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Nguyen HD, Hoang TL, Vu GH. An in silico investigation of the toxicological effects and biological activities of 3-phenoxybenzoic acid and its metabolite products. Xenobiotica 2024; 54:322-341. [PMID: 38833509 DOI: 10.1080/00498254.2024.2361457] [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: 04/19/2024] [Revised: 05/12/2024] [Accepted: 05/26/2024] [Indexed: 06/06/2024]
Abstract
We aimed to elucidate the toxic effects and biological activities of 3-phenoxybenzoic acid (3PBA) and its metabolite products. Numerous in silico methods were used to identify the toxic effects and biological activities of 3PBA, including PASS online, molecular docking, ADMETlab 2.0, ADMESWISS, MetaTox, and molecular dynamic simulation. Ten metabolite products were identified via Phase II reactions (O-glucuronidation, O-sulfation, and methylation). All of the investigated compounds were followed by Lipinski's rule, indicating that they were stimulants or inducers of hazardous processes. Because of their high gastrointestinal absorption and ability to reach the blood-brain barrier, the studied compounds' physicochemical and pharmacokinetic properties matched existing evidence of harmful effects, including haematemesis, reproductive dysfunction, allergic dermatitis, toxic respiration, and neurotoxicity. The studied compounds have been linked to the apoptotic pathway, the reproductivity system, neuroendocrine disruptors, phospholipid-translocating ATPase inhibitors, and JAK2 expression. An O-glucuronidation metabolite product demonstrated higher binding affinity and interaction with CYP2C9, CYP3A4, caspase 3, and caspase 8 than 3PBA and other metabolite products, whereas metabolite products from methylation were predominant and more toxic. Our in silico findings partly meet the 3Rs principle by minimizing animal testing before more study is needed to identify the detrimental effects of 3PBA on other organs (liver, kidneys). Future research directions may involve experimental validation of in silico predictions, elucidation of molecular mechanisms, and exploration of therapeutic interventions. These findings contribute to our understanding of the toxicological profile of 3PBA and its metabolites, which has implications for risk assessment and regulatory decisions.
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Affiliation(s)
- Hai Duc Nguyen
- Division of Microbiology, Tulane National Private Research Center, Tulane University, Covington, LA, USA
| | - Thuy Linh Hoang
- College of Pharmacy, California Northstate University College of Pharmacy, CA, USA
| | - Giang Huong Vu
- Department of Public Heath, Hong Bang Health Center, Hai Phong, Vietnam
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Tayyeb JZ, Mondal S, Anisur Rahman M, Kumar S, Bayıl I, Akash S, Hossain MS, Alqahtani T, Zaki MEA, Oliveira JIN. Identification of Helicobacter pylori-carcinogenic TNF-alpha-inducing protein inhibitors via daidzein derivatives through computational approaches. J Cell Mol Med 2024; 28:e18358. [PMID: 38693868 PMCID: PMC11063725 DOI: 10.1111/jcmm.18358] [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: 12/30/2023] [Revised: 03/10/2024] [Accepted: 03/18/2024] [Indexed: 05/03/2024] Open
Abstract
Gastric cancer is considered a class 1 carcinogen that is closely linked to infection with Helicobacter pylori (H. pylori), which affects over 1 million people each year. However, the major challenge to fight against H. pylori and its associated gastric cancer due to drug resistance. This research gap had led our research team to investigate a potential drug candidate targeting the Helicobacter pylori-carcinogenic TNF-alpha-inducing protein. In this study, a total of 45 daidzein derivatives were investigated and the best 10 molecules were comprehensively investigated using in silico approaches for drug development, namely pass prediction, quantum calculations, molecular docking, molecular dynamics simulations, Lipinski rule evaluation, and prediction of pharmacokinetics. The molecular docking study was performed to evaluate the binding affinity between the target protein and the ligands. In addition, the stability of ligand-protein complexes was investigated by molecular dynamics simulations. Various parameters were analysed, including root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF), radius of gyration (Rg), hydrogen bond analysis, principal component analysis (PCA) and dynamic cross-correlation matrix (DCCM). The results has confirmed that the ligand-protein complex CID: 129661094 (07) and 129664277 (08) formed stable interactions with the target protein. It was also found that CID: 129661094 (07) has greater hydrogen bond occupancy and stability, while the ligand-protein complex CID 129664277 (08) has greater conformational flexibility. Principal component analysis revealed that the ligand-protein complex CID: 129661094 (07) is more compact and stable. Hydrogen bond analysis revealed favourable interactions with the reported amino acid residues. Overall, this study suggests that daidzein derivatives in particular show promise as potential inhibitors of H. pylori.
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Affiliation(s)
- Jehad Zuhair Tayyeb
- Department of Clinical Biochemistry, College of MedicineUniversity of JeddahJeddahSaudi Arabia
| | - Shibam Mondal
- Pharmacy Discipline, School of Life SciencesKhulna UniversityKhulnaBangladesh
| | | | - Swapon Kumar
- Department of PharmacyJahangirnagar UniversitySavarBangladesh
| | - Imren Bayıl
- Department of Bioinformatics and Computational BiologyGaziantep UniversityGaziantepTurkey
| | - Shopnil Akash
- Department of PharmacyDaffodil International UniversityDhakaBangladesh
| | | | - Taha Alqahtani
- Department of Pharmacology, College of PharmacyKing Khalid UniversityAbhaSaudi Arabia
| | - Magdi E. A. Zaki
- Department of Chemistry, College of ScienceImam Mohammad Ibn Saud Islamic UniversityRiyadhSaudi Arabia
| | - Jonas Ivan Nobre Oliveira
- Department of Biophysics and Pharmacology, Bioscience CenterFederal University of Rio Grande do NorteNatalBrazil
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Wiraswati HL, Bashari MH, Alfarafisa NM, Ma’ruf IF, Sholikhah EN, Wahyuningsih TD, Satriyo PB, Mustofa M, Satria D, Damayanti E. Pyrazoline B-Paclitaxel or Doxorubicin Combination Drugs Show Synergistic Activity Against Cancer Cells: In silico Study. Adv Appl Bioinform Chem 2024; 17:33-46. [PMID: 38435441 PMCID: PMC10908341 DOI: 10.2147/aabc.s452281] [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: 11/29/2023] [Accepted: 02/10/2024] [Indexed: 03/05/2024] Open
Abstract
Background Multidrug resistance in various cancer types is a major obstacle in cancer treatment. The concept of a single drug molecular target often causes treatment failure due to the complexity of the cellular processes. Therefore, combination chemotherapy, in which two or more anticancer drugs are co-administered, can overcome this problem because it potentially have synergistic efficacy besides reducing resistance, and drug doses. Previously, we reported that pyrazoline B had promising anticancer activity in both in silico and in vitro studies. To increase the efficacy of this drug, co-administration with established anticancer drugs such as doxorubicin and paclitaxel is necessary. Materials and Methods In this study, we used an in silico approach to predict the synergistic effect of pyrazoline B with paclitaxel or doxorubicin using various computational frameworks and compared the results with those of an established study on the combination of doxorubicin-cyclophosphamide and paclitaxel-ascorbic acid. Results and Discussion Drug interaction analysis showed the combination was safe with no contraindications or side effects. Furthermore, molecular docking studies revealed that doxorubicin-pyrazoline B and doxorubicin-cyclophosphamide may synergistically inhibit cancer cell proliferation by inhibiting the binding of topoisomerase I to the DNA chain. Moreover, the combination of pyrazoline B-paclitaxel may has synergistic activity to cause apoptosis by inhibiting Bcl2 binding to the Bax fragment or inhibiting cell division by inhibiting α-β tubulin disintegration. Paclitaxel-ascorbic acid had a synergistic effect on the inhibition of α-β tubulin disintegration. Conclusion The results show that this combination is promising for further in vitro and in vivo studies.
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Affiliation(s)
- Hesti Lina Wiraswati
- Department of Biomedical Sciences, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
- Oncology and Stem Cells Working Group, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | - Muhammad Hasan Bashari
- Department of Biomedical Sciences, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
- Oncology and Stem Cells Working Group, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | - Nayla Majeda Alfarafisa
- Department of Biomedical Sciences, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
- Oncology and Stem Cells Working Group, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | - Ilma Fauziah Ma’ruf
- Research Center for Pharmaceutical Ingredients and Traditional Medicine, National Research and Innovation Agency, Bogor, Indonesia
| | - Eti Nurwening Sholikhah
- Department of Pharmacology and Therapy, Faculty of Medicine Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Tutik Dwi Wahyuningsih
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Pamungkas Bagus Satriyo
- Department of Pharmacology and Therapy, Faculty of Medicine Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Mustofa Mustofa
- Department of Pharmacology and Therapy, Faculty of Medicine Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Denny Satria
- Department of Pharmaceutical Biology, Faculty of Pharmacy, Universitas Sumatera Utara, Medan, Indonesia
| | - Ema Damayanti
- Research Center for Food Technology and Processing, National Research and Innovation Agency, Gunungkidul, Indonesia
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Oliveira LPS, Lima LR, Silva LB, Cruz JN, Ramos RS, Lima LS, Cardoso FMN, Silva AV, Rodrigues DP, Rodrigues GS, Proietti-Junior AA, dos Santos GB, Campos JM, Santos CBR. Hierarchical Virtual Screening of Potential New Antibiotics from Polyoxygenated Dibenzofurans against Staphylococcus aureus Strains. Pharmaceuticals (Basel) 2023; 16:1430. [PMID: 37895901 PMCID: PMC10610096 DOI: 10.3390/ph16101430] [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: 08/16/2023] [Revised: 09/25/2023] [Accepted: 10/01/2023] [Indexed: 10/29/2023] Open
Abstract
Staphylococcus aureus is a microorganism with high morbidity and mortality due to antibiotic-resistant strains, making the search for new therapeutic options urgent. In this context, computational drug design can facilitate the drug discovery process, optimizing time and resources. In this work, computational methods involving ligand- and structure-based virtual screening were employed to identify potential antibacterial agents against the S. aureus MRSA and VRSA strains. To achieve this goal, tetrahydroxybenzofuran, a promising antibacterial agent according to in vitro tests described in the literature, was adopted as the pivotal molecule and derivative molecules were considered to generate a pharmacophore model, which was used to perform virtual screening on the Pharmit platform. Through this result, twenty-four molecules were selected from the MolPort® database. Using the Tanimoto Index on the BindingDB web server, it was possible to select eighteen molecules with greater structural similarity in relation to commercial antibiotics (methicillin and oxacillin). Predictions of toxicological and pharmacokinetic properties (ADME/Tox) using the eighteen most similar molecules, showed that only three exhibited desired properties (LB255, LB320 and LB415). In the molecular docking study, the promising molecules LB255, LB320 and LB415 showed significant values in both molecular targets. LB320 presented better binding affinity to MRSA (-8.18 kcal/mol) and VRSA (-8.01 kcal/mol) targets. Through PASS web server, the three molecules, specially LB320, showed potential for antibacterial activity. Synthetic accessibility (SA) analysis performed on AMBIT and SwissADME web servers showed that LB255 and LB415 can be considered difficult to synthesize and LB320 is considered easy. In conclusion, the results suggest that these ligands, particularly LB320, may bind strongly to the studied targets and may have appropriate ADME/Tox properties in experimental studies.
