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Bouzammit R, Belchkar S, El fadili M, Kanzouai Y, Mujwar S, Alanazi MM, Chalkha M, Nakkabi A, Bakhouch M, Gal E, Gaina LI, al houari G. New Triazole-Isoxazole Hybrids as Antibacterial Agents: Design, Synthesis, Characterization, In Vitro, and In Silico Studies. Molecules 2024; 29:2510. [PMID: 38893386 PMCID: PMC11174038 DOI: 10.3390/molecules29112510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 05/22/2024] [Accepted: 05/23/2024] [Indexed: 06/21/2024] Open
Abstract
Novel isoxazole-triazole conjugates have been efficiently synthesized using 3-formylchromone as starting material according to a multi-step synthetic approach. The structures of the target conjugates and intermediate products were characterized by standard spectroscopic techniques (1H NMR and 13C NMR) and confirmed by mass spectrometry (MS). The all-synthesized compounds were screened for their antibacterial activity against three ATCC reference strains, namely Staphylococcus aureus ATCC 25923, Staphylococcus aureus ATCC BAA-44, and Escherichia coli ATCC 25922 as well as one strain isolated from the hospital environment Pseudomonas aeruginosa. The findings indicate that conjugate 7b exhibits a stronger antibacterial response against the tested Escherichia coli ATCC 25922 and Pseudomonas aeruginosa pathogenic strains compared to the standard antibiotics. Furthermore, hybrid compound 7b proved to have a bactericidal action on the Escherichia coli ATCC 25922 strain, as evidenced by the results of the MBC determination. Moreover, the ADMET pharmacokinetic characteristics revealed a favorable profile for the examined compound, as well as a good level of oral bioavailability. Molecular docking and molecular dynamics simulations were performed to explore the inhibition mechanism and binding energies of conjugate 7b with the proteins of Escherichia coli and Pseudomonas aeruginosa bacterial strains. The in silico results corroborated the data observed in the in vitro evaluation for compound 7b.
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Affiliation(s)
- Rachid Bouzammit
- Engineering Laboratory of Organometallic and Molecular Materials and Environment, Faculty of Sciences Dhar El Mahraz, University Sidi Mohamed Ben Abdellah, P.O. Box 1796, Atlas, Fez 30000, Morocco; (Y.K.); (M.C.); (A.N.); (G.a.h.)
| | - Salim Belchkar
- Laboratory of Epidemiology and Research in Health Sciences, Faculty of Medicine, Pharmacy and Dentistry, University Sidi Mohammed Ben Abdellah, Fez 30070, Morocco;
| | - Mohamed El fadili
- LIMAS Laboratory, Chemistry Department, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, P.O. Box 1796, Atlas, Fez 30000, Morocco;
| | - Youssra Kanzouai
- Engineering Laboratory of Organometallic and Molecular Materials and Environment, Faculty of Sciences Dhar El Mahraz, University Sidi Mohamed Ben Abdellah, P.O. Box 1796, Atlas, Fez 30000, Morocco; (Y.K.); (M.C.); (A.N.); (G.a.h.)
| | - Somdutt Mujwar
- Chitkara College of Pharmacy, Chitkara University, Rajpura 140401, Punjab, India;
| | - Mohammed M. Alanazi
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia;
| | - Mohammed Chalkha
- Engineering Laboratory of Organometallic and Molecular Materials and Environment, Faculty of Sciences Dhar El Mahraz, University Sidi Mohamed Ben Abdellah, P.O. Box 1796, Atlas, Fez 30000, Morocco; (Y.K.); (M.C.); (A.N.); (G.a.h.)
- Laboratory of Materials Engineering for the Environment and Natural Ressources, Faculty of Sciences and Techniques, University of Moulay Ismail of Meknès, B.P 509, Boutalamine, Errachidia 52000, Morocco
| | - Asmae Nakkabi
- Engineering Laboratory of Organometallic and Molecular Materials and Environment, Faculty of Sciences Dhar El Mahraz, University Sidi Mohamed Ben Abdellah, P.O. Box 1796, Atlas, Fez 30000, Morocco; (Y.K.); (M.C.); (A.N.); (G.a.h.)
