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Jangwan NS, Khan M, Das R, Altwaijry N, Sultan AM, Khan R, Saleem S, Singh MF. From petals to healing: consolidated network pharmacology and molecular docking investigations of the mechanisms underpinning Rhododendron arboreum flower's anti-NAFLD effects. Front Pharmacol 2024; 15:1366279. [PMID: 38863975 PMCID: PMC11165132 DOI: 10.3389/fphar.2024.1366279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Accepted: 04/25/2024] [Indexed: 06/13/2024] Open
Abstract
Rhododendron arboreum: Sm., also known as Burans is traditionally used as an anti-inflammatory, anti-diabetic, hepatoprotective, adaptogenic, and anti-oxidative agent. It has been used since ancient times in Indian traditional medicine for various liver disorders. However, the exact mechanism behind its activity against NAFLD is not known. The aim of the present study is to investigate the molecular mechanism of Rhododendron arboreum flower (RAF) in the treatment of NAFLD using network pharmacology and molecular docking methods. Bioactives were also predicted for their drug-likeness score, probable side effects and ADMET profile. Protein-protein interaction (PPI) data was obtained using the STRING platform. For the visualisation of GO analysis, a bioinformatics server was employed. Through molecular docking, the binding affinity between potential targets and active compounds were assessed. A total of five active compounds of RAF and 30 target proteins were selected. The targets with higher degrees were identified through the PPI network. GO analysis indicated that the NAFLD treatment with RAF primarily entails a response to the fatty acid biosynthetic process, lipid metabolic process, regulation of cell death, regulation of stress response, and cellular response to a chemical stimulus. Molecular docking and molecular dynamic simulation exhibited that rutin has best binding affinity among active compounds and selected targets as indicated by the binding energy, RMSD, and RMSF data. The findings comprehensively elucidated toxicity data, potential targets of bioactives and molecular mechanisms of RAF against NAFLD, providing a promising novel strategy for future research on NAFLD treatment.
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Affiliation(s)
- Nitish Singh Jangwan
- Department of Pharmacognosy and Phytochemistry, School of Pharmaceutical Sciences, Delhi Pharmaceutical Sciences and Research University, New Delhi, India
| | - Mausin Khan
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences and Technology, Sardar Bhagwan Singh University, Dehradun, Uttarakhand, India
| | - Richa Das
- Department of Biotechnology, Parul Institute of Applied Science, Parul University, Vadodara, Gujarat, India
| | - Najla Altwaijry
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Ahlam Mansour Sultan
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Ruqaiyah Khan
- Department of Basic Health Sciences, Deanship of Preparatory Year for the Health Colleges, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Shakir Saleem
- Department of Public Health, College of Health Sciences, Saudi Electronic University, Riyadh, Saudi Arabia
| | - Mamta F. Singh
- College of Pharmacy, COER University, Roorkee, Uttarakhand, India
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S AS, Vellapandian C. In silico and pharmacokinetic assessment of echinocystic acid effectiveness in Alzheimer's disease like pathology. Future Sci OA 2024; 10:FSO904. [PMID: 38827791 PMCID: PMC11140647 DOI: 10.2144/fsoa-2023-0150] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 09/12/2023] [Indexed: 06/05/2024] Open
Abstract
Aim: Alzheimer's disease causes dementia which impairs the cognitive domains. Methodology: The pharmacokinetic characteristics and biological activity of echinocystic acid are predicted in this work using in silico or computational approaches, including pkCSM, Swiss ADME, OSIRIS® property explorer, PASS online web resource and MOLINSPIRATION® software. Results & discussion: The compound has lipid metabolism regulating property as major role in decreasing the progression of Alzheimer's disease and it has no major side effects and ADR. The drug also has anti-inflammatory properties which can help in regulating the innate immunity that plays a major role in Alzheimer's disease. Conclusion: From the computational screening, we infer that, echinocystic acid can regulate memory loss, cognitive disability and also slow down the progression of Alzheimer's disease-like pathology.
