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Kausar N, Shier WT, Ahmed M, Maryam, Albekairi NA, Alshammari A, Saleem M, Imran M, Muddassar M. Investigation of the insecticidal potential of curcumin derivatives that target the Helicoverpa armigera sterol carrier protein-2. Heliyon 2024; 10:e29695. [PMID: 38660259 PMCID: PMC11040122 DOI: 10.1016/j.heliyon.2024.e29695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 04/12/2024] [Accepted: 04/12/2024] [Indexed: 04/26/2024] Open
Abstract
Cotton bollworm (Helicoverpa armigera) is a highly polyphagous, widely prevalent, and persistent Old World insect pest that affects numerous important crops that are directly consumed by people, including tomato, cotton, pigeon pea, chickpea, rice, sorghum, and cowpea. Insects do not synthesize steroids but obtain them from their diet. Inhibition of dietary uptake of steroids by insects is a potentially effective insecticidal mechanism that should not be toxic to humans and other mammals, who synthesize their steroids. Ten curcumin derivatives were tested against H. armigera sterol carrier protein-2 (HaSCP-2) for their potential as insecticidal agents. Curcumin derivatives were initially docked at the binding site of HaSCP-2 to determine their binding affinities and plausible binding modes. The binding modes predominantly show hydrophobic interactions of derivatives with Phe53, Phe110, and Phe89 as core interacting residues in the active site. Validation of in silico results was carried out by performing a fluorescence binding and displacement assay to determine the binding affinities of curcumin derivatives. Among a collection of curcumin derivatives tested, Cur10 showed the lowest IC50 value of 9.64 μM, while Cur07 was 19.86 μM, and Cur06 was 20.79 μM. There was a significant negative correlation between the ability of the curcumin derivatives tested to displace the fluorescent probe from the sterol binding site of HaSCP-2 and to inhibit Sf9 insect cell growth in culture, which is consistent with the curcumin derivatives acting by the novel mechanism of blocking sterol uptake. Then molecular dynamics simulation studies validated the predicted binding modes and the interactions of curcumin derivatives with HaSCP-2 protein. In conclusion, these studies support the potential use of curcumin derivatives as insecticidal agents.
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Affiliation(s)
- Naeema Kausar
- Department of Biosciences, COMSATS University Islamabad, Park Road, Islamabad, 45550, Pakistan
| | - Wayne Thomas Shier
- College of Pharmacy, Department of Medicinal Chemistry, University of Minnesota, 55455, USA
| | - Mahmood Ahmed
- Department of Chemistry, Division of Science and Technology, University of Education, College Road, Lahore, Pakistan
| | - Maryam
- Department of Biosciences, COMSATS University Islamabad, Park Road, Islamabad, 45550, Pakistan
| | - Norah A. Albekairi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Abdulrahman Alshammari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Muhammad Saleem
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Muhammad Imran
- KAM-School of Life Sciences, FC College (A Chartered University), Lahore, 54000, Pakistan
| | - Muhammad Muddassar
- Department of Biosciences, COMSATS University Islamabad, Park Road, Islamabad, 45550, Pakistan
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Ye H, Lin Q, Mei Q, Liu Q, Cao S. Study on mechanism of transdermal administration of eugenol for pain treatment by network pharmacology and molecular docking technology. Heliyon 2024; 10:e29722. [PMID: 38681628 PMCID: PMC11046106 DOI: 10.1016/j.heliyon.2024.e29722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 04/12/2024] [Accepted: 04/14/2024] [Indexed: 05/01/2024] Open
Abstract
The objective of this study was to explore the pharmacological mechanism of transdermal administration of eugenol (EUG) for pain treatment. Firstly, network pharmacology techniques were employed to identify the potential targets responsible for the analgesic effect of EUG. Subsequently, molecular docking technology was used to validate interactions between EUG and the crystal structure of the core target protein. Finally, the impact of EUG on the expression and activation of TRPV1 receptors in HaCaT cells was evaluated through in vitro experiments, thus confirming the analysis of network pharmacology. The study suggested that the transdermal administration of EUG for pain treatment might target the TRPV1 receptor. Molecular docking revealed that EUG could spontaneously bind to the TRPV1 receptor with a high binding ability. The analysis of Western blot (WB) and intracellular Ca2+ levels demonstrated that EUG could increase the expression of TRPV1 in HaCaT cells, activating TRPV1 to induce intracellular Ca2+ influx (P < 0.05). These findings suggested that the initial application of EUG would cause a brief stimulation of TRPV1 receptors and upregulation of TRPV1 expression. Upon continued exposure, EUG would act as a TRPV1 agonist, increasing intracellular Ca2+ levels that might be associated with desensitization of pain sensations.