- Laboratory of Materials Engineering for the Environment and Natural Ressources, Faculty of Sciences and Techniques, University of Moulay Ismail of Meknès, B.P 509, Boutalamine, Errachidia 52000, Morocco
| | - Mohamed Bakhouch
- Bioorganic Chemistry Team, Faculty of Science, Chouaïb Doukkali University, P.O. Box 24, El Jadida 24000, Morocco;
| | - Emese Gal
- Research Center on Fundamental and Applied Heterochemistry, Faculty of Chemistry and Chemical Engineering, Babeş-Bolyai University, 11 Arany Janos Str., RO-400028 Cluj-Napoca, Romania; (E.G.); (L.I.G.)
| | - Luiza Ioana Gaina
- Research Center on Fundamental and Applied Heterochemistry, Faculty of Chemistry and Chemical Engineering, Babeş-Bolyai University, 11 Arany Janos Str., RO-400028 Cluj-Napoca, Romania; (E.G.); (L.I.G.)
| | - Ghali al houari
- Engineering Laboratory of Organometallic and Molecular Materials and Environment, Faculty of Sciences Dhar El Mahraz, University Sidi Mohamed Ben Abdellah, P.O. Box 1796, Atlas, Fez 30000, Morocco; (Y.K.); (M.C.); (A.N.); (G.a.h.)
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Sadik A, Viswaswar JP, Rajamoney A, Rekha A, Raj DM, Prakashan D, Vasudevan M, Visakh JS, Renuka D, Hely S, Shaji SK, Chandran PR, Kumar G, Vijayan Nair S, Haripriyan J. Mitigation of quorum sensing mediated virulence factors of Pseudomonas aeruginosa: the role of Meldrum's acid activated furan. Front Microbiol 2024; 14:1272240. [PMID: 38235424 PMCID: PMC10791761 DOI: 10.3389/fmicb.2023.1272240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 10/05/2023] [Indexed: 01/19/2024] Open
Abstract
The rapid emergence of drug resistant pathogens is a major threat which has warranted the development of alternative strategies to combat infectious diseases. In this work, we have tested the anti-virulent activity of Meldrum's acid activated furan (MAF) and 1,3-dimethyl barbituric acid activated furan (BAF) against Chromobacterium violaceum and Pseudomonas aeruginosa. It was found that MAF significantly reduced the violacein production and biofilm formation of C. violaceum at sub-inhibitory concentrations. The quorum sensing (QS) regulated virulence factors of P. aeruginosa including biofilm formation, motility, pigment production, and elastase activity were also found to be reduced considerably at sub-inhibitory concentrations of MAF. Additionally, MAF downregulated the expression of genes in the QS circuitry of P. aeruginosa, demonstrating the potential of MAF in lowering the pathogenicity of P. aeruginosa. In silico studies demonstrated the potential of MAF to compete with the signaling molecules of C. violaceum and P. aeruginosa for the QS receptor interaction. In vivo studies using Caenorhabditis elegans demonstrated the anti-pathogenicity of MAF by enhancing the survival of P. aeruginosa-infected C. elegans. These results suggest that activated furan compounds could be potential inhibitors of QS-mediated virulence factors in C. violaceum and P. aeruginosa, encouraging their use in combating multidrug-resistant pathogens.