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Affiliation(s)
- Ankul Singh S
- Department of Pharmacology, SRM College of Pharmacy, SRM Institute of Science & Technology, Kattankulathur, Tamil nadu, 603203, India (Bharat)
| | - Chitra Vellapandian
- Department of Pharmacology, SRM College of Pharmacy, SRM Institute of Science & Technology, Kattankulathur, Tamil nadu, 603203, India (Bharat)
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Sahoo M, Behera DU, Gaur M, Subudhi E. Molecular docking, molecular dynamics simulation, and MM/PBSA analysis of ginger phytocompounds as a potential inhibitor of AcrB for treating multidrug-resistant Klebsiella pneumoniae infections. J Biomol Struct Dyn 2024:1-17. [PMID: 38165647 DOI: 10.1080/07391102.2023.2299741] [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: 08/17/2023] [Accepted: 12/20/2023] [Indexed: 01/04/2024]
Abstract
The emergence of Multidrug resistance (MDR) in human pathogens has defected the existing antibiotics and compelled us to understand more about the basic science behind alternate anti-infective drug discovery. Soon, proteome analysis identified AcrB efflux pump protein as a promising drug target using plant-driven phytocompounds used in traditional medicine systems with lesser side effects. Thus, the present study aims to explore the novel, less toxic, and natural inhibitors of Klebsiella pneumoniae AcrB pump protein from 69 Zingiber officinale phyto-molecules available in the SpiceRx database through computational-biology approaches. AcrB protein's homology-modelling was carried out to get a 3D structure. The multistep-docking (HTVS, SP, and XP) were employed to eliminate less-suitable compounds in each step based on the docking score. The chosen hit-compounds underwent induced-fit docking (IFD). Based on the XP GScore, the top three compounds, epicatechin (-10.78), 6-gingerol (-9.71), and quercetin (-9.09) kcal/mol, were selected for further calculation of binding free energy (MM/GBSA). Furthermore, the short-listed compounds were assessed for their drug-like properties based on in silico ADMET properties and Pa, Pi values. In addition, the molecular dynamics simulation (MDS) studies for 250 ns elucidated the binding mechanism of epicatechin, 6-gingerol, and quercetin to AcrB. From the dynamic binding free energy calculations using MM/PBSA, 6-gingerol exhibited a strong binding affinity towards AcrB. Further, the 6-gingerol complex's energy fluctuation was observed from the free energy landscape. In conclusion, 6-gingerol has a promising inhibiting potential against the AcrB efflux pump and thus necessitates further validation through in vitro and in vivo experiments.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Maheswata Sahoo
- Centre for Biotechnology, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar, Odisha, India
| | | | - Mahendra Gaur
- Drug Development, and Analysis Laboratory, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar, India
- Department of Biotechnology, Punjabi University, Patiala, India
| | - Enketeswara Subudhi
- Centre for Biotechnology, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar, Odisha, India
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Arthur MN, Bebla K, Broni E, Ashley C, Velazquez M, Hua X, Radhakrishnan R, Kwofie SK, Miller WA. Design of Inhibitors That Target the Menin-Mixed-Lineage Leukemia Interaction. COMPUTATION (BASEL, SWITZERLAND) 2024; 12:3. [PMID: 38938622 PMCID: PMC11209892 DOI: 10.3390/computation12010003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/29/2024]
Abstract
The prognosis of mixed-lineage leukemia (MLL) has remained a significant health concern, especially for infants. The minimal treatments available for this aggressive type of leukemia has been an ongoing problem. Chromosomal translocations of the KMT2A gene are known as MLL, which expresses MLL fusion proteins. A protein called menin is an important oncogenic cofactor for these MLL fusion proteins, thus providing a new avenue for treatments against this subset of acute leukemias. In this study, we report results using the structure-based drug design (SBDD) approach to discover potential novel MLL-mediated leukemia inhibitors from natural products against menin. The three-dimensional (3D) protein model was derived from Protein Databank (Protein ID: 4GQ4), and EasyModeller 4.0 and I-TASSER were used to fix missing residues during rebuilding. Out of the ten protein models generated (five from EasyModeller and I-TASSER each), one model was selected. The selected model demonstrated the most reasonable quality and had 75.5% of residues in the most favored regions, 18.3% of residues in additionally allowed regions, 3.3% of residues in generously allowed regions, and 2.9% of residues in disallowed regions. A ligand library containing 25,131 ligands from a Chinese database was virtually screened using AutoDock Vina, in addition to three known menin inhibitors. The top 10 compounds including ZINC000103526876, ZINC000095913861, ZINC000095912705, ZINC000085530497, ZINC000095912718, ZINC000070451048, ZINC000085530488, ZINC000095912706, ZINC000103580868, and ZINC000103584057 had binding energies of -11.0, -10.7, -10.6, -10.2, -10.2, -9.9, -9.9, -9.9, -9.9, and -9.9 