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Affiliation(s)
- Lana P. S. Oliveira
- Graduate Program in Biotechnology and Biodiversity-Network BIONORTE, Federal University of Amapá, Macapá 68903-419, Brazil; (L.P.S.O.); (R.S.R.); (F.M.N.C.); (A.V.S.); (A.A.P.-J.)
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, Brazil; (L.R.L.); (L.B.S.); (J.N.C.)
| | - Lúcio R. Lima
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, Brazil; (L.R.L.); (L.B.S.); (J.N.C.)
- Graduate Program in Network in Pharmaceutical Innovation, Federal University of Amapá, Macapá 68902-280, Brazil
- Graduate Program in Medicinal Chemistry and Molecular Modeling, Health Science Institute, Federal Univesity of Pará, Belém 66075-110, Brazil
| | - Luciane B. Silva
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, Brazil; (L.R.L.); (L.B.S.); (J.N.C.)
- Graduate Program in Medicinal Chemistry and Molecular Modeling, Health Science Institute, Federal Univesity of Pará, Belém 66075-110, Brazil
| | - Jorddy N. Cruz
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, Brazil; (L.R.L.); (L.B.S.); (J.N.C.)
| | - Ryan S. Ramos
- Graduate Program in Biotechnology and Biodiversity-Network BIONORTE, Federal University of Amapá, Macapá 68903-419, Brazil; (L.P.S.O.); (R.S.R.); (F.M.N.C.); (A.V.S.); (A.A.P.-J.)
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, Brazil; (L.R.L.); (L.B.S.); (J.N.C.)
| | - Luciana S. Lima
- Special Laboratory of Applied Microbiology, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, Brazil;
| | - Francy M. N. Cardoso
- Graduate Program in Biotechnology and Biodiversity-Network BIONORTE, Federal University of Amapá, Macapá 68903-419, Brazil; (L.P.S.O.); (R.S.R.); (F.M.N.C.); (A.V.S.); (A.A.P.-J.)
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, Brazil; (L.R.L.); (L.B.S.); (J.N.C.)
- Special Laboratory of Applied Microbiology, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, Brazil;
| | - Aderaldo V. Silva
- Graduate Program in Biotechnology and Biodiversity-Network BIONORTE, Federal University of Amapá, Macapá 68903-419, Brazil; (L.P.S.O.); (R.S.R.); (F.M.N.C.); (A.V.S.); (A.A.P.-J.)
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, Brazil; (L.R.L.); (L.B.S.); (J.N.C.)
| | - Dália P. Rodrigues
- Laboratory of Bacterial Enteric Pathogens, Oswaldo Cruz Foundation, FIOCRUZ, Rio de Janeiro 21045-900, Brazil;
| | - Gabriela S. Rodrigues
- Graduate Program in Health Sciences, Institute of Collective Health, Federal University of Western Pará, Santarém 68270-000, Brazil; (G.S.R.); (G.B.d.S.)
| | - Aldo A. Proietti-Junior
- Graduate Program in Biotechnology and Biodiversity-Network BIONORTE, Federal University of Amapá, Macapá 68903-419, Brazil; (L.P.S.O.); (R.S.R.); (F.M.N.C.); (A.V.S.); (A.A.P.-J.)
- Special Laboratory of Applied Microbiology, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, Brazil;
| | - Gabriela B. dos Santos
- Graduate Program in Health Sciences, Institute of Collective Health, Federal University of Western Pará, Santarém 68270-000, Brazil; (G.S.R.); (G.B.d.S.)
| | - Joaquín M. Campos
- Department of Pharmaceutical and Organic Chemistry, Faculty of Pharmacy, Institute of Biosanitary Research ibs. GRANADA, University of Granada, 18071 Granada, Spain;
| | - Cleydson B. R. Santos
- Graduate Program in Biotechnology and Biodiversity-Network BIONORTE, Federal University of Amapá, Macapá 68903-419, Brazil; (L.P.S.O.); (R.S.R.); (F.M.N.C.); (A.V.S.); (A.A.P.-J.)
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, Brazil; (L.R.L.); (L.B.S.); (J.N.C.)
- Graduate Program in Network in Pharmaceutical Innovation, Federal University of Amapá, Macapá 68902-280, Brazil
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Akash S, Bibi S, Biswas P, Mukerjee N, Khan DA, Hasan MN, Sultana NA, Hosen ME, Jardan YAB, Nafidi HA, Bourhia M. Revolutionizing anti-cancer drug discovery against breast cancer and lung cancer by modification of natural genistein: an advanced computational and drug design approach. Front Oncol 2023; 13:1228865. [PMID: 37817764 PMCID: PMC10561655 DOI: 10.3389/fonc.2023.1228865] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 08/15/2023] [Indexed: 10/12/2023] Open
Abstract
Breast and lung cancer are two of the most lethal forms of cancer, responsible for a disproportionately high number of deaths worldwide. Both doctors and cancer patients express alarm about the rising incidence of the disease globally. Although targeted treatment has achieved enormous advancements, it is not without its drawbacks. Numerous medicines and chemotherapeutic drugs have been authorized by the FDA; nevertheless, they can be quite costly and often fall short of completely curing the condition. Therefore, this investigation has been conducted to identify a potential medication against breast and lung cancer through structural modification of genistein. Genistein is the active compound in Glycyrrhiza glabra (licorice), and it exhibits solid anticancer efficiency against various cancers, including breast cancer, lung cancer, and brain cancer. Hence, the design of its analogs with the interchange of five functional groups-COOH, NH2 and OCH3, Benzene, and NH-CH2-CH2-OH-have been employed to enhance affinities compared to primary genistein. Additionally, advanced computational studies such as PASS prediction, molecular docking, ADMET, and molecular dynamics simulation were conducted. Firstly, the PASS prediction spectrum was analyzed, revealing that the designed genistein analogs exhibit improved antineoplastic activity. In the prediction data, breast and lung cancer were selected as primary targets. Subsequently, other computational investigations were gradually conducted. The mentioned compounds have shown acceptable results for in silico ADME, AMES toxicity, and hepatotoxicity estimations, which are fundamental for their oral medication. It is noteworthy that the initial binding affinity was only -8.7 kcal/mol against the breast cancer targeted protein (PDB ID: 3HB5). However, after the modification of the functional group, when calculating the binding affinities, it becomes apparent that the binding affinities increase gradually, reaching a maximum of -11.0 and -10.0 kcal/mol. Similarly, the initial binding affinity was only -8.0 kcal/mol against lung cancer (PDB ID: 2P85), but after the addition of binding affinity, it reached -9.5 kcal/mol. Finally, a molecular dynamics simulation was conducted to study the molecular models over 100 ns and examine the stability of the docked complexes. The results indicate that the selected complexes remain highly stable throughout the 100-ns molecular dynamics simulation runs, displaying strong correlations with the binding of targeted ligands within the active site of the selected protein. It is important to further investigate and proceed to clinical or wet lab experiments to determine the practical value of the proposed compounds.
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Affiliation(s)
- Shopnil Akash
- Faculty of Allied Health Science, Department of Pharmacy, Daffodil International University, Dhaka, Bangladesh
| | - Shabana Bibi
- Department of Biosciences, Shifa Tameer-e-Millat University, Islamabad, Pakistan
| | - Partha Biswas
- Laboratory of Pharmaceutical Biotechnology and Bioinformatics, Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Nobendu Mukerjee
- Department of Microbiology, West Bengal State University, Kolkata, India
| | - Dhrubo Ahmed Khan
- Laboratory of Pharmaceutical Biotechnology and Bioinformatics, Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Md. Nazmul Hasan
- Laboratory of Pharmaceutical Biotechnology and Bioinformatics, Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Nazneen Ahmeda Sultana
- Faculty of Allied Health Science, Department of Pharmacy, Daffodil International University, Dhaka, Bangladesh
| | - Md. Eram Hosen
- Professor Joarder DNA and Chromosome Research Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Yousef A. Bin Jardan
- Department of Food Science, Faculty of Agricultural and Food Sciences, Laval University, Quebec City, QC, Canada
| | - Hiba-Allah Nafidi
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Mohammed Bourhia
- Laboratory of Chemistry and Biochemistry, Faculty of Medicine and Pharmacy, Ibn Zohr University, Laayoune, Morocco
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Broni E, Ashley C, Velazquez M, Khan S, Striegel A, Sakyi PO, Peracha S, Bebla K, Sodhi M, Kwofie SK, Ademokunwa A, Miller WA. In Silico Discovery of Potential Inhibitors Targeting the RNA Binding Loop of ADAR2 and 5-HT2CR from Traditional Chinese Natural Compounds. Int J Mol Sci 2023; 24:12612. [PMID: 37628792 PMCID: PMC10454645 DOI: 10.3390/ijms241612612] [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: 07/01/2023] [Revised: 08/02/2023] [Accepted: 08/06/2023] [Indexed: 08/27/2023] Open
Abstract
Adenosine deaminase acting on RNA 2 (ADAR2) is an important enzyme involved in RNA editing processes, particularly in the conversion of adenosine to inosine in RNA molecules. Dysregulation of ADAR2 activity has been implicated in various diseases, including neurological disorders (including schizophrenia), inflammatory disorders, viral infections, and cancers. Therefore, targeting ADAR2 with small molecules presents a promising therapeutic strategy for modulating RNA editing and potentially treating associated pathologies. However, there are limited compounds that effectively inhibit ADAR2 reactions. This study therefore employed computational approaches to virtually screen natural compounds from the traditional Chinese medicine (TCM) library. The shortlisted compounds demonstrated a stronger binding affinity to the ADAR2 (<-9.5 kcal/mol) than the known inhibitor, 8-azanebularine (-6.8 kcal/mol). The topmost compounds were also observed to possess high binding affinity towards 5-HT2CR with binding energies ranging from -7.8 to -12.9 kcal/mol. Further subjecting the top ADAR2-ligand complexes to molecular dynamics simulations and molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) calculations revealed that five potential hit compounds comprising ZINC000014637370, ZINC000085593577, ZINC000042890265, ZINC000039183320, and ZINC000101100339 had favorable binding free energies of -174.911, -137.369, -117.236, -67.023, and -64.913 kJ/mol, respectively, with the human ADAR2 protein. Residues Lys350, Cys377, Glu396, Cys451, Arg455, Ser486, Gln488, and Arg510 were also predicted to be crucial in ligand recognition and binding. This finding will provide valuable insights into the molecular interactions between ADAR2 and small molecules, aiding in the design of future ADAR2 inhibitors with potential therapeutic applications. The potential lead compounds were also profiled to have insignificant toxicities. A structural similarity search via DrugBank revealed that ZINC000039183320 and ZINC000014637370 were similar to naringin and naringenin, which are known adenosine deaminase (ADA) inhibitors. These potential novel ADAR2 inhibitors identified herein may be beneficial in treating several neurological disorders, cancers, viral infections, and inflammatory disorders caused by ADAR2 after experimental validation.