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Affiliation(s)
- Ajmal Sadik
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Kerala, India
| | - Jithin P. Viswaswar
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Kerala, India
| | - Ambili Rajamoney
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Kerala, India
| | - Anjali Rekha
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Kerala, India
| | - Darsana M. Raj
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Kerala, India
| | - Deepthi Prakashan
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Kerala, India
| | - Mydhili Vasudevan
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Kerala, India
| | - J. S. Visakh
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Kerala, India
| | - Dhannya Renuka
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Kerala, India
| | - Sreetha Hely
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Kerala, India
| | | | - Prakash R. Chandran
- Department of Chemistry, Mannam Memorial N.S.S. College, Kottiyam, Kerala, India
| | - Geetha Kumar
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Kerala, India
| | - Sobha Vijayan Nair
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Kerala, India
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Fu J, He F, Xiao J, Liao Z, He L, He J, Guo J, Liu S. Rapid AMR prediction in Pseudomonas aeruginosa combining MALDI-TOF MS with DNN model. J Appl Microbiol 2023; 134:lxad248. [PMID: 37930836 DOI: 10.1093/jambio/lxad248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/14/2023] [Accepted: 10/31/2023] [Indexed: 11/08/2023]
Abstract
BACKGROUND Pseudomonas aeruginosa is a significant clinical pathogen that poses a substantial threat due to its extensive drug resistance. The rapid and precise identification of this resistance is crucial for effective clinical treatment. Although matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been used for antibiotic susceptibility differentiation of some bacteria in recent years, the genetic diversity of P. aeruginosa complicates population analysis. Rapid identification of antimicrobial resistance (AMR) in P. aeruginosa based on a large amount of MALDI-TOF-MS data has not yet been reported. In this study, we employed publicly available datasets for P. aeruginosa, which contain data on bacterial resistance and MALDI-TOF-MS spectra. We introduced a deep neural network model, synergized with a strategic sampling approach (SMOTEENN) to construct a predictive framework for AMR of three widely used antibiotics. RESULTS The framework achieved area under the curve values of 90%, 85%, and 77% for Tobramycin, Cefepime, and Meropenem, respectively, surpassing conventional classifiers. Notably, random forest algorithm was used to assess the significance of features and post-hoc analysis was conducted on the top 10 features using Cohen's d. This analysis revealed moderate effect sizes (d = 0.5-0.8) in Tobramycin and Cefepime models. Finally, putative AMR biomarkers were identified in this study. CONCLUSIONS This work presented an AMR prediction tool specifically designed for P. aeruginosa, which offers a hopeful pathway for clinical decision-making.
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Affiliation(s)
- Jiaojiao Fu
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, P. R. China
- Chongqing Key Laboratory of Sichuan-Chongqing Co-construction for Diagnosis and Treatment of Infectious Diseases Integrated Traditional Chinese and Western Medicine, Chengdu 611137, P. R. China
| | - Fangting He
- Department of Laboratory Medicine, Chengdu Second People's Hospital, Chengdu 600021, P. R. China
| | - Jinming Xiao
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, P. R. China
| | - Zhengyue Liao
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, P. R. China
- Chongqing Key Laboratory of Sichuan-Chongqing Co-construction for Diagnosis and Treatment of Infectious Diseases Integrated Traditional Chinese and Western Medicine, Chengdu 611137, P. R. China
| | - Liying He
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, P. R. China
| | - Jing He
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, P. R. China
- Chongqing Key Laboratory of Sichuan-Chongqing Co-construction for Diagnosis and Treatment of Infectious Diseases Integrated Traditional Chinese and Western Medicine, Chengdu 611137, P. R. China
| | - Jinlin Guo
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, P. R. China
- Chongqing Key Laboratory of Sichuan-Chongqing Co-construction for Diagnosis and Treatment of Infectious Diseases Integrated Traditional Chinese and Western Medicine, Chengdu 611137, P. R. China
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, P. R. China
| | - Sijing Liu
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, P. R. China
- Chongqing Key Laboratory of Sichuan-Chongqing Co-construction for Diagnosis and Treatment of Infectious Diseases Integrated Traditional Chinese and Western Medicine, Chengdu 611137, P. R. China
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Niranjan V, Uttarkar A, Ramakrishnan A, Muralidharan A, Shashidhara A, Acharya A, Tarani A, Kumar J. De Novo Design of Anti-COVID Drugs Using Machine Learning-Based Equivariant Diffusion Model Targeting the Spike Protein. Curr Issues Mol Biol 2023; 45:4261-4284. [PMID: 37232740 DOI: 10.3390/cimb45050271] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/07/2023] [Accepted: 04/25/2023] [Indexed: 05/27/2023] Open
Abstract
The drug discovery and research for an anti-COVID-19 drug has been ongoing despite repurposed drugs in the market. Over time, these drugs were discontinued due to side effects. The search for effective drugs is still under process. The role of Machine Learning (ML) is critical in the search for novel drug compounds. In the current work, using the equivariant diffusion model, we built novel compounds targeting the spike protein of SARS-CoV-2. Using the ML models, 196 de novo compounds were generated which had no hits on any major chemical databases. These novel compounds fulfilled all the criteria of ADMET properties to be lead-like and drug-like compounds. Of the 196 compounds, 15 were docked with high confidence in the target. These compounds were further subjected to molecular docking, the best compound having an IUPAC name of (4aS,4bR,8aS,8bS)-4a,8a-dimethylbiphenylene-1,4,5,8(4aH,4bH,8aH,8bH)-tetraone and a binding score of -6.930 kcal/mol. The principal compound is labeled as CoECG-M1. Density Function Theory (DFT) and Quantum optimization was carried out along with the study of ADMET properties. This suggests that the compound has potential drug-like properties. The docked complex was further subjected to MD simulations, GBSA, and metadynamics simulations to gain insights into the stability of binding. The model can be in the future modified to improve the positive docking rate.