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Affiliation(s)
- Haoting Ye
- Department of Pharmacy, Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Qiuxiao Lin
- Department of Pharmacy, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Qinghua Mei
- Department of Pharmacy, Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Qiuqiong Liu
- Department of Pharmacy, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Siwei Cao
- Department of Pharmacy, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
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Soltani Rad MN, Behrouz S, Shahbazkhani K, Behrouz M, Zarenezhad E, Ghanbariasad A. Design, synthesis, anticancer and in silico assessment of 8-piperazinyl caffeinyl-triazolylmethyl hybrid conjugates. RSC Adv 2023; 13:24656-24673. [PMID: 37601597 PMCID: PMC10436028 DOI: 10.1039/d3ra04817a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 08/15/2023] [Indexed: 08/22/2023] Open
Abstract
In this paper, we have assessed the design, synthesis, characterization, anticancer properties, toxicity, and in silico study of 8-piperazinyl caffeinyl-triazolylmethyl derivatives as new caffeine hybrid conjugates. These compounds consist of four moieties comprising 8-caffeinyl, piperazinyl, 1,2,3-triazolyl, and alkyl substituents. The synthesis of these compounds was started by bromination of caffeine to attain 8-BC, SNAr reaction with piperazine to acquire 8-PC, N-propargylation of 8-PC and finally click Huisgen cycloaddition with diverse alkyl azides. These compounds were in vitro tested against two significant cancer cell lines comprising breast cancer MCF-7 (ATCC HTB-22) and melanoma cancer A-375 (ATCC CRL-1619) cell lines and activities compared with methotrexate (MTX) as a reference drug. Anticancer assessments indicated 12j (IC50 = 323 ± 2.6) and 12k (IC50 = 175 ± 3.2) were the most potent compounds against A-375 and MCF-7 cell growth, respectively and their activities were even stronger than MTX (IC50 = 418 ± 2 for A375 and IC50 = 343 ± 3.6 for MCF-7). Toxicities were determined by screening compounds against normal cell line HEK-293 (ATCC CRL-11268) and indicated that except 12i (IC50 = 371 ± 2.3), 12j (IC50 = 418 ± 2.4), and MTX (IC50 = 199 ± 2.4), all compounds are non-toxic. Docking was conducted for 12j and 12k and determined the strong binding affinities to B-RAF kinase and hDHFR enzymes, respectively. In silico pharmacokinetic and physiochemical profiles of tested compounds were investigated which indicated that most compounds obeyed Lipinski's rule of five (RO5). The DFT study on M06-2X/6-311G (d,p) was used to indicate HOMO, LUMO, MEP, and other parameters for a better understanding of 12j and 12k reactivity. Owing to anticancer properties, toxicity, and in silico data, 12j and 12k can be proposed for further research in the future.