kcal/mol, respectively. To confirm the stability of the menin-ligand complexes and the binding mechanisms, molecular dynamics simulations including molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) computations were performed. The amino acid residues that were found to be potentially crucial in ligand binding included Phe243, Met283, Cys246, Tyr281, Ala247, Ser160, Asn287, Asp185, Ser183, Tyr328, Asn249, His186, Leu182, Ile248, and Pro250. MI-2-2 and PubChem CIDs 71777742 and 36294 were shown to possess anti-menin properties; thus, this justifies a need to experimentally determine the activity of the identified compounds. The compounds identified herein were found to have good pharmacological profiles and had negligible toxicity. Additionally, these compounds were predicted as antileukemic, antineoplastic, chemopreventive, and apoptotic agents. The 10 natural compounds can be further explored as potential novel agents for the effective treatment of MLL-mediated leukemia.
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Affiliation(s)
- Moses N. Arthur
- Department of Parasitology, Noguchi Memorial Institute for Medical Research (NMIMR), College of Health Sciences (CHS), University of Ghana, Legon, Accra LG 581, Ghana
- Biomedical Engineering Department, University of Rochester, Rochester, NY 14627, USA
| | - Kristeen Bebla
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
- Department of Molecular Pharmacology & Neuroscience, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
| | - Emmanuel Broni
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
| | - Carolyn Ashley
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
| | - Miriam Velazquez
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
| | - Xianin Hua
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ravi Radhakrishnan
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Samuel K. Kwofie
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic & Applied Sciences, University of Ghana, Legon, Accra LG 77, Ghana
- Department of Biochemistry, Cell and Molecular Biology, West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Accra LG 54, Ghana
| | - Whelton A. Miller
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
- Department of Molecular Pharmacology & Neuroscience, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
- Department of Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA
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Zhang C, Sui Y, Liu S, Yang M. Anti-Viral Activity of Bioactive Molecules of Silymarin against COVID-19 via In Silico Studies. Pharmaceuticals (Basel) 2023; 16:1479. [PMID: 37895950 PMCID: PMC10610370 DOI: 10.3390/ph16101479] [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: 09/04/2023] [Revised: 10/11/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
The severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) infection drove the global coronavirus disease 2019 (COVID-19) pandemic, causing a huge loss of human life and a negative impact on economic development. It is an urgent necessity to explore potential drugs against viruses, such as SARS-CoV-2. Silymarin, a mixture of herb-derived polyphenolic flavonoids extracted from the milk thistle, possesses potent antioxidative, anti-apoptotic, and anti-inflammatory properties. Accumulating research studies have demonstrated the killing activity of silymarin against viruses, such as dengue virus, chikungunya virus, and hepatitis C virus. However, the anti-COVID-19 mechanisms of silymarin remain unclear. In this study, multiple disciplinary approaches and methodologies were applied to evaluate the potential mechanisms of silymarin as an anti-viral agent against SARS-CoV-2 infection. In silico approaches such as molecular docking, network pharmacology, and bioinformatic methods were incorporated to assess the ligand-protein binding properties and analyze the protein-protein interaction network. The DAVID database was used to analyze gene functions, such as the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and Gene Ontology (GO) enrichment. TCMSP and GeneCards were used to identify drug target genes and COVID-19-related genes. Our results revealed that silymarin compounds, such as silybin A/B and silymonin, displayed triplicate functions against SARS-CoV-2 infection, including directly binding with human angiotensin-converting enzyme 2 (ACE2) to inhibit SARS-CoV-2 entry into the host cells, directly binding with viral proteins RdRp and helicase to inhibit viral replication and proliferation, and regulating host immune response to indirectly inhibit viral infection. Specifically, the targets of silymarin molecules in immune regulation were screened out, such as proinflammatory cytokines TNF and IL-6 and cell growth factors VEGFA and EGF. In addition, the molecular mechanism of drug-target protein interaction was investigated, including the binding pockets of drug molecules in human ACE2 and viral proteins, the formation of hydrogen bonds, hydrophobic interactions, and other drug-protein ligand interactions. Finally, the drug-likeness results of candidate molecules passed the criteria for drug screening. Overall, this study demonstrates the molecular mechanism of silymarin molecules against SARS-CoV-2 infection.