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Affiliation(s)
- Vidya Niranjan
- Department of Biotechnology, R V College of Engineering, Mysuru Road, Kengeri, Bangalore 560059, Karnataka, India
| | - Akshay Uttarkar
- Department of Biotechnology, R V College of Engineering, Mysuru Road, Kengeri, Bangalore 560059, Karnataka, India
| | - Ananya Ramakrishnan
- Department of Biotechnology, R V College of Engineering, Mysuru Road, Kengeri, Bangalore 560059, Karnataka, India
| | - Anagha Muralidharan
- Department of Biotechnology, R V College of Engineering, Mysuru Road, Kengeri, Bangalore 560059, Karnataka, India
| | - Abhay Shashidhara
- Department of Biotechnology, R V College of Engineering, Mysuru Road, Kengeri, Bangalore 560059, Karnataka, India
| | - Anushri Acharya
- Department of Biotechnology, R V College of Engineering, Mysuru Road, Kengeri, Bangalore 560059, Karnataka, India
| | - Avila Tarani
- Department of Biotechnology, R V College of Engineering, Mysuru Road, Kengeri, Bangalore 560059, Karnataka, India
| | - Jitendra Kumar
- Bangalore Bioinnovation Centre (BBC), Helix Biotech Park, Electronics City Phase 1, Bengaluru 560100, Karnataka, India
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Lima EMF, Almeida FAD, Sircili MP, Bueris V, Pinto UM. N-acetylcysteine (NAC) attenuates quorum sensing regulated phenotypes in Pseudomonas aeruginosa PAO1. Heliyon 2023; 9:e14152. [PMID: 36923901 PMCID: PMC10009464 DOI: 10.1016/j.heliyon.2023.e14152] [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: 07/26/2022] [Revised: 02/22/2023] [Accepted: 02/22/2023] [Indexed: 03/05/2023] Open
Abstract
The expression of many virulence genes in bacteria is regulated by quorum sensing (QS), and the inhibition of this mechanism has been intensely investigated. N-acetylcysteine (NAC) has good antibacterial activity and is able to interfere with biofilm-related respiratory infections, but little is known whether this compound has an effect on bacterial QS communication. This work aimed to evaluate the potential of NAC as a QS inhibitor (QSI) in Pseudomonas aeruginosa PAO1 through in silico and in vitro analyses, as well as in combination with the antibiotic tobramycin. Initially, a molecular docking analysis was performed between the QS regulatory proteins, LasR and RhlR, of P. aeruginosa with NAC, 3-oxo-C12-HSL, C4-HSL, and furanone C30. The NAC sub-inhibitory concentration was determined by growth curves. Then, we performed in vitro tests using the QS reporter strains P. aeruginosa lasB-gfp and rhlA-gfp, as well as the expression of QS-related phenotypes. Finally, the synergistic effect of NAC with the antibiotic tobramycin was calculated by fractional inhibitory concentrations index (FICi) and investigated against bacterial growth, pigment production, and biofilm formation. In the molecular docking study, NAC bound to LasR and RhlR proteins in a similar manner to the AHL cognate, suggesting that it may be able to bind to QS receptor proteins in vivo. In the biosensor assay, the GFP signal was turned down in the presence of NAC at 1000, 500, 250, and 125 μM for lasB-gfp and rhlA-gfp (p < 0.05), suggesting a QS inhibitory effect. Pyocyanin and rhamnolipids decreased (p < 0.05) up to 34 and 37%, respectively, in the presence of NAC at 125 μM. Swarming and swimming motilities were inhibited (p < 0.05) by NAC at 250 to 10000 μM. Additionally, 2500 and 10000 μM of NAC reduced biofilm formation. NAC-tobramycin combination showed synergistic effect with FICi of 0.8, and the best combination was 2500-1.07 μM, inhibiting biofilm formation up to 60%, besides reducing pyocyanin and pyoverdine production. Confocal microscopy images revealed a stronger, dense, and compact biofilm of P. aeruginosa PAO1 control, while the biofilm treated with NAC-tobramycin became thinner and more dispersed. Overall, NAC at low concentrations showed promising anti-QS properties against P. aeruginosa PAO1, adding to its already known effect as an antibacterial and antibiofilm agent.