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Affiliation(s)
- Mohammad Navid Soltani Rad
- Department of Chemistry, Shiraz University of Technology Shiraz 71555-313 Iran +98 71 3735 4520 +98 71 3735 4500
- Medicinal Chemistry Research Laboratory, Novel Technology for Health Research Center, Shiraz University of Technology Shiraz 71555-313 Iran
| | - Somayeh Behrouz
- Department of Chemistry, Shiraz University of Technology Shiraz 71555-313 Iran +98 71 3735 4520 +98 71 3735 4500
- Medicinal Chemistry Research Laboratory, Novel Technology for Health Research Center, Shiraz University of Technology Shiraz 71555-313 Iran
| | - Kiana Shahbazkhani
- Department of Chemistry, Shiraz University of Technology Shiraz 71555-313 Iran +98 71 3735 4520 +98 71 3735 4500
| | - Marzieh Behrouz
- Department of Chemistry, Shiraz University of Technology Shiraz 71555-313 Iran +98 71 3735 4520 +98 71 3735 4500
| | - Elham Zarenezhad
- Non-communicable Diseases Research Center, Fasa University of Medical Sciences Fasa Iran
| | - Ali Ghanbariasad
- Department of Medical Biotechnology, School of Medicine, Fasa University of Medical Sciences Fasa Iran
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Oladejo DO, duselu GO, Dokunmu TM, Isewon I, Oyelade J, Okafor E, Iweala EEJ, Adebiyi E. In silico Structure Prediction, Molecular Docking, and Dynamic Simulation of Plasmodium falciparum AP2-I Transcription Factor. Bioinform Biol Insights 2023; 17:11779322221149616. [PMID: 36704725 PMCID: PMC9871981 DOI: 10.1177/11779322221149616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 12/18/2022] [Indexed: 01/22/2023] Open
Abstract
Plasmodium falciparum Apicomplexan Apetala 2 Invasion (PfAP2-I) transcription factor (TF) is a protein that regulates the expression of a subset of gene families involved in P. falciparum red blood cell (RBC) invasion. Inhibiting PfAP2-I TF with small molecules represents a potential new antimalarial therapeutic target to combat drug resistance, which this study aims to achieve. The 3D model structure of PfAP2-I was predicted ab initio using ROBETTA prediction tool and was validated using Save server 6.0 and MolProbity. Computed Atlas of Surface Topography of proteins (CASTp) 3.0 was used to predict the active sites of the PfAP2-I modeled structure. Pharmacophore modeling of the control ligand and PfAP2-I modeled structure was carried out using the Pharmit server to obtain several compounds used for molecular docking analysis. Molecular docking and postdocking studies were conducted using AutoDock vina and Discovery studio. The designed ligands' toxicity predictions and in silico drug-likeness were performed using the SwissADME predictor and OSIRIS Property Explorer. The modeled protein structure from the ROBETTA showed a validation result of 96.827 for ERRAT, 90.2% of the amino acid residues in the most favored region for the Ramachandran plot, and MolProbity score of 1.30 in the 98th percentile. Five (5) best hit compounds from molecular docking analysis were selected based on their binding affinity (between -8.9 and -11.7 Kcal/mol) to the active site of PfAP2-I and were considered for postdocking studies. For the absorption, distribution, metabolism, elimination, and toxicity (ADMET) properties, compound MCULE-7146940834 had the highest drug score (0.63) and drug-likeness (6.76). MCULE-7146940834 maintained a stable conformation within the flexible protein's active site during simulation. The good, estimated binding energies, drug-likeness, drug score, and molecular dynamics simulation interaction observed for MCULE-7146940834 against PfAP2-I show that MCULE-7146940834 can be considered a lead candidate for PfAP2-I inhibition. Experimental validations should be carried out to ascertain the efficacy of these predicted best hit compounds.
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Affiliation(s)
- David O Oladejo
- Covenant Applied Informatics and
Communication Africa Centre of Excellence (CApIC-ACE), Covenant University, Ota,
Nigeria
- Department of Biochemistry, College of
Science and Technology, Covenant University, Ota, Nigeria
| | - Gbolahan O duselu
- Department of Chemistry, College of
Science and Technology, Covenant University, Ota, Nigeria
| | - Titilope M Dokunmu
- Covenant Applied Informatics and
Communication Africa Centre of Excellence (CApIC-ACE), Covenant University, Ota,
Nigeria
- Department of Biochemistry, College of
Science and Technology, Covenant University, Ota, Nigeria
| | - Itunuoluwa Isewon
- Covenant Applied Informatics and
Communication Africa Centre of Excellence (CApIC-ACE), Covenant University, Ota,
Nigeria
- Department of Computer and Information
Science, College of Science and Technology, Covenant University, Ota, Nigeria
| | - Jelili Oyelade
- Covenant Applied Informatics and
Communication Africa Centre of Excellence (CApIC-ACE), Covenant University, Ota,
Nigeria
- Department of Computer and Information
Science, College of Science and Technology, Covenant University, Ota, Nigeria
| | - Esther Okafor
- Department of Biochemistry, College of
Science and Technology, Covenant University, Ota, Nigeria
| | - Emeka EJ Iweala
- Covenant Applied Informatics and