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Affiliation(s)
- Chunye Zhang
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65212, USA;
| | - Yuxiang Sui
- School of Life Science, Shanxi Normal University, Linfen 041004, China;
| | - Shuai Liu
- The First Affiliated Hospital, Zhejiang University, Hangzhou 310006, China;
| | - Ming Yang
- Department of Surgery, University of Missouri, Columbia, MO 65212, USA
- NextGen Precision Health Institute, University of Missouri, Columbia, MO 65212, USA
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Choudhary R, Walhekar V, Muthal A, Kumar D, Bagul C, Kulkarni R. Machine learning facilitated structural activity relationship approach for the discovery of novel inhibitors targeting EGFR. J Biomol Struct Dyn 2023; 41:12445-12463. [PMID: 36762704 DOI: 10.1080/07391102.2023.2175263] [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: 11/10/2022] [Accepted: 01/03/2023] [Indexed: 02/11/2023]
Abstract
This research manuscript aims to find the most effective epidermal growth factor receptor (EGFR) inhibitors from millions of in house compounds through Machine Learning (ML) techniques. ML-based structure activity relationship (SAR) models were validated to predict biological activity of untested novel molecules. Six ML algorithms, including k nearest neighbour (KNN), decision tree (DT), Logistic Regression, support vector machine (SVM), multilinear regression (MLR), and random forest (RF), were used to build for activity prediction. Among these, RF classifier (accuracy for train and test set is 90% and 81%) and RF regressor (R2 and MSE for trainset is 0.83 and 0.29 and for test set, 0.69 and 0.46) showed good predictive performance. Also, the six most essential features that affect the biological activity parameter and highly contribute to model development were successfully selected by the variable importance technique. RF regression model was used to predict the biological activity expressed as pIC50 of nearly ten million molecules while RF classification model classifies those molecules into active, moderately active, and least active according to their predicted pIC50. Based on two models, thousand molecules from million molecules with higher predicted pIC50 values and classified as active were selected for molecular docking. Based on the docking scores, predicted pIC50, and binding interactions with MET769 residue, compounds, i.e., Zinc257233137, Zinc257232249, and Zinc101379788, were identified as potential EGFR inhibitors with predicted pIC50 7.72, 7.85, and 7.70. Dynamics studies were also performed on Zinc257233137 to illustrate that it has good binding free energy and stable hydrogen bonding interactions with EGFR. These molecules can be used for further research and proved to be the novel drugs for EGFR in cancer treatment.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rekha Choudhary
- Department of Pharmaceutical Chemistry, BVDU'S Poona College of Pharmacy, Pune, Maharashtra, India
| | - Vinayak Walhekar
- Department of Pharmaceutical Chemistry, BVDU'S Poona College of Pharmacy, Pune, Maharashtra, India
| | - Amol Muthal
- Department of Pharmacology, BVDU'S Poona College of Pharmacy, Pune, Maharashtra, India
| | - Dilip Kumar
