can be described by two partition constants: PWI (between aqueous/interfacial regions) and POI (between oil/interfacial regions). The effects of emulsifier concentration expressed in terms of the volume fraction, ΦI, and O/W ratio were also evaluated on its distribution. SIM-53B is predominantly distributed (>90%) in the interfacial region of 1:9 (O/W) olive oil-in-water emulsions at the lowest emulsifier volume fraction (ΦI = 0.005) and only a small fraction is located in the aqueous (<5%) and the oil (<5%) regions. Besides, the concentration of SIM-53B in the interfacial region of the emulsions is ~170-190-fold higher than the stoichiometric concentration, emphasizing the compartmentalization effects. Results suggest that the emulsifier volume fraction is a key parameter that may modulate significantly its concentration in the interface. Our study suggests that cyanothiophene-based compounds may be interesting additives for potential lipid protection in biomembranes or other lipid-based systems.
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Affiliation(s)
- Sonia Losada-Barreiro
- Physical Chemistry Department, Chemistry Faculty, University of Vigo, E-36310 Vigo, Spain;
- REQUIMTE-LAQV, Chemistry and Biochemistry Department, Science Faculty, University of Porto, PT-4169-007 Porto, Portugal
- Correspondence: (S.L.-B.); (M.S.)
| | - Matej Sova
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia;
- Correspondence: (S.L.-B.); (M.S.)
| | - Janez Mravljak
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia;
| | - Luciano Saso
- Department of Physiology and Pharmacology “Vittorio Erspamer”, Sapienza University of Rome, 00185 Rome, Italy;
| | - Carlos Bravo-Díaz
- Physical Chemistry Department, Chemistry Faculty, University of Vigo, E-36310 Vigo, Spain;
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Vijaya Prabhu S, Singh SK. Atom-based 3D-QSAR, induced fit docking, and molecular dynamics simulations study of thieno[2,3-b]pyridines negative allosteric modulators of mGluR5. J Recept Signal Transduct Res 2018; 38:225-239. [PMID: 29806525 DOI: 10.1080/10799893.2018.1476542] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Atom-based three dimensional-quantitative structure-activity relationship (3D-QSAR) model was developed on the basis of 5-point pharmacophore hypothesis (AARRR) with two hydrogen bond acceptors (A) and three aromatic rings for the derivatives of thieno[2,3-b]pyridine, which modulates the activity to inhibit the mGluR5 receptor. Generation of a highly predictive 3D-QSAR model was performed using the alignment of predicted pharmacophore hypothesis for the training set (R2 = 0.84, SD = 0.26, F = 45.8, N = 29) and test set (Q2 = 0.74, RMSE = 0.235, Pearson-R = 0.94, N = 9). The best pharmacophore hypothesis AARRR was selected, and developed three dimensional-quantitative structure activity relationship (3D-QSAR) model also supported the outcome of this study by means of favorable and unfavorable electron withdrawing group and hydrophobic regions of most active compound 42d and least active compound 18b. Following, induced fit docking and binding free energy calculations reveals the reliable binding orientation of the compounds. Finally, molecular dynamics simulations for 100 ns were performed to depict the protein-ligand stability. We anticipate that the resulted outcome could be supportive to discover potent negative allosteric modulators for metabotropic glutamate receptor 5 (mGluR5).
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Affiliation(s)
- Sitrarasu Vijaya Prabhu
- a Department of Bioinformatics, Computer Aided Drug Design and Molecular Modeling Lab , Alagappa University , Karaikudi , India
| | - Sanjeev Kumar Singh
- a Department of Bioinformatics, Computer Aided Drug Design and Molecular Modeling Lab , Alagappa University , Karaikudi , India
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