Communication Africa Centre of Excellence (CApIC-ACE), Covenant University, Ota,
Nigeria
- Department of Biochemistry, College of
Science and Technology, Covenant University, Ota, Nigeria
| | - Ezekiel Adebiyi
- Covenant Applied Informatics and
Communication Africa Centre of Excellence (CApIC-ACE), Covenant University, Ota,
Nigeria
- Department of Computer and Information
Science, College of Science and Technology, Covenant University, Ota, Nigeria
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Oduselu GO, Afolabi R, Ademuwagun I, Vaughan A, Adebiyi E. Structure-based pharmacophore modeling, virtual screening, and molecular dynamics simulation studies for identification of Plasmodium falciparum 5-aminolevulinate synthase inhibitors. Front Med (Lausanne) 2023; 9:1022429. [PMID: 36714108 PMCID: PMC9877529 DOI: 10.3389/fmed.2022.1022429] [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: 08/18/2022] [Accepted: 12/23/2022] [Indexed: 01/13/2023] Open
Abstract
Plasmodium falciparum (Pf) 5-aminolevulinic acid synthase (5-ALAS) is an essential enzyme with high selectivity during liver stage development, signifying its potential as a prophylactic antimalarial drug target. The aim of this study was to identify important potential lead compounds which can serve as inhibitors of Pf 5-ALAS using pharmacophore modeling, virtual screening, qualitative structural assessment, in silico ADMET (Absorption, Distribution, Metabolism, Excretion and Toxicity) evaluation and molecular dynamics simulation. The best model of the tertiary structure of Pf 5-ALAS was obtained using MolProbity, while the following databases were explored for the pharmacophore-based virtual screening: CHEMBL, ChemDiv, ChemSpace, MCULE, MCULE-ULTIMATE, MolPort, NCI Open Chemical Repository, LabNetwork and ZINC databases. 2,621 compounds were screened against the modeled Pf 5-ALAS using AutoDock vina. The post-screening analysis was carried out using Discovery Studio while molecular dynamics simulation was performed on the best hits using NAMD-VMD and Galaxy Europe platform. Compound CSMS00081585868 was observed as the best hit with a binding affinity of -9.9 kcal/mol and predicted Ki of 52.10 nM, engaging in seven hydrogen bonds with the target's active site amino acid residues. The in silico ADMET prediction showed that all ten best hits possessed relatively good pharmacokinetic properties. The qualitative structural assessment of the best hit, CSMS00081585868, revealed that the presence of two pyridine scaffolds bearing hydroxy and fluorine groups linked by a pyrrolidine scaffold contributed significantly to its ability to have a strong binding affinity with the receptor. The best hit also showed stability in the active site of Pf 5-ALAS as confirmed from the RMSD obtained during the MD simulation.
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Affiliation(s)
- Gbolahan O. Oduselu
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State, Nigeria
- Department of Chemistry, Covenant University, Ota, Ogun State, Nigeria
| | - Rufus Afolabi
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State, Nigeria
- Department of Biochemistry, Covenant University, Ota, Ogun State, Nigeria
| | - Ibitayo Ademuwagun
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State, Nigeria
- Department of Biochemistry, Covenant University, Ota, Ogun State, Nigeria
| | - Ashley Vaughan
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA, United States
| | - Ezekiel Adebiyi
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Ogun State, Nigeria
- Department of Computer and Information Science, Covenant University, Ota, Ogun State, Nigeria
- Covenant Applied Informatics and Communications ACE (CApIC-ACE), Covenant University, Ota, Ogun State, Nigeria
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
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Degfie T, Ombito JO, Demissie TB, Eswaramoorthy R, Dekebo A, Endale M. Antibacterial and Antioxidant Activities, in silico Molecular Docking, ADMET and DFT Analysis of Compounds from Roots of Cyphostemma cyphopetalum. Adv Appl Bioinform Chem 2022; 15:79-97. [PMID: 36330228 PMCID: PMC9624657 DOI: 10.2147/aabc.s377336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 09/28/2022] [Indexed: 11/06/2022] Open
Abstract
Background Cyphostemma cyphopetalum is a medicinal plant traditionally used to treat various ailments. Limited studies on C. cyphopetalum inspired us to investigate the chemical nature and therapeutic potential of the plant. Methods Silica gel column chromatographic separation was used for isolation. 