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Affiliation(s)
- Emília Maria França Lima
- Food Research Center, Department of Food and Experimental Nutrition, Faculty of Pharmaceutical Sciences, University of Sao Paulo (USP), São Paulo, SP, Brazil
| | - Felipe Alves de Almeida
- Instituto de Laticínios Cândido Tostes (ILCT), Empresa de Pesquisa Agropecuária de Minas Gerais (EPAMIG), Juiz de Fora, MG, Brazil
| | | | - Vanessa Bueris
- Microbiology Department, Institute of Biomedical Science, University of São Paulo (USP), São Paulo, SP, Brazil
| | - Uelinton Manoel Pinto
- Food Research Center, Department of Food and Experimental Nutrition, Faculty of Pharmaceutical Sciences, University of Sao Paulo (USP), São Paulo, SP, Brazil
- Corresponding author.
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Pandit A, Shukla AK, Deepika, Vaidya D, Kumari A, Kumar A. In vitro Assessment of Anti-Microbial Activity of Aloe vera (Barbadensis miller) Supported through Computational Studies. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2023. [DOI: 10.1134/s1068162023020188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
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Design of Novel Coumarin Derivatives as NUDT5 Antagonists That Act by Restricting ATP Synthesis in Breast Cancer Cells. MOLECULES (BASEL, SWITZERLAND) 2022; 28:molecules28010089. [PMID: 36615284 PMCID: PMC9822328 DOI: 10.3390/molecules28010089] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/06/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022]
Abstract
Breast cancer, a heterogeneous disease, is among the most frequently diagnosed diseases and is the second leading cause of death due to cancer among women after lung cancer. Phytoactives (plant-based derivatives) and their derivatives are safer than synthetic compounds in combating chemoresistance. In the current work, a template-based design of the coumarin derivative was designed to target the ADP-sugar pyrophosphatase protein. The novel coumarin derivative (2R)-2-((S)-sec-butyl)-5-oxo-4-(2-oxochroman-4-yl)-2,5-dihydro-1H-pyrrol-3-olate was designed. Molecular docking studies provided a docking score of -6.574 kcal/mol and an MM-GBSA value of -29.15 kcal/mol. Molecular dynamics simulation studies were carried out for 500 ns, providing better insights into the interaction. An RMSD change of 2.4 Å proved that there was a stable interaction and that there was no conformational change induced to the receptor. Metadynamics studies were performed to calculate the unbinding energy of the principal compound with NUDT5, which was found to be -75.171 kcal/mol. In vitro validation via a cytotoxicity assay (MTT assay) of the principal compound was carried out with quercetin as a positive control in the MCF7 cell line and with an IC50 value of 55.57 (+/-) 0.7 μg/mL. This work promoted the research of novel natural derivatives to discover their anticancer activity.