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Affiliation(s)
- 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
- Department of Molecular Pharmacology & Neuroscience, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
| | - Sufia Khan
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
- Department of Biology, Loyola University Chicago, Chicago, IL 60660, USA
| | - Andrew Striegel
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
- Department of Chemical and Biochemistry, College of Science, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Patrick O. Sakyi
- Department of Chemistry, School of Physical and Mathematical Sciences, College of Basic and Applied Sciences, University of Ghana, Legon, Accra P.O. Box LG 56, Ghana
- Department of Chemical Sciences, School of Sciences, University of Energy and Natural Resources, Sunyani P.O. Box 214, Ghana
| | - Saqib Peracha
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, 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
| | - Monsheel Sodhi
- Department of Molecular Pharmacology & Neuroscience, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
| | - Samuel K. Kwofie
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic & Applied Sciences, University of Ghana, Legon, Accra P.O. Box 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 P.O. Box LG 54, Ghana
| | - Adesanya Ademokunwa
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
- Department of Cognitive and Behavioral Neuroscience, Loyola University Chicago, Chicago, IL 60660, USA
| | - 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
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Uddin KM, Sakib M, Siraji S, Uddin R, Rahman S, Alodhayb A, Alibrahim KA, Kumer A, Matin MM, Bhuiyan MMH. Synthesis of New Derivatives of Benzylidinemalononitrile and Ethyl 2-Cyano-3-phenylacrylate: In Silico Anticancer Evaluation. ACS OMEGA 2023; 8:25817-25831. [PMID: 37521603 PMCID: PMC10373203 DOI: 10.1021/acsomega.3c01123] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 06/16/2023] [Indexed: 08/01/2023]
Abstract
In this study, microwave-assisted Knoevenagel condensation was used to produce two novel series of derivatives (1-6) from benzylidenemalononitrile and ethyl 2-cyano-3-phenylacrylate. The synthesized compounds were characterized using Fourier transform infrared (FT-IR) and 1H NMR spectroscopies. The pharmacodynamics, toxicity profiles, and biological activities of the compounds were evaluated through an in silico study using prediction of activity spectra for substances (PASS) and Absorption, Distribution, Metabolism, Excretion, and Toxicity (ADMET) studies. According to the PASS prediction results, compounds 1-6 showed greater antineoplastic potency for breast cancer than other types of cancer. Molecular docking was employed to investigate the binding mode and interaction sites of the derivatives (1-6) with three human cancer targets (HER2, EGFR, and human FPPS), and the protein-ligand interactions of these derivatives were compared to those reference standards Tyrphostin 1 (AG9) and Tyrphostin 23 (A23). Compound 3 showed a stronger effect on two cell lines (HER2 and FPPS) than the reference drugs. A 20 ns molecular dynamics (MD) simulation was also conducted to examine the ligand's behavior at the active binding site of the modeled protein, utilizing the lowest docking energy obtained from the molecular docking study. Enthalpies (ΔH), Gibbs free energies (ΔG), entropies (ΔS), and frontier molecular orbital parameters (highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO-LUMO) gap, hardness, and softness) were calculated to confirm the thermodynamic stability of all derivatives. The consistent results obtained from the in silico studies suggest that compound 3 has potential as a new anticancer and antiparasitic drug. Further research is required to validate its efficacy.
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Affiliation(s)
- Kabir M. Uddin
- Department
of Biochemistry and Microbiology, North
South University, Bashundhara, Dhaka 1217, Bangladesh
| | - Mohiuddin Sakib
- Department
of Biochemistry and Microbiology, North
South University, Bashundhara, Dhaka 1217, Bangladesh
| | - Siam Siraji
- Department
of Biochemistry and Microbiology, North
South University, Bashundhara, Dhaka 1217, Bangladesh
| | - Riaz Uddin
- Biorganic
and Medicinal Chemistry Laboratory, Department of Chemistry, University of Chittagong, Chattogram 4331, Bangladesh
| | - Shofiur Rahman
- Biological
and Environmental Sensing Research Unit, King Abdullah Institute for
Nanotechnology, King Saud University, Riyadh 11451, Saudi Arabia
| | - Abdullah Alodhayb
- Biological
and Environmental Sensing Research Unit, King Abdullah Institute for
Nanotechnology, King Saud University, Riyadh 11451, Saudi Arabia
- Research
Chair for Tribology, Surface, and Interface Sciences, Department of
Physics and Astronomy, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Khuloud A. Alibrahim
- Department
of Chemistry, College of Science, Princess
Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Ajoy Kumer
- Department
of Chemistry, European University of Bangladesh, Gabtoli, Dhaka 1216, Bangladesh
| | - M. Mahbubul Matin
- Biorganic
and Medicinal Chemistry Laboratory, Department of Chemistry, University of Chittagong, Chattogram 4331, Bangladesh
| | - Md. Mosharef H. Bhuiyan
- Biorganic
and Medicinal Chemistry Laboratory, Department of Chemistry, University of Chittagong, Chattogram 4331, Bangladesh
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8
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Varbanov M, Philippot S, González-Cardenete MA. Anticoronavirus Evaluation of Antimicrobial Diterpenoids: Application of New Ferruginol Analogues. Viruses 2023; 15:1342. [PMID: 37376641 DOI: 10.3390/v15061342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/02/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
The abietane diterpene (+)-ferruginol (1), like other natural and semisynthetic abietanes, is distinguished for its interesting pharmacological properties such as antimicrobial activity, including antiviral. In this study, selected C18-functionalized semisynthetic abietanes prepared from the commercially available (+)-dehydroabietylamine or methyl dehydroabietate were tested in vitro against human coronavirus 229E (HCoV-229E). As a result, a new ferruginol analogue caused a relevant reduction in virus titer as well as the inhibition of a cytopathic effect. A toxicity prediction based on in silico analysis was also performed as well as an estimation of bioavailability. This work demonstrates the antimicrobial and specifically antiviral activity of two tested compounds, making these molecules interesting for the development of new antivirals.
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Affiliation(s)
- Mihayl Varbanov
- Université de Lorraine, CNRS, L2CM, F-54000 Nancy, France
- Laboratoire de Virologie, CHRU de Nancy Brabois, 54500 Vandoeuvre-lès-Nancy, France
| | | | - Miguel A González-Cardenete
- Instituto de Tecnologia Química (UPV-CSIC), Universitat Politècnica de Valencia-Consejo Superior de Investigaciones Científicas, Avenida de los Naranjos s/n, 46022 Valencia, Spain
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9
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Rodrigues ET, Peretti P, Bezerra RM, Biancardi MF, Sousa FFO, Mendes EP, Dutra JBR, Silveira CCR, Castro CH, Cruz JN, Santos CBR, Santos FCA, Pinheiro MT. Pharmacological Characteristics of the Hydroethanolic Extract of Acmella oleracea (L) R. K. Jansen Flowers: ADME/Tox In Silico and In Vivo Antihypertensive and Chronic Toxicity Evaluation. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2023; 2023:1278720. [PMID: 37159592 PMCID: PMC10163967 DOI: 10.1155/2023/1278720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 03/28/2023] [Accepted: 03/30/2023] [Indexed: 05/11/2023]
Abstract
Acmella oleracea (L.) R. K. Jansen, popularly known as jambu in Northern Brazil, is widely used in folk medicine and local cuisine. Its consumption in different ways reinforces the need for safety assessments. In this study, the major compounds found in the hydroethanolic extract of A. oleracea flowers (EHFAO) were characterized by ultra-performance liquid mass spectrometry (UHPLC-ESI-QTOF-MS/MS). The effects of oral administration of 100/mg/kg of EHFAO extract over 60 days in male spontaneously hypertensive (SHR) and Wistar (WR) rats and the in silico ADME/Tox predictions, lipophilicity, and water solubility were accomplished for the compounds identified. Spilanthol was detected as the foremost major compound at a concentration of 97.7%, followed by 1.53% scopoletin and 0.77% d-limonene. The treatment with EHFAO did not alter the animals´ weight over the studied period. Moderate alterations were observed solely in the hepatic enzymes AST (WR = 97 UI/L and SHR = 150 UI/L ∗ p < 0.05) and ALT (WR = 55 UI/L and SHR = 95 UI/L ∗ p < 0.05), while no relevant histopathological alterations were found. The in-silico study confirmed the in vivo findings, as the identified compounds were considered highly bioactive orally, due to their drug similarity profiles, adequate lipid solubility, bioavailability, and pharmacokinetics. Therefore, the chronic treatment with EHFAO was found safe at the concentration of 100/mg/kg, with no interference in the blood pressure levels neither appreciable toxic effects.