1D and 2D NMR spectroscopic analysis and literature data were used for structural elucidation. Agar well diffusion assay was used for evaluation of antibacterial activity against E. coli, P. aeruginosa, and S. aureus. DPPH assay was used to evaluate radical scavenging activities. Molecular docking was done by AutoDock Vina 4.2 open-source program. DFT calculations were performed using the Gaussian 16 program package. Results Dichloromethane/methanol (1:1) roots extract afforded a new hydroxyl-spongiane diterpenoid lactone derivative, 3-hydroxyisoagatholactone (1), along with β-sitosterol (2) and ε-viniferin (3) whereas methanol extract afforded trans-resveratrol (4), gnetin H (5), tricuspidatol A (6), ε-viniferin-diol (7) and parthenostilbenin B (8). At 50 μg/mL, compound 3 recorded the highest inhibition against E. coli (8.55 ± 0.45 mm) and S. aureus (9.30 ±1.39 mm). Against P. aeruginosa, compound 5 consistently outperformed chloramphenicol (11.76 ± 0.77 mm, at 30 g/mL). Maximum binding affinity were observed by compound 3 against DNA gyrase B (-7.6 kcal/mol) where as compound 5 displayed maximum binding against PqsA (-8.8 kcal/mol) and S. aureus PK (-5.8 kcal/mol). Compounds 1, 3 and 4 satisfy Lipinski’s rule of five. Trans-resveratrol (4) demonstrated strong DPPH scavenging activity at 12.5 g/mL, with IC50 values of 0.052 µg/mL, compared to ascorbic acid (IC50 value of 0.0012 µg/mL). Conclusion In this work, eight compounds were identified from the roots extracts of C. cyphopetalum including a new hydroxyl-spongiane diterpenoid lactone, 3-hydroxyisoagatholactone (1). Compounds 3 and 5 exhibited good antibacterial activity and binding affinities. The docking result is in agreement with the invitro antibacterial study. Overall, the study result suggests that the isolated compounds have the potential to be used as therapeutic agents, which supports the traditional uses of C. cyphpetalum roots.
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Affiliation(s)
- Teshome Degfie
- Department of Applied Chemistry, School of Applied Natural Science, Adama Science and Technology University, Adama, Ethiopia
| | - Japheth O Ombito
- Department of Chemistry, University of Botswana, Gaborone, Botswana
| | - Taye B Demissie
- Department of Chemistry, University of Botswana, Gaborone, Botswana
| | - Rajalakshmanan Eswaramoorthy
- Department of Biomaterials, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India
| | - Aman Dekebo
- Department of Applied Chemistry, School of Applied Natural Science, Adama Science and Technology University, Adama, Ethiopia,Institute of Pharmaceutical Sciences, Adama Science and Technology University, Adama, Ethiopia
| | - Milkyas Endale
- Department of Applied Chemistry, School of Applied Natural Science, Adama Science and Technology University, Adama, Ethiopia,Correspondence: Milkyas Endale; Teshome Degfie, Department of Applied Chemistry, School of Applied Natural Science, Adama Science and Technology University, P.O. Box 1888, Adama, Ethiopia, Email ;
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Bhat BA, Mir WR, Sheikh BA, Alkanani M, Mir MA. Metabolite fingerprinting of phytoconstituents from Fritillaria cirrhosa D. Don and molecular docking analysis of bioactive peonidin with microbial drug target proteins. Sci Rep 2022; 12:7296. [PMID: 35508512 PMCID: PMC9068770 DOI: 10.1038/s41598-022-10796-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 04/07/2022] [Indexed: 12/15/2022] Open
Abstract
Fritillaria cirrhosa D. Don (Liliaceae), a valuable and critically endangered medicinal herb of northwest India, including Jammu and Kashmir, grows in temperate to alpine regions of the Himalaya. It is known as the traditional herb for cardiovascular diseases, respiratory diseases, and metabolic disorders. The plant bulbs are precious and are used to cure many other health complications. The current study analysed the phytoconstituents by liquid chromatography-mass spectrometry (LC–MS) of different crude extracts (methanolic, petroleum ether, and ethyl acetate) of F. cirrhosa. The LC–MS analysis from the bulbs of F. cirrhosa yielded 88 bioactive compounds, with the vast majority having therapeutic applications. Further, determination of minimum inhibitory concentrations (MICs) by broth microdilution method of F. cirrhosa against tested bacterial and fungal pathogens showed remarkable results with MICs ranging between 6.25–200 µg/mL and 50–400 µg/mL, respectively. Subsequently, these 88 identified phytocompounds were tested for their bioactivity through ADMET prediction by SwissADME and in silico molecular docking studies. Results revealed that Peonidin might have maximum antibacterial and antifungal activity against various microbial protein drug targets among the phytochemical compounds identified. Furthermore, the highest binding affinity complex was subjected to molecular dynamic simulation (MDS) analysis using Desmond Schrodinger v3.8. The root-mean-square deviation (RMSD) graphs obtained through the molecular dynamic simulations indicated the true bonding interactions, further validated using the root-mean-square fluctuation (RMSF) graphs which provided a better understanding of the amino acids present in the proteins responsible for the molecular motions and fluctuations. To our best knowledge, this is the first description of the phytochemical constituents of the bulbs of F.cirrhosa analyzed through LC–MS, which show pharmacological significance. The in silico molecular docking and molecular dynamics study of peonidin was also performed to confirm its broad-spectrum activities based on the binding interactions with the antibacterial and antifungal target proteins. The present study results will create a way for the invention of herbal medicines for several ailments by using F. cirrhosa plants, which may lead to the development of novel drugs.