- Department of Pharmaceutical Chemistry, BVDU'S Poona College of Pharmacy, Pune, Maharashtra, India
- Department of Entomology, University of California, Davis, Davis, California, USA
- UC Davis Comprehensive Cancer Centre, University of California, Davis, Davis, California, USA
| | - Chandrakant Bagul
- Department of Pharmaceutical Chemistry, BVDU'S Poona College of Pharmacy, Pune, Maharashtra, India
| | - Ravindra Kulkarni
- Department of Pharmaceutical Chemistry, BVDU'S Poona College of Pharmacy, Pune, Maharashtra, India
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Parihar A, Ahmed SS, Sharma P, Choudhary NK, Akter F, Ali MA, Sonia ZF, Khan R. Plant-based bioactive molecules for targeting of endoribonuclease using steered molecular dynamic simulation approach: a highly conserved therapeutic target against variants of SARS-CoV-2. MOLECULAR SIMULATION 2022. [DOI: 10.1080/08927022.2022.2113811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Affiliation(s)
- Arpana Parihar
- Industrial Waste Utilization, Nano and Biomaterials, CSIR-Advanced Materials and Processes Research Institute (AMPRI), Bhopal, India
| | - Sayeda Samina Ahmed
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Dhaka, Bangladesh
| | - Palak Sharma
- NIMS Institute of Allied Medical Science and Technology, NIMS University, Jaipur, India
| | | | - Farjana Akter
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Dhaka, Bangladesh
| | - Md Ackas Ali
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Dhaka, Bangladesh
| | - Zannatul Ferdous Sonia
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Dhaka, Bangladesh
| | - Raju Khan
- Industrial Waste Utilization, Nano and Biomaterials, CSIR-Advanced Materials and Processes Research Institute (AMPRI), Bhopal, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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In Silico Study of Alkaloids: Neferine and Berbamine Potentially Inhibit the SARS-CoV-2 RNA-Dependent RNA Polymerase. J CHEM-NY 2022. [DOI: 10.1155/2022/7548802] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19, has been a global concern. While there have been some vaccines and drugs, the rapid emergence of variants due to mutations has threatened public health. As the de novo drug development process is expensive and time-consuming, repurposing existing antiviral drugs against SARS-CoV-2 is an alternative and promising approach to mitigate the current situation. Several studies have indicated that some natural products exhibit inhibitory activities against SARS-CoV-2. This study is aimed at analyzing the potential of natural alkaloids, using various computational tools, as drug candidates against SARS-CoV-2. The molecular docking analysis predicted that naturally occurring alkaloids can bind with RNA-dependent RNA-polymerase (RdRP). The QSAR analysis was conducted by using the way2drug/PASS online web resource, and the pharmacokinetics and toxicity properties of these alkaloids were predicted using pkCSM, SwissADME, and ProTox-II webserver. Among the different alkaloids studied, neferine and berbamine were repurposed as potential drug candidates based on their binding affinity and interactions with RdRP. Further, molecular dynamics simulation of 90 ns revealed the conformational stability of the neferine-RdRP complex.