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Affiliation(s)
- Emanuelle T. Rodrigues
- Laboratory of Biotechnology in Natural Products, Faculty of Pharmacy, Department of Biological and Health Sciences, Federal University of Amapá, Macapá, Amapá, Brazil
- Graduate Program in Health Sciences, Department of Biological and Health Sciences, Federal University of Amapá, Macapá, Amapá, Brazil
| | - Paulo Peretti
- Laboratory of Biotechnology in Natural Products, Faculty of Pharmacy, Department of Biological and Health Sciences, Federal University of Amapá, Macapá, Amapá, Brazil
- Graduate Program in Health Sciences, Department of Biological and Health Sciences, Federal University of Amapá, Macapá, Amapá, Brazil
| | - Roberto M. Bezerra
- Graduate Program in Health Sciences, Department of Biological and Health Sciences, Federal University of Amapá, Macapá, Amapá, Brazil
- Laboratory of Atomic Absorption and Bioprospecting, Department of Biological and Health Sciences, Federal University of Amapá, Macapá, Amapá, Brazil
| | - Manoel F. Biancardi
- Department of Histology, Embryology and Cell Biology, Laboratory of Microscopy Applied to Reproduction, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Francisco F. O. Sousa
- Laboratory of Quality Control and Bromatology, Faculty of Pharmacy, Department of Biological and Health Sciences, Federal University of Amapá, Macapá, Amapá, Brazil
| | - Elizabeth P. Mendes
- Department of Physiological Sciences, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - João B. R. Dutra
- Department of Physiological Sciences, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Goiás, Brazil
- Integrated Laboratory of Cardiovascular and Neurological Pathophysiology, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Carla C. R. Silveira
- Department of Physiological Sciences, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Goiás, Brazil
- Integrated Laboratory of Cardiovascular and Neurological Pathophysiology, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Carlos H. Castro
- Department of Physiological Sciences, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Goiás, Brazil
- Integrated Laboratory of Cardiovascular and Neurological Pathophysiology, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Jorddy N. Cruz
- Laboratory of Biotechnology in Natural Products, Faculty of Pharmacy, Department of Biological and Health Sciences, Federal University of Amapá, Macapá, Amapá, Brazil
| | - Cleydson B. R. Santos
- Laboratory of Biotechnology in Natural Products, Faculty of Pharmacy, Department of Biological and Health Sciences, Federal University of Amapá, Macapá, Amapá, Brazil
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá, Amapá, Brazil
| | - Fernanda C. A. Santos
- Laboratory of Atomic Absorption and Bioprospecting, Department of Biological and Health Sciences, Federal University of Amapá, Macapá, Amapá, Brazil
| | - Mayara T. Pinheiro
- Laboratory of Biotechnology in Natural Products, Faculty of Pharmacy, Department of Biological and Health Sciences, Federal University of Amapá, Macapá, Amapá, Brazil
- Graduate Program in Health Sciences, Department of Biological and Health Sciences, Federal University of Amapá, Macapá, Amapá, Brazil
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10
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Tessema FB, Gonfa YH, Asfaw TB, Tadesse MG, Bachheti RK. Antioxidant Activity of Flavonoids and Phenolic Acids from Dodonaea angustifolia Flower: HPLC Profile and PASS Prediction. J CHEM-NY 2023. [DOI: 10.1155/2023/8315711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023] Open
Abstract
Background. Dodonaea angustifolia is a known medicinal plant across East Arica. The flower of D. angustifolia is not well investigated in terms of phytochemistry and biological activities. This study aims to investigate the presence of flavonoids and phenolic acids in the flower of D. angustifolia and its antioxidant activity. Methods. Preliminary phytochemical screening was carried out using the standard protocols. Antioxidant activity evaluation using DPPH assay and total phenol content (TPC) and total flavonoid content (TFC) determinations in the flower extract were compared with the values of the leaf extract. UHPLC-DAD analysis was managed to develop the profile of the flower extract. Prediction of biological activity spectra for substances (PASS) was done using an online server for antioxidant and related activities. Results. Preliminary phytochemical screening and TPC and TFC values confirmed the presence of flavonoids and phenolic acids. From the HPLC analysis of flavonoids, quercetin, myricetin, rutin, and phenolic acids such as chlorogenic acid, gallic acid, and syringic acid were detected and quantified. The biological activity spectrum was predicted for the detected and quantified polyphenols. Conclusions. D. angustifolia flower is a rich source of flavonoids and phenolic acids, which are extractable and can be checked for further biological activity. It was possible to identify and quantify phenolic compounds through HPLC analysis in the methanol extract of D. angustifolia flower. The PASS biological activity prediction results showed that there were stronger antioxidant activities for the identified flavonoids. Future work will emphasize the isolation and characterization of active principles responsible for bioactivity.
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11
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Broni E, Ashley C, Adams J, Manu H, Aikins E, Okom M, Miller WA, Wilson MD, Kwofie SK. Cheminformatics-Based Study Identifies Potential Ebola VP40 Inhibitors. Int J Mol Sci 2023; 24:ijms24076298. [PMID: 37047270 PMCID: PMC10094735 DOI: 10.3390/ijms24076298] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/21/2023] [Accepted: 03/24/2023] [Indexed: 03/30/2023] Open
Abstract
The Ebola virus (EBOV) is still highly infectious and causes severe hemorrhagic fevers in primates. However, there are no regulatorily approved drugs against the Ebola virus disease (EVD). The highly virulent and lethal nature of EVD highlights the need to develop therapeutic agents. Viral protein 40 kDa (VP40), the most abundantly expressed protein during infection, coordinates the assembly, budding, and release of viral particles into the host cell. It also regulates viral transcription and RNA replication. This study sought to identify small molecules that could potentially inhibit the VP40 protein by targeting the N-terminal domain using an in silico approach. The statistical quality of AutoDock Vina’s capacity to discriminate between inhibitors and decoys was determined, and an area under the curve of the receiver operating characteristic (AUC-ROC) curve of 0.791 was obtained. A total of 29,519 natural-product-derived compounds from Chinese and African sources as well as 2738 approved drugs were successfully screened against VP40. Using a threshold of −8 kcal/mol, a total of 7, 11, 163, and 30 compounds from the AfroDb, Northern African Natural Products Database (NANPDB), traditional Chinese medicine (TCM), and approved drugs libraries, respectively, were obtained after molecular docking. A biological activity prediction of the lead compounds suggested their potential antiviral properties. In addition, random-forest- and support-vector-machine-based algorithms predicted the compounds to be anti-Ebola with IC50 values in the micromolar range (less than 25 μM). A total of 42 natural-product-derived compounds were identified as potential EBOV inhibitors with desirable ADMET profiles, comprising 1, 2, and 39 compounds from NANPDB (2-hydroxyseneganolide), AfroDb (ZINC000034518176 and ZINC000095485942), and TCM, respectively. A total of 23 approved drugs, including doramectin, glecaprevir, velpatasvir, ledipasvir, avermectin B1, nafarelin acetate, danoprevir, eltrombopag, lanatoside C, and glycyrrhizin, among others, were also predicted to have potential anti-EBOV activity and can be further explored so that they may be repurposed for EVD treatment. Molecular dynamics simulations coupled with molecular mechanics Poisson–Boltzmann surface area calculations corroborated the stability and good binding affinities of the complexes (−46.97 to −118.9 kJ/mol). The potential lead compounds may have the potential to be developed as anti-EBOV drugs after experimental testing.
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Affiliation(s)
- Emmanuel Broni
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, Legon, Accra LG 77, Ghana
- Department of Parasitology, Noguchi Memorial Institute for Medical Research (NMIMR), College of Health Sciences (CHS), University of Ghana, Legon, Accra LG 581, Ghana
- 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
| | - Joseph Adams
- Department of Parasitology, Noguchi Memorial Institute for Medical Research (NMIMR), College of Health Sciences (CHS), University of Ghana, Legon, Accra LG 581, Ghana
| | - Hammond Manu
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, Legon, Accra LG 77, Ghana
| | - Ebenezer Aikins
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, Legon, Accra LG 77, Ghana
| | - Mary Okom
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, Legon, Accra LG 77, Ghana
| | - Whelton A. Miller
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
- Department of Molecular Pharmacology and Neuroscience, Loyola University Medical Center, Maywood, IL 60153, USA
- Department of Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA
- Correspondence: (W.A.M.III); (S.K.K.); Tel.: +1(708)-2168451 (W.A.M.III); +23-320-3797922 (S.K.K.)
| | - Michael D. Wilson
- Department of Parasitology, Noguchi Memorial Institute for Medical Research (NMIMR), College of Health Sciences (CHS), University of Ghana, Legon, Accra LG 581, Ghana
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
| | - Samuel K. Kwofie
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic and 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
- Correspondence: (W.A.M.III); (S.K.K.); Tel.: +1(708)-2168451 (W.A.M.III); +23-320-3797922 (S.K.K.)
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12
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Moharana M, Pattanayak SK, Khan F. Molecular recognition of bio-active triterpenoids from Swertia chirayita towards hepatitis Delta antigen: a mechanism through docking, dynamics simulation, Gibbs free energy landscape. J Biomol Struct Dyn 2023; 41:14651-14664. [PMID: 36856037 DOI: 10.1080/07391102.2023.2184173] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 02/18/2023] [Indexed: 03/02/2023]
Abstract
Medicinal plants the underpinning of indigenous herbal serve, are the possible source of key compounds for the development of new drugs. Hepatitis D, one of the most widespread infectious diseases associated with global public health issues. Therefore, we aim to screen natural compounds to find out potent inhibitor towards hepatitis delta antigen. Through ADMET investigation, we have screened twenty phytochemicals for this study. Additionally, using molecular docking, these phytochemicals were docked with the HDV protease which signifies the phytochemicals beta-amyrin, chiratenol, episwertenol and swertanone have a significant capability to bind with hepatitis D virus protein. The docking study was further accompanied by analyzes RMSD, RMSF, Rg, SASA, Hbond number, and principal component analysis through 100 ns MD simulations. Based on our principal component analysis, beta-amyrin, chiratenol, episwertenol and swertanone phytochemicals can be a potential drug candidates for inhibition of hepatitis D. The above observation is also supported by our Gibbs free energy landscape study. The potential therapeutic characteristics of the phytochemicals against hepatitis D inhibition offer additional support for the in vitro and in vivo studies in future.
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Affiliation(s)
- Maheswata Moharana
- Department of Chemistry, National Institute of Technology, Raipur, India
| | | | - Fahmida Khan
- Department of Chemistry, National Institute of Technology, Raipur, India
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13
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Galantamine Based Novel Acetylcholinesterase Enzyme Inhibitors: A Molecular Modeling Design Approach. Molecules 2023; 28:molecules28031035. [PMID: 36770702 PMCID: PMC9919016 DOI: 10.3390/molecules28031035] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 12/31/2022] [Accepted: 01/09/2023] [Indexed: 01/22/2023] Open
Abstract
Acetylcholinesterase (AChE) enzymes play an essential role in the development of Alzheimer's disease (AD). Its excessive activity causes several neuronal problems, particularly psychopathies and neuronal cell death. A bioactive pose on the hAChE B site of the human acetylcholinesterase (hAChE) enzyme employed in this investigation, which was obtained from the Protein Data Bank (PDB ID 4EY6), allowed for the prediction of the binding affinity and free binding energy between the protein and the ligand. Virtual screening was performed to obtain structures similar to Galantamine (GNT) with potential hAChE activity. The top 200 hit compounds were prioritized through the use of filters in ZincPharmer, with special features related to the pharmacophore. Critical analyses were carried out, such as hierarchical clustering analysis (HCA), ADME/Tox predictions, molecular docking, molecular simulation studies, synthetic accessibility (SA), lipophilicity, water solubility, and hot spots to confirm the stable binding of the two promising molecules (ZINC16951574-LMQC2, and ZINC08342556-LMQC5). The metabolism prediction, with metabolites M3-2, which is formed by Glutathionation reaction (Phase II), M1-2, and M2-2 formed from the reaction of S-oxidation and Aliphatic hydroxylation (Phase I), were both reactive but with no side effects. Theoretical synthetic routes and prediction of synthetic accessibility for the most promising compounds are also proposed. In conclusion, this study shows that in silico modeling can be used to create new drug candidate inhibitors for hAChE. The compounds ZINC16951574-LMQC2, and ZINC08342556-LMQC5 are particularly promising for oral administration because they have a favorable drug-likeness profile, excellent lipid solubility, high bioavailability, and adequate pharmacokinetics.