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Affiliation(s)
- Basharat Ahmad Bhat
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar, 190006, India
| | - Wajahat Rashid Mir
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar, 190006, India
| | - Bashir Ahmad Sheikh
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar, 190006, India
| | - Mustafa Alkanani
- College of Applied Medical Sciences, Almaarefa University, Riyadh, 11597, Kingdom of Saudi Arabia
| | - Manzoor Ahmad Mir
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar, 190006, India.
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Floris B, Galloni P, Conte V, Sabuzi F. Tailored Functionalization of Natural Phenols to Improve Biological Activity. Biomolecules 2021; 11:1325. [PMID: 34572538 PMCID: PMC8467377 DOI: 10.3390/biom11091325] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 08/31/2021] [Accepted: 09/02/2021] [Indexed: 12/11/2022] Open
Abstract
Phenols are widespread in nature, being the major components of several plants and essential oils. Natural phenols' anti-microbial, anti-bacterial, anti-oxidant, pharmacological and nutritional properties are, nowadays, well established. Hence, given their peculiar biological role, numerous studies are currently ongoing to overcome their limitations, as well as to enhance their activity. In this review, the functionalization of selected natural phenols is critically examined, mainly highlighting their improved bioactivity after the proper chemical transformations. In particular, functionalization of the most abundant naturally occurring monophenols, diphenols, lipidic phenols, phenolic acids, polyphenols and curcumin derivatives is explored.
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Affiliation(s)
- Barbara Floris
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Via della Ricerca Scientifica, snc, 00133 Roma, Italy
| | - Pierluca Galloni
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Via della Ricerca Scientifica, snc, 00133 Roma, Italy
| | - Valeria Conte
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Via della Ricerca Scientifica, snc, 00133 Roma, Italy
| | - Federica Sabuzi
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Via della Ricerca Scientifica, snc, 00133 Roma, Italy
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Anza M, Endale M, Cardona L, Cortes D, Eswaramoorthy R, Zueco J, Rico H, Trelis M, Abarca B. Antimicrobial Activity, in silico Molecular Docking, ADMET and DFT Analysis of Secondary Metabolites from Roots of Three Ethiopian Medicinal Plants. Adv Appl Bioinform Chem 2021; 14:117-132. [PMID: 34447254 PMCID: PMC8384431 DOI: 10.2147/aabc.s323657] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 08/10/2021] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Uvaria scheffleri (Annonaceae), Clematis burgensis (Ranunculaceae), and Euphorbia schimperiana (Euphorbiaceae) are medicinal plants traditionally used to treat cough, tuberculosis, asthma, sore throat and skin infections. METHODS Silica gel column chromatographic separation was used to isolate compounds. Crude extract and isolated compounds were evaluated for antimicrobial activity against Staphylococcus aureus, Escherichia coli, and Candida albicans via the broth dilution method. Docking studies were performed with E. coli DNA-Gyrase B and human DNA topoisomerase IIα by using AutoDock Vina. ADMET were predicted by SwissADME, PreADMET, and OSIRIS Property predictions. The optimized structures and molecular electrostatic potential surface of the isolated compounds were predicted by DFT analysis using B3LYP/6-31G basis levels. RESULTS Silica gel column chromatographic separation afforded five compounds 1-5 of which N-methyl-2,3-bis(2-hydroxybenzyl)-1Н-indol (1) is reported herein for the first time, along with known C-benzylated dihydrochalcone uvaretin (2), bis(2-ethylheptyl) phthalate (3), lupeol (4) and suberosin derivative (5). Dichloromethane roots extract of U. scheffleri showed potent antibacterial activity against S. aureus (MIC = 6.25 µg/mL) compared to gentamicin (MIC=5 µg/mL). In silico, molecular docking analysis of compounds (1and 3-5) showed strong interaction with E. coli DNA gyrase B with a binding energy value ranging from -6.9 to -6.0 kcal/mol compared to ciprofloxacin -7.2 kcal/mol, whereas analysis against human topoisomerase IIα showed binding energy value ranging from -5.9 to -5.3 kcal/mol compared to vosaroxin (-6.2 kcal/mol). CONCLUSION The results obtained suggest that N-methyl-2,3-bis(2-hydroxybenzyl)-1Н-indol (1) and coumarin (5) are potential topoisomerase II α inhibitors and might be used as anticancer agents. The ADMET studies showed the highest drug-likeness properties for studied compounds other than bis(2-ethylheptyl) phthalate (3). DFT calculations suggested that studied compounds showed the lowest gap energy and were chemically reactive, and isolated compounds may serve as potential drug candidates that corroborate with the traditional uses of studied plants.