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Mycobacterium Time-Series Genome Analysis Identifies AAC2′ as a Potential Drug Target with Naloxone Showing Potential Bait Drug Synergism. Molecules 2022; 27:molecules27196150. [PMID: 36234683 PMCID: PMC9571707 DOI: 10.3390/molecules27196150] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/15/2022] [Accepted: 09/15/2022] [Indexed: 11/16/2022] Open
Abstract
The World Health Organization has put drug resistance in tuberculosis on its list of significant threats, with a critical emphasis on resolving the genetic differences in Mycobacterium tuberculosis. This provides an opportunity for a better understanding of the evolutionary progression leading to anti-microbial resistance. Anti-microbial resistance has a great impact on the economic stability of the global healthcare sector. We performed a timeline genomic analysis from 2003 to 2021 of 578 mycobacterium genomes to understand the pattern underlying genomic variations. Potential drug targets based on functional annotation was subjected to pharmacophore-based screening of FDA-approved phyto-actives. Reaction search, MD simulations, and metadynamics studies were performed. A total of 4,76,063 mutations with a transition/transversion ratio of 0.448 was observed. The top 10 proteins with the least number of mutations were high-confidence drug targets. Aminoglycoside 2′-N-acetyltransferase protein (AAC2′), conferring resistance to aminoglycosides, was shortlisted as a potential drug target based on its function and role in bait drug synergism. Gentamicin-AAC2′ binding pose was used as a pharmacophore template to screen 10,570 phyto-actives. A total of 66 potential hits were docked to obtain naloxone as a lead—active with a docking score of −6.317. Naloxone is an FDA-approved drug that rapidly reverses opioid overdose. This is a classic case of a repurposed phyto-active. Naloxone consists of an amine group, but the addition of the acetyl group is unfavorable, with a reaction energy of 612.248 kcal/mol. With gentamicin as a positive control, molecular dynamic simulation studies were performed for 200 ns to check the stability of binding. Metadynamics-based studies were carried out to compare unbinding energy with gentamicin. The unbinding energies were found to be −68 and −74 kcal/mol for naloxone and gentamycin, respectively. This study identifies naloxone as a potential drug candidate for a bait drug synergistic approach against Mycobacterium tuberculosis.
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Uttarkar A, Niranjan V. Brefeldin A variant via combinatorial screening acts as an effective antagonist inducing structural modification in EPAC2. MOLECULAR SIMULATION 2022. [DOI: 10.1080/08927022.2022.2110271] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Akshay Uttarkar
- Department of Biotechnology, R V College of Engineering, Rashtreeya Sikshana Samithi Trust, Bengaluru, India
| | - Vidya Niranjan
- Department of Biotechnology, R V College of Engineering, Rashtreeya Sikshana Samithi Trust, Bengaluru, India
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Anju VT, Busi S, Kumar S, Suchiang K, Kumavath R, Ranganathan S, Ampasala DR, Dyavaiah M. Alantolactone modulates the production of quorum sensing mediated virulence factors and biofilm formation in Pseudomonas aeruginosa. BIOFOULING 2022; 38:331-347. [PMID: 35469529 DOI: 10.1080/08927014.2022.2064747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 04/05/2022] [Accepted: 04/06/2022] [Indexed: 06/14/2023]
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen in immunocompromised patients and accounts for mortality worldwide. Quorum sensing (QS) and QS mediated biofilm formation of P. aeruginosa increase the severity of infection in the host. New and effective therapeutics are in high demand to eliminate Pseudomonas infections. The current study investigated the quorum quenching and biofilm inhibition properties of alantolactone (ATL) against P. aeruginosa PAO1. The production of key virulence factors and biofilm components were affected in bacteria when treated with sub-MIC of ATL and further validated by qRT-PCR studies. The anti-infective potential of ATL was corroborated in an in vivo model with improved survival of infected Caenorhabditis elegans and reduced bacterial colonization. In silico studies suggested the molecular interactions of ATL to QS proteins as stable. Finally, ATL was explored in the present study to inhibit QS pathways and holds the potential to develop into an effective anti-infective agent against P. aeruginosa.