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14
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Tullius Scotti M, Herrera-Acevedo C, Barros de Menezes RP, Martin HJ, Muratov EN, Ítalo de Souza Silva Á, Faustino Albuquerque E, Ferreira Calado L, Coy-Barrera E, Scotti L. MolPredictX: Online Biological Activity Predictions by Machine Learning Models. Mol Inform 2022; 41:e2200133. [PMID: 35961924 DOI: 10.1002/minf.202200133] [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: 06/06/2022] [Accepted: 08/12/2022] [Indexed: 01/05/2023]
Abstract
Here we report the development of MolPredictX, an innovate and freely accessible web interface for biological activity predictions of query molecules. MolPredictX utilizes in-house QSAR models to provide 27 qualitative predictions (active or inactive), and quantitative probabilities for bioactivity against parasitic (Trypanosoma and Leishmania), viral (Dengue, Sars-CoV and Hepatitis C), pathogenic yeast (Candida albicans), bacterial (Salmonella enterica and Escherichia coli), and Alzheimer disease enzymes. In this article, we introduce the methodology and usability of this webtool, highlighting its potential role in the development of new drugs against a variety of diseases. MolPredictX is undergoing continuous development and is freely available at https://www.molpredictx.ufpb.br/.
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Affiliation(s)
- Marcus Tullius Scotti
- Programa de Pós-Graduação de Produtos Naturais e Sintéticos Bioativos, Universidade Federal da Paraíba, 58051-900, João Pessoa-PB, Brazil
| | - Chonny Herrera-Acevedo
- Programa de Pós-Graduação de Produtos Naturais e Sintéticos Bioativos, Universidade Federal da Paraíba, 58051-900, João Pessoa-PB, Brazil.,Department of Chemical Engineering, Universidad ECCI, Carrera 19 # 49-20, 111311, Bogotá D.C., Colombia
| | - Renata Priscila Barros de Menezes
- Programa de Pós-Graduação de Produtos Naturais e Sintéticos Bioativos, Universidade Federal da Paraíba, 58051-900, João Pessoa-PB, Brazil
| | - Holli-Joi Martin
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Eugene N Muratov
- Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Ávilla Ítalo de Souza Silva
- Programa de Pós-Graduação de Produtos Naturais e Sintéticos Bioativos, Universidade Federal da Paraíba, 58051-900, João Pessoa-PB, Brazil
| | - Emmanuella Faustino Albuquerque
- Programa de Pós-Graduação de Produtos Naturais e Sintéticos Bioativos, Universidade Federal da Paraíba, 58051-900, João Pessoa-PB, Brazil
| | - Lucas Ferreira Calado
- Programa de Pós-Graduação de Produtos Naturais e Sintéticos Bioativos, Universidade Federal da Paraíba, 58051-900, João Pessoa-PB, Brazil
| | - Ericsson Coy-Barrera
- Bioorganic Chemistry Laboratory, Facultad de Ciencias Básicas y Aplicadas, Universidad Militar Nueva Granada, Cajicá, 250247, Colombia
| | - Luciana Scotti
- Programa de Pós-Graduação de Produtos Naturais e Sintéticos Bioativos, Universidade Federal da Paraíba, 58051-900, João Pessoa-PB, Brazil
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15
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Yadav RP, Chatterjee S, Chatterjee A, Pal DK, Ghosh S, Acharya K, Das M. Identification of novel mycocompounds as inhibitors of PI3K/AKT/mTOR pathway against RCC. J Recept Signal Transduct Res 2022; 42:599-607. [PMID: 36125981 DOI: 10.1080/10799893.2022.2123515] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
PI3K/AKT/mTOR pathway is one of the frequently disrupted signaling pathways in renal cell carcinoma (RCC) that plays a significant role in tumor formation, disease progression and therapeutic resistance. Therefore, novel natural molecules targeting the critical proteins of this pathway will provide the best alternative to existing drugs, which are toxic and develops resistance. Recent studies have recognized the anti-cancer therapeutic potential of mycocompounds. The current study is focused on screening various mycocompounds from Astraeus hygrometricus against key cancer signaling proteins phosphoinositide 3-kinase (PI3K), protein kinase B, PKB (AKT1) and mammalian target of rapamycin (mTOR). We also studied in-silico cancer cells cytotoxicity and ADMET (absorption, distribution, metabolism, excretion and toxicity) profiles to elucidate the molecular mechanism against RCC and also to uncover the pharmacokinetic profile of these compounds. Astrakurkurone and Ergosta-4,6, 8-(14) 22-tetraene-3-one were the two most efficacious compounds with highest interaction scores and bonding. These compounds were both active against RCC4 and VMRC-RCZ cell lines of RCC. The ADME profiles of both were satisfactory based on druglikeness and bioavailability score criteria. Thus, this proposed study identified astrakurkurone and ergosta-4,6, 8-(14) 22-tetraene-3-one as potential anticancer drug candidates, and provides comparative structural insight into their binding to the 3 protein kinases.
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Affiliation(s)
| | | | | | - Dilip Kumar Pal
- Department of Urology, Institute of Post Graduate Medical Education & Research, Kolkata, India
| | - Sudakshina Ghosh
- Department of Zoology, Vidyasagar College for Women, Kolkata, India
| | - Krishnendu Acharya
- Molecular and Applied Mycology and Plant Pathology Laboratory, Centre of Advanced Study, Department of Botany, University of Calcutta, Kolkata, India
| | - Madhusudan Das
- Department of Zoology, University of Calcutta, Kolkata, India
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16
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Investigating the Anticancer Activity of G-Rh1 Using In Silico and In Vitro Studies (A549 Lung Cancer Cells). MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27238311. [PMID: 36500403 PMCID: PMC9890317 DOI: 10.3390/molecules27238311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/11/2022] [Accepted: 11/16/2022] [Indexed: 11/30/2022]
Abstract
Ginsenoside Rh1 (G-Rh1), a possible bioactive substance isolated from the Korean Panax ginseng Meyer, has a wide range of pharmacological effects. In this study, we have investigated the anticancer efficacy of G-Rh1 via in silico and in vitro methodologies. This study mainly focuses on the two metastatic regulators, Rho-associated protein kinase 1 (ROCK1) and RhoA, along with other standard apoptosis regulators. The ROCK1 protein is a member of the active serine/threonine kinase family that is crucial for many biological processes, including cell division, differentiation, and death, as well as many cellular processes and muscle contraction. The abnormal activation of ROCK1 kinase causes several disorders, whereas numerous studies have also shown that RhoA is expressed highly in various cancers, including colon, lung, ovarian, gastric, and liver malignancies. Hence, inhibiting both ROCK1 and RhoA will be promising in preventing metastasis. Therefore, the molecular level interaction of G-Rh1 with the ROCK1 and RhoA active site residues from the preliminary screening clearly shows its inhibitory potential. Molecular dynamics simulation and principal component analysis give essential insights for comprehending the conformational changes that result from G-Rh1 binding to ROCK1 and RhoA. Further, MTT assay was employed to examine the potential cytotoxicity in vitro against human lung cancer cells (A549) and Raw 264.7 Murine macrophage cells. Thus, G-Rh1 showed significant cytotoxicity against human lung adenocarcinoma (A549) at 100 µg/mL. In addition, we observed an elevated level of reactive oxygen species (ROS) generation, perhaps promoting cancer cell toxicity. Additionally, G-Rh1 suppressed the mRNA expression of RhoA, ROCK1, MMP1, and MMP9 in cancer cell. Accordingly, G-Rh1 upregulated the p53, Bax, Caspase 3, caspase 9 while Bcl2 is downregulated intrinsic pathway. The findings from our study propose that the anticancer activity of G-Rh1 may be related to the induction of apoptosis by the RhoA/ROCK1 signaling pathway. As a result, this study evaluated the functional drug-like compound G-Rh1 from Panax ginseng in preventing and treating lung cancer adenocarcinoma via regulating metastasis and apoptosis.
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17
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Dankwa B, Broni E, Enninful KS, Kwofie SK, Wilson MD. Consensus docking and MM-PBSA computations identify putative furin protease inhibitors for developing potential therapeutics against COVID-19. Struct Chem 2022; 33:2221-2241. [PMID: 36118173 PMCID: PMC9470509 DOI: 10.1007/s11224-022-02056-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 09/05/2022] [Indexed: 12/16/2022]
Abstract
The coronavirus disease 2019 (COVID-19) is a pandemic that has severely posed substantial health challenges and claimed millions of lives. Though vaccines have been produced to stem the spread of this disease, the death rate remains high since drugs used for treatment have therapeutic challenges. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes the disease, has a slew of potential therapeutic targets. Among them is the furin protease, which has a cleavage site on the virus’s spike protein. The cleavage site facilitates the entry of the virus into human cells via cell–cell fusion. This critical involvement of furin in the disease pathogenicity has made it a viable therapeutic strategy against the virus. This study employs the consensus docking approach using HYBRID and AutoDock Vina to virtually screen a pre-filtered library of 3942 natural product compounds of African origin against the human furin protease (PDB: 4RYD). Twenty of these compounds were selected as hits after meeting molecular docking cut-off of − 7 kcal.mol−1, pose alignment inspection, and having favorable furin-ligand interactions. An area under the curve (AUC) value of 0.72 was computed from the receiver operator characteristic (ROC) curve, and Boltzmann-enhanced discrimination of the ROC curve (BEDROC) value of 0.65 showed that AutoDock Vina was a reasonable tool for selecting actives for this target. Seven of these hits were proposed as potential leads having had bonding interactions with catalytic triad residues Ser368, His194, and Asp153, and other essential residues in the active site with plausible binding free energies between − 189 and − 95 kJ/mol from the Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) calculations as well as favorable ADME/Tox properties. The molecules were also predicted as antiviral, anti-inflammatory, membrane permeability inhibitors, RNA synthesis inhibitors, cytoprotective, and hepatoprotective with probable activity (Pa) above 0.5 and probable inactivity values below 0.1. Some of them also have anti-influenza activity. Influenza virus has many similarities with SARS-CoV-2 in their mode of entry into human cells as both are facilitated by the furin protease. Pinobanksin 3-(E)-caffeate, one of the potential leads is a propolis compound. Propolis compounds have shown inhibitory effects against ACE2, TMPRSS2, and PAK1 signaling pathways of SARS-CoV-2 in previous studies. Likewise, quercitrin is structurally similar to isoquercetin, which is currently in clinical trials as possible medication for COVID-19.