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Affiliation(s)
- Mathewos Anza
- Department of Applied Chemistry, School of Applied Natural Science, Adama Science and Technology University, Adama, Ethiopia
| | - Milkyas Endale
- Department of Applied Chemistry, School of Applied Natural Science, Adama Science and Technology University, Adama, Ethiopia
| | - Luz Cardona
- Department of Organic Chemistry, Faculty of Chemistry, University of Valencia, Burjassot, Spain
| | - Diego Cortes
- Department of Pharmacology, Faculty of Pharmacy, University of Valencia, Burjassot, Spain
| | - Rajalakshmanan Eswaramoorthy
- Department of Applied Chemistry, School of Applied Natural Science, Adama Science and Technology University, Adama, Ethiopia
| | - Jesus Zueco
- Department of Microbiology and Ecology, Faculty of Pharmacy, University of Valencia, Burjassot, Spain
| | - Hortensia Rico
- Department of Microbiology and Ecology, Faculty of Pharmacy, University of Valencia, Burjassot, Spain
| | - Maria Trelis
- Parasites and Health Research Group, Department of Pharmacy, Pharmaceutical Technology and Parasitology, Faculty of Pharmacy, University of Valencia, Burjassot, Spain
| | - Belen Abarca
- Department of Organic Chemistry, Faculty of Chemistry, University of Valencia, Burjassot, Spain
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10
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Pasha A, Mondal S, Panigrahi N. Synthesis of Novel Aryl (4-Aryl-1H-Pyrrol-3-yl) (Thiophen-2-yl) Methanone Derivatives: Molecular Modelling, In Silico ADMET, Anti-Inflammatory and Anti-Ulcer Activities. Antiinflamm Antiallergy Agents Med Chem 2020; 20:182-195. [PMID: 33200699 DOI: 10.2174/1871523019999201116191622] [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: 07/10/2020] [Revised: 10/10/2020] [Accepted: 10/18/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Due to the presence of both five-membered heterocyclics like pyrrole and thiophene in one molecule considerable attention was made for their enormous pharmacological activities out of which include anti-inflammatory and anti-ulcer activities. OBJECTIVE Chalcones with toluenesulfonylmethyl isocyanide (TosMIC) undergo synthesis to form some new aryl (4-aryl-1H-pyrrol-3-yl) (thiophen-2-yl) methanone derivatives. Molecular docking of synthesized compounds with protein receptors of anti-inflammatory COX-1(3N8Y), COX-2 (1PXX) along with anti-ulcer H+/K+ATPase enzyme (2XZB) followed with drug-likeness, and in silico ADMET properties. MATERIALS AND METHODS The multicomponent reaction was carried out by the intermediate formation of α, β-unsaturated ketone from carbonyl compounds which on sequential addition undergoes [3+2] cycloaddition reaction in same medium affords aryl (4-aryl-1H-pyrrol-3-yl) (thiophen-2-yl) methanone derivatives by addition of TosMIC in basic medium had resulted in series of compounds PY1 to PY12. All the new synthesized compounds were screened for their in-vitro anti-inflammatory activity by bovine serum albumin method followe with COX assay, and in-vivo by using carrageenan-induced rat paw edema method of the selected compounds PY1, PY5 and PY12 which is also screened for anti-ulcer activity by pylorus ligation method, respectively. Molecular docking was performed using autodock tools, drug-likeness by OSIRIS property explorer and admetSAR properties. RESULTS AND DISCUSSION From the synthesized compounds of aryl (4-aryl-1H-pyrrol-3-yl) (thiophen- 2-yl) methanone derivatives PY5 showed decent in-vitro and in-vivo anti-inflammatory along selectivity index of 6.2 for COX-1 with IC50(μM) value of 9.54 over diclofenac with 8.74 and PY1 showed decent in-vivo anti-ulcer activities along with drug-likeness and in silico ADMET predictions revealed that all the synthesized compounds have minimal toxic effects with good absorption as well as solubility characteristics. The selected compounds may serve as potential lead compounds for developing new anti-inflammatory and anti-ulcer drugs. CONCLUSION From the newly synthesized molecules PY5 was found to be effective for anti-inflammatory and PY1 was found to be effective for anti-ulcer activities further derivitization and designed of modification to achieve more compounds with potent anti-inflammatory and anti-ulcer activities.