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Gilmiyarova FN, Kolotyeva NA, Gusyakova OA. Predicted and Experimentally Validated Lactate Characteristics: New Possibilities for Controlling Endothelial Cell Metabolism. J EVOL BIOCHEM PHYS+ 2022. [DOI: 10.1134/s0022093022030176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Rowaiye AB, Ogugua AJ, Ibeanu G, Bur D, Asala MT, Ogbeide OB, Abraham EO, Usman HB. Identifying potential natural inhibitors of Brucella melitensis Methionyl-tRNA synthetase through an in-silico approach. PLoS Negl Trop Dis 2022; 16:e0009799. [PMID: 35312681 PMCID: PMC8970508 DOI: 10.1371/journal.pntd.0009799] [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: 09/08/2021] [Revised: 03/31/2022] [Accepted: 02/16/2022] [Indexed: 12/12/2022] Open
Abstract
Background Brucellosis is an infectious disease caused by bacteria of the genus Brucella. Although it is the most common zoonosis worldwide, there are increasing reports of drug resistance and cases of relapse after long term treatment with the existing drugs of choice. This study therefore aims at identifying possible natural inhibitors of Brucella melitensis Methionyl-tRNA synthetase through an in-silico approach. Methods Using PyRx 0.8 virtual screening software, the target was docked against a library of natural compounds obtained from edible African plants. The compound, 2-({3-[(3,5-dichlorobenzyl) amino] propyl} amino) quinolin-4(1H)-one (OOU) which is a co-crystallized ligand with the target was used as the reference compound. Screening of the molecular descriptors of the compounds for bioavailability, pharmacokinetic properties, and bioactivity was performed using the SWISSADME, pkCSM, and Molinspiration web servers respectively. The Fpocket and PLIP webservers were used to perform the analyses of the binding pockets and the protein ligand interactions. Analysis of the time-resolved trajectories of the Apo and Holo forms of the target was performed using the Galaxy and MDWeb servers. Results The lead compounds, Strophanthidin and Isopteropodin are present in Corchorus olitorius and Uncaria tomentosa (Cat’s-claw) plants respectively. Isopteropodin had a binding affinity score of -8.9 kcal / ml with the target and had 17 anti-correlating residues in Pocket 1 after molecular dynamics simulation. The complex formed by Isopteropodin and the target had a total RMSD of 4.408 and a total RMSF of 9.8067. However, Strophanthidin formed 3 hydrogen bonds with the target at ILE21, GLY262 and LEU294, and induced a total RMSF of 5.4541 at Pocket 1. Conclusion Overall, Isopteropodin and Strophanthidin were found to be better drug candidates than OOU and they showed potentials to inhibit the Brucella melitensis Methionyl-tRNA synthetase at Pocket 1, hence abilities to treat brucellosis. In-vivo and in-vitro investigations are needed to further evaluate the efficacy and toxicity of the lead compounds. The cure for brucellosis involves a long course of treatment with a combination of antibiotics. However, some of the drugs are not recommended for very young children and pregnant women. Moreover, cases of relapse and resistance to these drugs are reported. With the Brucella Methionyl-tRNA synthetase as a target, molecular docking and virtual screening was used to identify possible drug candidates from a library of 1524 compounds obtained from edible African plants. Two lead compounds, Strophanthidin and Isopteropodin usually present in Corchorus olitorius and Uncaria tomentosa (Cat’s claw) plants showed potentials to inhibit the Brucella melitensis Methionyl-tRNA synthetase. Their bioactivities were also confirmed in their molecular dynamic simulation with the target protein. Consequently, both compounds have potentials for safety and efficacy in the treatment of brucellosis.
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Affiliation(s)
| | - Akwoba Joseph Ogugua
- Department of Veterinary Public Health and Preventive Medicine, University of Nigeria, Nsukka, Nigeria
- * E-mail:
| | - Gordon Ibeanu
- Department of Pharmaceutical Science, North Carolina Central University, Durham, North Carolina, United States of America
| | - Doofan Bur
- Department of Medical Biotechnology, National Biotechnology Development Agency, Abuja, Nigeria
| | - Mercy Titilayo Asala
- Department of Medical Biotechnology, National Biotechnology Development Agency, Abuja, Nigeria
| | | | | | - Hamzah Bundu Usman
- Department of Plant Science and Biotechnology, Federal University Gusau, Gusau, Nigeria