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Affiliation(s)
- Bismark Dankwa
- Department of Parasitology, Noguchi Memorial Institute for Medical Research (NMIMR), College of Health Sciences (CHS), University of Ghana, Legon, Accra LG 581, Ghana
- Department of Computer Science, School of Physical & Mathematical Science, College of Basic & Applied Sciences, University of Ghana, LG 163 Legon, Accra Ghana
| | - Emmanuel Broni
- Department of Parasitology, Noguchi Memorial Institute for Medical Research (NMIMR), College of Health Sciences (CHS), University of Ghana, Legon, Accra LG 581, Ghana
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic & Applied Sciences, University of Ghana, Legon, Accra LG 77, Ghana
- Department of Medicine, Loyola University Medical Center, Maywood, IL 60153 USA
| | - Kweku S. Enninful
- Department of Parasitology, Noguchi Memorial Institute for Medical Research (NMIMR), College of Health Sciences (CHS), University of Ghana, Legon, Accra LG 581, Ghana
| | - 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
| | - Michael D. Wilson
- Department of Parasitology, Noguchi Memorial Institute for Medical Research (NMIMR), College of Health Sciences (CHS), University of Ghana, Legon, Accra LG 581, Ghana
- Department of Medicine, Loyola University Medical Center, Maywood, IL 60153 USA
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Palladium(II) Complexes of Substituted Salicylaldehydes: Synthesis, Characterization and Investigation of Their Biological Profile. Pharmaceuticals (Basel) 2022; 15:ph15070886. [PMID: 35890184 PMCID: PMC9323974 DOI: 10.3390/ph15070886] [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: 06/22/2022] [Revised: 07/06/2022] [Accepted: 07/14/2022] [Indexed: 02/04/2023] Open
Abstract
Five palladium(II) complexes of substituted salicylaldehydes (X-saloH, X = 4-Et2N (for 1), 3,5-diBr (for 2), 3,5-diCl (for 3), 5-F (for 4) or 4-OMe (for 5)) bearing the general formula [Pd(X-salo)2] were synthesized and structurally characterized. The crystal structure of complex [Pd(4-Et2N-salo)2] was determined by single-crystal X-ray crystallography. The complexes can scavenge 1,1-diphenyl-picrylhydrazyl and 2,2′-azinobis(3-ethylbenzothiazoline-6-sulfonic acid) radicals and reduce H2O2. They are active against two Gram-positive (Staphylococcus aureus and Bacillus subtilis) and two Gram-negative (Escherichia coli and Xanthomonas campestris) bacterial strains. The complexes interact strongly with calf-thymus DNA via intercalation, as deduced by diverse techniques and via the determination of their binding constants. Complexes interact reversibly with bovine and human serum albumin. Complementary insights into their possible mechanisms of bioactivity at the molecular level were provided by molecular docking calculations, exploring in silico their ability to bind to calf-thymus DNA, Escherichia coli and Staphylococcus aureus DNA-gyrase, 5-lipoxygenase, and membrane transport lipid protein 5-lipoxygenase-activating protein, contributing to the understanding of the role complexes 1–5 can play both as antioxidant and antibacterial agents. Furthermore, in silico predictive tools have been employed to study the chemical reactivity, molecular properties and drug-likeness of the complexes, and also the drug-induced changes of gene expression profile (as protein- and mRNA-based prediction results), the sites of metabolism, the substrate/metabolite specificity, the cytotoxicity for cancer and non-cancer cell lines, the acute rat toxicity, the rodent organ-specific carcinogenicity, the anti-target interaction profiles, the environmental ecotoxicity, and finally the activity spectra profile of the compounds.
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Antioxidant Activity and Cytotoxicity of Aromatic Oligosulfides. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27123961. [PMID: 35745083 PMCID: PMC9229798 DOI: 10.3390/molecules27123961] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/16/2022] [Accepted: 06/18/2022] [Indexed: 01/05/2023]
Abstract
Natural or synthetic antioxidants with biomimetic fragments protect the functional and structural integrity of biological molecules at a minimum concentration, and may be used as potential chemotherapeutic agents. This paper is devoted to in silico and in vitro evaluation of the antioxidant and cytotoxic properties of synthetic analogues of natural compounds—aromatic oligosulfides. The antiradical and SOD-protective activity of oligosulfides was demonstrated in the reaction with O2–• generated in enzymatic and non-enzymatic systems. It was found that phenol-containing disulfides significantly reduced the accumulation level of hydroperoxides and secondary carbonyl thiobarbituric acid reactive substances, which are primary products of oleic acid peroxidation. The antioxidant efficiency of bis(3,5-di-tert-butyl-4-hydroxyphenyl) disulfide increased over time due to the synergistic action of the 2,6-di-tert-butylphenol fragment and the disulfide linker. The highest cytotoxicity on the A-549 and HCT-116 cell lines was found for bis(3,4-dimethoxyphenyl) disulfide. Significant induction of apoptosis in HCT-116 cells in the presence of bis(3,4-dimethoxyphenyl) disulfide indicates the prospect of its use as an antitumor agent. The significant and moderate dependences revealed between various types of activities of the studied aromatic oligosulfides can be used in the development of a strategy for the synthesis and study of target-oriented compounds with predictable biological activity.
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Khanal P, Patil VS, Bhandare VV, Dwivedi PS, Shastry C, Patil B, Gurav SS, Harish DR, Roy S. Computational investigation of benzalacetophenone derivatives against SARS-CoV-2 as potential multi-target bioactive compounds. Comput Biol Med 2022; 146:105668. [PMID: 35667894 PMCID: PMC9135652 DOI: 10.1016/j.compbiomed.2022.105668] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 05/22/2022] [Accepted: 05/23/2022] [Indexed: 02/08/2023]
Abstract
Benzalacetophenones, precursors of flavonoids are aromatic ketones and enones and possess the immunostimulant as well as antiviral activities. Thus, benzalacetophenones were screened against the COVID-19 that could be lethal in patients with compromised immunity. We considered ChEBI recorded benzalacetophenone derivative(s) and evaluated their activity against 3C-like protease (3CLpro), papain-like protease (PLpro), and spike protein of SARS-Cov-2 to elucidate their possible role as antiviral agents. The probable targets for each compound were retrieved from DIGEP-Pred at 0.5 pharmacological activity and all the modulated proteins were enriched to identify the probably regulated pathways, biological processes, cellular components, and molecular functions. In addition, molecular docking was performed using AutoDock 4 and the best-identified hits were subjected to all-atom molecular dynamics simulation and binding energy calculations using molecular mechanics Poisson-Boltzmann surface area (MMPBSA). The compound 4-hydroxycordoin showed the highest druglikeness score and regulated nine proteins of which five were down-regulated and four were upregulated. Similarly, enrichment analysis identified the modulation of multiple pathways concerned with the immune system as well as pathways related to infectious and non-infectious diseases. Likewise, 3'-(3-methyl-2-butenyl)-4′-O-β-d-glucopyranosyl-4,2′-dihydroxychalcone with 3CLpro, 4-hydroxycordoin with PLpro and mallotophilippen D with spike protein receptor-binding domain showed highest binding affinity, revealed stable interactions during the simulation, and scored binding free energy of −26.09 kcal/mol, −16.28 kcal/mol, and −39.2 kcal/mol, respectively. Predicted anti-SARS-CoV-2 activities of the benzalacetophenones reflected the requirement of wet lab studies to develop novel antiviral candidates.
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Dwivedi PSR, Patil VS, Khanal P, Bhandare VV, Gurav S, Harish DR, Patil BM, Roy S. System biology-based investigation of Silymarin to trace hepatoprotective effect. Comput Biol Med 2022; 142:105223. [PMID: 35033877 DOI: 10.1016/j.compbiomed.2022.105223] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 01/04/2022] [Accepted: 01/04/2022] [Indexed: 02/08/2023]
Abstract
Silymarin is used as a hepatoprotective agent since ancient times which could be via its potent anti-oxidant effect. However, the mode of silymarin for the hepatoprotective effect has not been established with the targets involved in hepatic cirrhosis. The present study investigated the multiple interactions of the flavonolignans from Silybum marianum with targets involved in hepatic cirrhosis using a series of system biology approaches. Chemo-informative tools and databases i.e. DIGEP-Pred and DisGeNET were used to predict the targets of flavonolignans and proteins involved in liver cirrhosis respectively. Further, STRING was used to enrich the protein-protein interaction for the flavonolignans-modulated targets. Similarly, molecular docking was performed using AutoDock Vina. Additionally, molecular dynamics simulation and MM-PBSA calculations were carried out for the lead-hit complexes by GROMACS. Thirteen flavonolignans were identified from S. marianum, in which silymonin exhibited the highest drug-likeness score i.e. 1.09. Similarly, CTNNB1 was found to be regulated by the 12 different flavonolignans and was majorly expressed within the compound(s)-protein(s)-pathway(s) network. Further, silymonin had the highest binding affinity; binding energy -9.2 kcal/mol with the CTNNB1 and formed very stable hydrogen bond interactions with Arg332, Ser336, Lys371, and Arg475 throughout 100 ns molecular dynamic production run. The binding free energy of CTNNB1-silymonin complex was found to be -15.83 ± 2.71 kcal/mol. The hepatoprotective property of S. marianum may be due to the presence of silymonin and silychristin; this could majorly modulate CTNNB1, HMOX1, and CASP8 in combination with other flavonolignans. Our findings further suggest designing the in-vitro and in-vivo studies to validate the interaction of flavonolignans with identified targets to strengthen present findings of S. marianum as a hepatoprotective..