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Affiliation(s)
- Arif Pasha
- Department of Pharmaceutical Chemistry, GITAM Institute of Pharmacy, Rushikonda, GITAM (Deemed to be University), Visakhapatnam, Andhra Pradesh, 530045, India
| | - Sumanta Mondal
- Department of Pharmaceutical Chemistry, GITAM Institute of Pharmacy, Rushikonda, GITAM (Deemed to be University), Visakhapatnam, Andhra Pradesh, 530045, India
| | - Naresh Panigrahi
- Department of Pharmaceutical Chemistry, GITAM Institute of Pharmacy, Rushikonda, GITAM (Deemed to be University), Visakhapatnam, Andhra Pradesh, 530045, India
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Synthesis of hydroxyethyl methyl morpholinium azide (HEM Morph)N3: A highly efficient new task specific azide-based ionic liquid and its dual application as an azide source and media for synthesis of some novel aromatic O-oxime ethers-1,2,3-triazole conjugates as a potential antihistaminic agents. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2019.112245] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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12
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Oduselu GO, Ajani OO, Ajamma YU, Brors B, Adebiyi E. Homology Modelling and Molecular Docking Studies of Selected Substituted Benzo[ d]imidazol-1-yl)methyl)benzimidamide Scaffolds on Plasmodium falciparum Adenylosuccinate Lyase Receptor. Bioinform Biol Insights 2019; 13:1177932219865533. [PMID: 31391779 PMCID: PMC6669854 DOI: 10.1177/1177932219865533] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 06/29/2019] [Indexed: 12/22/2022] Open
Abstract
Plasmodium falciparum adenylosuccinate lyase (PfADSL) is an important enzyme in purine metabolism. Although several benzimidazole derivatives have been commercially developed into drugs, the template design as inhibitor against PfADSL has not been fully explored. This study aims to model the 3-dimensional (3D) structure of PfADSL, design and predict in silico absorption, distribution, metabolism, excretion and toxicity (ADMET) of 8 substituted benzo[d]imidazol-1-yl)methyl)benzimidamide compounds as well as predict the potential interaction modes and binding affinities of the designed ligands with the modelled PfADSL. PfADSL 3D structure was modelled using SWISS-MODEL, whereas the compounds were designed using ChemDraw Professional. ADMET predictions were done using OSIRIS Property Explorer and Swiss ADME, whereas molecular docking was done with AutoDock Tools. All designed compounds exhibited good in silico ADMET properties, hence can be considered safe for drug development. Binding energies ranged from -6.85 to -8.75 kcal/mol. Thus, they could be further synthesised and developed into active commercial antimalarial drugs.
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Affiliation(s)
- Gbolahan O Oduselu
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Nigeria
- Department of Chemistry, College of Science and Technology, Covenant University, Ota, Nigeria
| | - Olayinka O Ajani
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Nigeria
- Department of Chemistry, College of Science and Technology, Covenant University, Ota, Nigeria
| | - Yvonne U Ajamma
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Nigeria
| | - Benedikt Brors
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ezekiel Adebiyi
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Nigeria
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Computer and Information Science, Covenant University, Ota, Nigeria
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