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Haroun M, Tratrat C, Petrou A, Geronikaki A, Ivanov M, Ćirić A, Soković M, Nagaraja S, Venugopala KN, Balachandran Nair A, Elsewedy HS, Kochkar H. Exploration of the Antimicrobial Effects of Benzothiazolylthiazolidin-4-One and In Silico Mechanistic Investigation. Molecules 2021; 26:4061. [PMID: 34279400 PMCID: PMC8271899 DOI: 10.3390/molecules26134061] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/11/2021] [Accepted: 06/25/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Infectious diseases still affect large populations causing significant morbidity and mortality. Bacterial and fungal infections for centuries were the main factors of death and disability of millions of humans. Despite the progress in the control of infectious diseases, the appearance of resistance of microbes to existing drugs creates the need for the development of new effective antimicrobial agents. In an attempt to improve the antibacterial activity of previously synthesized compounds modifications to their structures were performed. METHODS Nineteen thiazolidinone derivatives with 6-Cl, 4-OMe, 6-CN, 6-adamantan, 4-Me, 6-adamantan substituents at benzothiazole ring were synthesized and evaluated against panel of four bacterial strains S. aureus, L. monocytogenes, E. coli and S. typhimirium and three resistant strains MRSA, E. coli and P. aeruginosa in order to improve activity of previously evaluated 6-OCF3-benzothiazole-based thiazolidinones. The evaluation of minimum inhibitory and minimum bactericidal concentration was determined by microdilution method. As reference compounds ampicillin and streptomycin were used. RESULTS All compounds showed antibacterial activity with MIC in range of 0.12-0.75 mg/mL and MBC at 0.25->1.00 mg/mL The most active compound among all tested appeared to be compound 18, with MIC at 0.10 mg/mL and MBC at 0.12 mg/mL against P. aeruginosa. as well as against resistant strain P. aeruginosa with MIC at 0.06 mg/mL and MBC at 0.12 mg/mL almost equipotent with streptomycin and better than ampicillin. Docking studies predicted that the inhibition of LD-carboxypeptidase is probably the possible mechanism of antibacterial activity of tested compounds. CONCLUSION The best improvement of antibacterial activity after modifications was achieved by replacement of 6-OCF3 substituent in benzothiazole moiety by 6-Cl against S. aureus, MRSA and resistant strain of E. coli by 2.5 folds, while against L. monocytogenes and S. typhimirium from 4 to 5 folds.
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Affiliation(s)
- Michelyne Haroun
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Saudi Arabia; (C.T.); (S.N.); (K.N.V.); (A.B.N.); (H.S.E.)
| | - Christophe Tratrat
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Saudi Arabia; (C.T.); (S.N.); (K.N.V.); (A.B.N.); (H.S.E.)
| | - Anthi Petrou
- School of Pharmacy, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
| | - Athina Geronikaki
- School of Pharmacy, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
| | - Marija Ivanov
- Mycological Laboratory, Department of Plant Physiology, Institute for Biological Research, Siniša Stanković-National Institute of Republic of Serbia, University of Belgrade, Bulevar Despota Stefana 142, 11000 Belgrade, Serbia; (M.I.); (A.Ć.); (M.S.)
| | - Ana Ćirić
- Mycological Laboratory, Department of Plant Physiology, Institute for Biological Research, Siniša Stanković-National Institute of Republic of Serbia, University of Belgrade, Bulevar Despota Stefana 142, 11000 Belgrade, Serbia; (M.I.); (A.Ć.); (M.S.)
| | - Marina Soković
- Mycological Laboratory, Department of Plant Physiology, Institute for Biological Research, Siniša Stanković-National Institute of Republic of Serbia, University of Belgrade, Bulevar Despota Stefana 142, 11000 Belgrade, Serbia; (M.I.); (A.Ć.); (M.S.)
| | - Sreeharsha Nagaraja
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Saudi Arabia; (C.T.); (S.N.); (K.N.V.); (A.B.N.); (H.S.E.)
- Department of Pharmaceutics, Vidya Siri College of Pharmacy, Off Sarjapura Road, Bengaluru 560 035, Karnataka, India
| | - Katharigatta Narayanaswamy Venugopala
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Saudi Arabia; (C.T.); (S.N.); (K.N.V.); (A.B.N.); (H.S.E.)
- Department of Biotechnology and Food Technology, Faculty of Applied Sciences, Durban University of Technology, Durban 4001, South Africa
| | - Anroop Balachandran Nair
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Saudi Arabia; (C.T.); (S.N.); (K.N.V.); (A.B.N.); (H.S.E.)
| | - Heba S. Elsewedy
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Saudi Arabia; (C.T.); (S.N.); (K.N.V.); (A.B.N.); (H.S.E.)
| | - Hafedh Kochkar
- Department of Chemistry, College of Science, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia;
- Basic & Applied Scientific Research Center, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
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