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Affiliation(s)
- Prarambh S R Dwivedi
- Department of Pharmacology, NGSM Institute of Pharmaceutical Sciences (NGSMIPS), Nitte (Deemed to be University), Mangalore, 575018, India
| | - Vishal S Patil
- Department of Pharmacology and Toxicology, KLE College of Pharmacy Belagavi, KLE Academy of Higher Education and Research (KAHER), Belagavi, 590010, India; ICMR-National Institute of Traditional Medicine, Belagavi, Karnataka, 590010, India
| | - Pukar Khanal
- Department of Pharmacology, NGSM Institute of Pharmaceutical Sciences (NGSMIPS), Nitte (Deemed to be University), Mangalore, 575018, India.
| | | | - Shailendra Gurav
- Department of Pharmacognosy, Goa College of Pharmacy, Panaji, Goa University - 403301, India
| | - Darasaguppe R Harish
- ICMR-National Institute of Traditional Medicine, Belagavi, Karnataka, 590010, India
| | - B M Patil
- Department of Pharmacology and Toxicology, KLE College of Pharmacy Belagavi, KLE Academy of Higher Education and Research (KAHER), Belagavi, 590010, India.
| | - Subarna Roy
- ICMR-National Institute of Traditional Medicine, Belagavi, Karnataka, 590010, India.
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Ibarra-Hernández JA, Gómez-Balderas R, Nivón-Ramírez D, García-Estrada JG, Mendoza-Jiménez DA, Martínez-Zaldívar A, Cruz-Sánchez TA, Tovar-Betancourt N, Luna-Mora RA, Penieres-Carrillo JG. Novel Compounds Based on Chalcone- and Pyrazoline-DIM Hybrids as Inhibitors of Staphylococcus aureus, Synthesis, DFT Studies, Biological Evaluation and Docking Studies. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Shah FH, Kim SJ. Identification of medicinal compounds as potential inhibitors for mutated isocitrate dehydrogenases against chondrosarcoma. Saudi J Biol Sci 2022; 29:161-167. [PMID: 35002404 PMCID: PMC8716869 DOI: 10.1016/j.sjbs.2021.08.077] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 08/19/2021] [Accepted: 08/22/2021] [Indexed: 11/12/2022] Open
Abstract
Virtual screening of 5000 novel medicinal compounds procured two compounds (5-galloylquinic acid and artocarpetin) capable of establishing interaction with both mutated IDH1 and IDH2 proteins implicated in chondrosarcoma. Cell lining prediction studies revealed that both 5-galloylquinic acid and artocarpetin sensitizes chondrosarcoma cell lines and has good cytotoxic influence on CHSA8926 and CHSA0011 cells. These compounds possess high acute toxicity values to incite adverse reaction and organ damage in rodents. ITGAV, CAPRIN-1, CCL5 COG5 and TNFRSF10B gene are successfully downregulated that are involved in the metastasis inflammation and chondrogenesis by these compounds. TP53 expression enhancer, free radical scavenger, MAP kinase stimulant, MM9 expression inhibitor and chemo preventive agent were some biological properties predicted by Prediction of Activity Spectra for substances (PASS) database. Artocarpetin had good ADME and druglikness properties as compared to 5-galloylquinic acid, as this compound had low bioavailability score and one lipinski violation for druglikness.
Chondrosarcoma is the third most common cartilaginous bone tumour that is insusceptible to radio- and chemotherapy and it is inclined to metastasis. These resistant qualities are facilitated by mutant variants of isocitrate dehydrogenases (IDH) 1–2 enzyme. These mutant enzymes promote oncogenesis of chondrocytes by changing their epigenetic wardrobe leading to tumour formation. Presently, there are lack of drugs available to be exploited as a remedy for this disease. On the other hand, majority of chemotherapeutic drugs induce cytotoxicity in the cancer cells at the cost of harming surrounding healthy cells, jeopardizing human life. The current study is focused on screening various medicinal compounds against IDH1 and IDH2 combined with insilico gene expression, cancer cells cytotoxicity and ADMET (absorption, distribution, metabolism, excretion and toxicity) studies to elucidate the molecular mechanism against chondrosarcoma and also to uncover pharmacokinetic profile of these compounds. Screening of 5000+ compounds filtered two efficacious compounds (Artocarpetin and 5-Galloylquinic acid) capable of establishing hydrogen bond connections with both IDH variants. Other studies showed that these compounds downregulate ITGAV, CARPIN1, CCL5 and COG5 and TNFRSF10B gene that reduces chondrogenesis and inflammation, Artocarpetin and 5-galloylquinic acid are TP53 expression enhancer and inhibit MM9 expression that promote immunomodulation and apoptosis in these cancers. These compounds are both active against CHSA8926 and CHSA011 cell line of chondrosarcoma. However, the ADME profile of 5-galloylquinic acid is slightly unsatisfactory based on druglikness and bioavailability score criteria as compared to artocarpetin. Both of these compounds are class-5 chemicals and require high doses to elicit adverse response. Our results suggest that artocarpetin and 5-galloylquinic acid are efficacious drug candidates and could be further exploited to validate these findings in vitro.
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Affiliation(s)
- Fahad Hassan Shah
- Department of Biological Sciences, College of Natural Sciences, Kongju National University, Gongju 32588, Republic of Korea
| | - Song Ja Kim
- Department of Biological Sciences, College of Natural Sciences, Kongju National University, Gongju 32588, Republic of Korea
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Iwaloye O, Elekofehinti OO, Kikiowo B, Fadipe TM, Akinjiyan MO, Ariyo EO, Aiyeku OO, Adewumi NA. Discovery of Traditional Chinese Medicine Derived Compounds as Wild Type and Mutant Plasmodium falciparum Dihydrofolate Reductase Inhibitors: Induced Fit Docking and ADME Studies. Curr Drug Discov Technol 2021; 18:554-569. [PMID: 32729419 DOI: 10.2174/1570163817999200729122753] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/28/2020] [Accepted: 06/04/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND In a bid to come up with effective compounds as inhibitors for antimalarial treatment, we built a library of 2,000 traditional Chinese medicine(TCM)-derived compounds retrieved from TCM Database@Taiwan. METHODS The active sites of both the wild type and mutant Plasmodium falciparum dihydrofolatereductase (pfDHFR) were explored using computational tools. pfDHFR, one of the prime drug targets in the prevention of malaria infection induced by the female anopheles mosquito has continued to offer resistance to drugs (antifolates) due to mutation in some of the key amino acid residues crucial for its inhibition. RESULTS We utilized virtual throughput screening and glide XP docking to screen the compounds, and 8 compounds were found to have promising docking scores with both the wild type and mutant pfDHFR. They were further subjected to Induce Fit Docking (IFD) to affirm their inhibitory potency. The ADME properties and biological activity spectrum of the compounds were also considered. The inhibition profile of the compounds revealed that a number of compounds formed intermolecular interactions with ASP54, ILE14, LEU164, SER108/ASN108, ARG122 and ASP58. Most of the compounds can be considered as drug candidates due to their antiprotozoal activities and accordance with the Lipinski's Rule of Five (ROF). CONCLUSION The outcome of the present study should further be investigated to attest the efficacy of these compounds as better drug candidates than the antifolates.
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Affiliation(s)
- Opeyemi Iwaloye
- Department of Biochemistry, Bioinformatics and Molecular Biology Unit, Federal University of Technology Akure, Ondo State, Nigeria
| | - Olusola Olalekan Elekofehinti
- Department of Biochemistry, Bioinformatics and Molecular Biology Unit, Federal University of Technology Akure, Ondo State, Nigeria
| | - Babatomiwa Kikiowo
- Department of Biochemistry, Adekunle Ajasin University, Akungba Akoko, Ondo State, Nigeria
| | - Toyin Mary Fadipe
- Department of Bioscience, International Institute of Agriculture, Ibadan, Oyo State, Nigeria
| | - Moses Orimoloye Akinjiyan
- Department of Biochemistry, Bioinformatics and Molecular Biology Unit, Federal University of Technology Akure, Ondo State, Nigeria
| | - Esther Opeyemi Ariyo
- Department of Biochemistry, Bioinformatics and Molecular Biology Unit, Federal University of Technology Akure, Ondo State, Nigeria
| | - Olabisi Olapade Aiyeku
- Department of Biochemistry, Bioinformatics and Molecular Biology Unit, Federal University of Technology Akure, Ondo State, Nigeria
| | - Nicholas Adeyemi Adewumi
- Department of Biochemistry, Bioinformatics and Molecular Biology Unit, Federal University of Technology Akure, Ondo State, Nigeria
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Kwofie SK, Broni E, Yunus FU, Nsoh J, Adoboe D, Miller WA, Wilson MD. Molecular Docking Simulation Studies Identifies Potential Natural Product Derived-Antiwolbachial Compounds as Filaricides against Onchocerciasis. Biomedicines 2021; 9:biomedicines9111682. [PMID: 34829911 PMCID: PMC8615632 DOI: 10.3390/biomedicines9111682] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 10/20/2021] [Accepted: 10/27/2021] [Indexed: 11/16/2022] Open
Abstract
Onchocerciasis is the leading cause of blindness and severe skin lesions which remain a major public health problem, especially in tropical areas. The widespread use of antibiotics and the long duration required for effective treatment continues to add to the increasing global menace of multi-resistant pathogens. Onchocerca volvulus harbors the endosymbiont bacteria Wolbachia, essential for the normal development of embryos, larvae and long-term survival of the adult worm, O. volvulus. We report here results of using structure-based drug design (SBDD) approach aimed at identifying potential novel Wolbachia inhibitors from natural products against the Wolbachia surface protein (WSP). The protein sequence of the WSP with UniProtKB identifier Q0RAI4 was used to model the three-dimensional (3D) structure via homology modelling techniques using three different structure-building algorithms implemented in Modeller, I-TASSER and Robetta. Out of the 15 generated models of WSP, one was selected as the most reasonable quality model which had 82, 15.5, 1.9 and 0.5% of the amino acid residues in the most favored regions, additionally allowed regions, generously allowed regions and disallowed regions, respectively, based on the Ramachandran plot. High throughput virtual screening was performed via Autodock Vina with a library comprising 42,883 natural products from African and Chinese databases, including 23 identified anti-Onchocerca inhibitors. The top six compounds comprising ZINC000095913861, ZINC000095486235, ZINC000035941652, NANPDB4566, acetylaleuritolic acid and rhemannic acid had binding energies of −12.7, −11.1, −11.0, −11, −10.3 and −9.5 kcal/mol, respectively. Molecular dynamics simulations including molecular mechanics Poisson-Boltzmann (MMPBSA) calculations reinforced the stability of the ligand-WSP complexes and plausible binding mechanisms. The residues Arg45, Tyr135, Tyr148 and Phe195 were predicted as potential novel critical residues required for ligand binding in pocket 1. Acetylaleuritolic acid and rhemannic acid (lantedene A) have previously been shown to possess anti-onchocercal activity. This warrants the need to evaluate the anti-WSP activity of the identified molecules. The study suggests the exploitation of compounds which target both pockets 1 and 2, by investigating their potential for effective depletion of Wolbachia. These compounds were predicted to possess reasonably good pharmacological profiles with insignificant toxicity and as drug-like. The compounds were computed to possess biological activity including antibacterial, antiparasitic, anthelmintic and anti-rickettsials. The six natural products are potential novel antiwolbachial agents with insignificant toxicities which can be explored further as filaricides for onchocerciasis.