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Affiliation(s)
- V T Anju
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Siddhardha Busi
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Sandeep Kumar
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Kitlangki Suchiang
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Ranjith Kumavath
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, Kerala, India
| | - Sampathkumar Ranganathan
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Dinakara Rao Ampasala
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Madhu Dyavaiah
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Pondicherry University, Puducherry, India
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Pang Y, Wang S, Tao J, Wang J, Xue Z, Wang R. Mechanism of berberine hydrochloride interfering with biofilm formation of Hafnia alvei. Arch Microbiol 2022; 204:126. [PMID: 34997845 DOI: 10.1007/s00203-021-02617-8] [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: 09/20/2021] [Revised: 11/27/2021] [Accepted: 11/30/2021] [Indexed: 11/02/2022]
Abstract
The mechanism of berberine hydrochloride (BBH) inhibiting the biofilm formation of Hafnia alvei was investigated in this study. The antibiofilm potential of BBH was evaluated by confocal laser scanning microscopy (CLSM) and scanning electron microscopy (SEM) as well as crystal violet staining. The quorum-sensing (QS) inhibition was revealed by determination of QS-related genes expression and related signal molecules production using real-time quantitative PCR (RT-qPCR) and high performance liquid chromatography (HPLC). The binding of BBH to receptor proteins was simulated by molecular docking and molecular dynamics simulations. It was found that BBH at sub-minimum inhibitory concentrations (sub-MICs) significantly reduced the biofilm formation of H. alvei in a dose dependent manner. BBH inhibited the bacterial swimming motility, decreased the transcription of halI and halR genes, and reduced the production of signal molecule C14-HSL. It bound to HalR protein mainly through Van der Waals force and electrostatic interaction force. Based on these results, it was concluded that BBH inhibits the biofilm formation of H. alvei and the mechanism is related to its interference with QS through down-regulating the expression of halI and halR genes.
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Affiliation(s)
- Yuesheng Pang
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, 102488, China
| | - Sha Wang
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, 102488, China
| | - Jiayue Tao
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, 102488, China
| | - Jing Wang
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, 102488, China
| | - Zhe Xue
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 102488, China.
| | - Rufeng Wang
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, 102488, China.
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Anju VT, Busi S, Ranganathan S, Ampasala DR, Kumar S, Suchiang K, Kumavath R, Dyavaiah M. Sesamin and sesamolin rescues Caenorhabditis elegans from Pseudomonas aeruginosa infection through the attenuation of quorum sensing regulated virulence factors. Microb Pathog 2021; 155:104912. [PMID: 33932548 DOI: 10.1016/j.micpath.2021.104912] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/21/2021] [Accepted: 04/21/2021] [Indexed: 10/21/2022]
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen emerging as a public health threat owing to their multidrug resistance profiles. The quorum sensing systems of P. aeruginosa play a pivotal role in the regulation of virulence and act as the target for the development of alternative therapeutics. The study discussed about anti-quorum sensing and antibiofilm properties of lignans (sesamin and sesamolin) found in Sesamum indicum (L.) against P. aeruginosa. The effect of lignans, sesamin and sesamolin on LasR/RhlR mediated virulence factor production, biofilm formation and bacterial motility were studied. To elucidate the mechanism of action of lignans on QS pathways, QS gene expression and in depth in silico analysis were performed. Both the lignans exerted anti-quorum sensing activity at 75 μg/ml without affecting the growth of bacteria. SA and SO exhibited decreased production of virulence factors such as pyocyanin, proteases, elastase and chitinase. The important biofilm constituents of P. aeruginosa including alginate, exopolysaccharides and rhamnolipids were strongly affected by the lignans. Likewise, plausible mechanism of action of lignans were determined through the down regulation of QS regulated gene expression, molecular docking and molecular simulation studies. The in vitro analysis was supported by C. elegans infection model. SA and SO rescued pre-infected worms within 8 days of post infection and reduced the colonization of bacteria inside the intestine due to the anti-infective properties of lignans. The lignans exhibited profound action on Las pathway rather than Rhl which was elucidated through in vitro and in silico assays. In silico pharmacokinetic analysis portrayed the opportunities to employ ligands as potential therapeutics for human use. The deep insights into the anti-QS, anti-biofilm and mechanism of action of lignans can contribute to the development of novel anti-infectives against pseuodmonal infections.
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Affiliation(s)
- V T Anju
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Pondicherry University, Puducherry, 605014, India
| | - Siddhardha Busi
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, 605014, India.
| | - Sampathkumar Ranganathan
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, 605014, India
| | - Dinakara Rao Ampasala
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, 605014, India
| | - Sandeep Kumar
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Pondicherry University, Puducherry, 605014, India
| | - Kitlangki Suchiang
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Pondicherry University, Puducherry, 605014, India
| | - Ranjith Kumavath
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kerala, 671316, India
| | - Madhu Dyavaiah
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Pondicherry University, Puducherry, 605014, India.
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