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Affiliation(s)
- Samuel K. Kwofie
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, PMB LG 77, Legon, Accra LG 77, Ghana; (E.B.); (F.U.Y.); (J.N.); (D.A.)
- West African Centre for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Accra LG 54, Ghana
- Correspondence: ; Tel.: +233-203-797922
| | - Emmanuel Broni
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, PMB LG 77, Legon, Accra LG 77, Ghana; (E.B.); (F.U.Y.); (J.N.); (D.A.)
- West African Centre for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Accra LG 54, Ghana
- Department of Parasitology, Noguchi Memorial Institute for Medical Research (NMIMR), College of Health Sciences (CHS), University of Ghana, P.O. Box LG 581, Legon, Accra LG 581, Ghana;
| | - Faruk U. Yunus
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, PMB LG 77, Legon, Accra LG 77, Ghana; (E.B.); (F.U.Y.); (J.N.); (D.A.)
| | - John Nsoh
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, PMB LG 77, Legon, Accra LG 77, Ghana; (E.B.); (F.U.Y.); (J.N.); (D.A.)
| | - Dela Adoboe
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, PMB LG 77, Legon, Accra LG 77, Ghana; (E.B.); (F.U.Y.); (J.N.); (D.A.)
| | - Whelton A. Miller
- Department of Medicine, Loyola University Medical Center, Maywood, IL 60153, USA;
- Department of Molecular Pharmacology and Neuroscience, Loyola University Medical Center, Maywood, IL 60153, USA
- Department of Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, IL 19104, USA
| | - Michael D. Wilson
- Department of Parasitology, Noguchi Memorial Institute for Medical Research (NMIMR), College of Health Sciences (CHS), University of Ghana, P.O. Box LG 581, Legon, Accra LG 581, Ghana;
- Department of Medicine, Loyola University Medical Center, Maywood, IL 60153, USA;
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Morita-Baylis-Hillman adducts derived from thymol: synthesis, in silico studies and biological activity against Giardia lamblia. Mol Divers 2021; 26:1969-1982. [PMID: 34482477 DOI: 10.1007/s11030-021-10308-1] [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: 07/10/2021] [Accepted: 08/26/2021] [Indexed: 10/20/2022]
Abstract
Giardiasis is a neglected disease, and there is a need for new molecules with less side effects and better activity against resistant strains. This work describes the evaluation of the giardicidal activity of thymol derivatives produced from the Morita-Baylis-Hillman reaction. Thymol acrylate was reacted with different aromatic aldehydes, using 1,4-diazabicyclo[2.2.2]octane (DABCO) as a catalyst. Eleven adducts (8 of them unpublished) with yields between 58 and 80% were obtained from this reaction, which were adequately characterized. The in silico prediction showed theoretical bioavailability after oral administration as well as antiparasitic activity against Giardia lamblia. Compound 4 showed better biological activity against G. lamblia. In addition to presenting antigiardial activity 24 times better than thymol, this MBHA was obtained in a short reaction time (3 h) with a yield (80%) superior to the other investigated molecules. The molecule was more active than the precursors (thymol and MBHA 12) and did not show cytotoxicity against HEK-293 or HT-29 cells. In conclusion, this study presents a new class of drugs with better antigiardial activity in relation to thymol, acting as a basis for the synthesis of new bioactive molecules. Molecular hybridization technique combined with the Morita-Baylis-Hillman reaction provided new thymol derivatives with giardicidal activity superior to the precursor molecules.
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Broni E, Kwofie SK, Asiedu SO, Miller WA, Wilson MD. A Molecular Modeling Approach to Identify Potential Antileishmanial Compounds Against the Cell Division Cycle (cdc)-2-Related Kinase 12 (CRK12) Receptor of Leishmania donovani. Biomolecules 2021; 11:458. [PMID: 33803906 PMCID: PMC8003136 DOI: 10.3390/biom11030458] [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: 02/27/2021] [Revised: 03/12/2021] [Accepted: 03/14/2021] [Indexed: 12/11/2022] Open
Abstract
The huge burden of leishmaniasis caused by the trypanosomatid protozoan parasite Leishmania is well known. This illness was included in the list of neglected tropical diseases targeted for elimination by the World Health Organization. However, the increasing evidence of resistance to existing antimonial drugs has made the eradication of the disease difficult to achieve, thus warranting the search for new drug targets. We report here studies that used computational methods to identify inhibitors of receptors from natural products. The cell division cycle-2-related kinase 12 (CRK12) receptor is a plausible drug target against Leishmania donovani. This study modelled the 3D molecular structure of the L. donovani CRK12 (LdCRK12) and screened for small molecules with potential inhibitory activity from African flora. An integrated library of 7722 African natural product-derived compounds and known inhibitors were screened against the LdCRK12 using AutoDock Vina after performing energy minimization with GROMACS 2018. Four natural products, namely sesamin (NANPDB1649), methyl ellagic acid (NANPDB1406), stylopine (NANPDB2581), and sennecicannabine (NANPDB6446) were found to be potential LdCRK12 inhibitory molecules. The molecular docking studies revealed two compounds NANPDB1406 and NANPDB2581 with binding affinities of -9.5 and -9.2 kcal/mol, respectively, against LdCRK12 which were higher than those of the known inhibitors and drugs, including GSK3186899, amphotericin B, miltefosine, and paromomycin. All the four compounds were predicted to have inhibitory constant (Ki) values ranging from 0.108 to 0.587 μM. NANPDB2581, NANPDB1649 and NANPDB1406 were also predicted as antileishmanial with Pa and Pi values of 0.415 and 0.043, 0.391 and 0.052, and 0.351 and 0.071, respectively. Molecular dynamics simulations coupled with molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) computations reinforced their good binding mechanisms. Most compounds were observed to bind in the ATP binding pocket of the kinase domain. Lys488 was predicted as a key residue critical for ligand binding in the ATP binding pocket of the LdCRK12. The molecules were pharmacologically profiled as druglike with inconsequential toxicity. The identified molecules have scaffolds that could form the backbone for fragment-based drug design of novel leishmanicides but warrant further studies to evaluate their therapeutic potential.
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Affiliation(s)
- Emmanuel Broni
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic & Applied Sciences, University of Ghana, Legon, Accra LG 77, Ghana;
| | - Samuel K. Kwofie
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic & Applied Sciences, University of Ghana, Legon, Accra LG 77, Ghana;
- West African Center for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Legon, Accra LG 54, Ghana
| | - Seth O. Asiedu
- Department of Parasitology, Noguchi Memorial Institute for Medical Research (NMIMR), College of Health Sciences (CHS), University of Ghana, Legon, Accra LG 581, Ghana; (S.O.A.); (M.D.W.)
| | - Whelton A. Miller
- Department of Medicine, Loyola University Medical Center, Maywood, IL 60153, USA;
- Department of Molecular Pharmacology and Neuroscience, Loyola University Medical Center, Maywood, IL 60153, USA
- Department of Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, IL 19104, USA
| | - Michael D. Wilson
- Department of Parasitology, Noguchi Memorial Institute for Medical Research (NMIMR), College of Health Sciences (CHS), University of Ghana, Legon, Accra LG 581, Ghana; (S.O.A.); (M.D.W.)
- Department of Medicine, Loyola University Medical Center, Maywood, IL 60153, USA;
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Density functional theory for the thermodynamic gas-phase investigation of butanol biofuel and its isomers mixed with gasoline and ethanol. J Mol Model 2021; 27:80. [PMID: 33575832 DOI: 10.1007/s00894-021-04681-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 01/17/2021] [Indexed: 10/22/2022]
Abstract
Herein, we present the results of our study on the thermodynamic properties of the isomers of butanol (n-butanol, 2-butanol, i-butanol, and t-butanol) to evaluate their thermodynamic potential as a complementary biofuel and/or substitute for ethanol and gasoline. The Gaussian09W software was used to perform molecular geometry optimization calculations using density functional theory with the B3lyp hybrid function using the base set 6-311++g(d,p) and the compound methods G3, G4, and CBS-QB3. Calculations of the fundamental frequency of the molecules were performed to obtain the molecular vibration modes for the respective frequencies. These calculations provided thermodynamic parameters such as the entropy, enthalpy, and specific molar heat at constant pressure, all as a function of the temperature. The parameter values obtained by each method were compared to the experimental values available in the literature. The results showed good accuracy, especially those obtained at the B3lyp/6-311++g(d,p) level for n-butanol. The error between the theoretical and experimental values for the combustion enthalpy of n-butanol was less than 4% at 298.15 K; due to the good prediction of its thermodynamic properties, we used n-butanol as a model for the prediction of other thermodynamic properties. We started a molecular docking study of four ligands, namely, n-butanol, ethanol, propanol, heptane, isooctane, and methanol interacting with butanol isomers. The highest values of affinity energy found were for N-butanol. The possible formation of hydrogen bonds, associations by means of London forces, hydrogen, and alkyl interactions were analyzed. n-Butanol was added to ethanol-gasoline mixtures in the temperature range of 298.15 to 600 K and the results suggest that n-butanol has a higher calorific value than gasoline-ethanol mixtures in G30E, G40E, G50E, G60E, G70E, G80E, G90E, and E100 blends. As such, n-butanol releases greater amounts of heat during combustion and is thus a viable alternative to biofuels.
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Khanal P, Chikhale R, Dey YN, Pasha I, Chand S, Gurav N, Ayyanar M, Patil BM, Gurav S. Withanolides from Withania somnifera as an immunity booster and their therapeutic options against COVID-19. J Biomol Struct Dyn 2021; 40:5295-5308. [PMID: 33459174 DOI: 10.1080/07391102.2020.1869588] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Traditionally, Withania somnifera is widely used as an immune booster, anti-viral, and for multiple medicinal purposes. The present study investigated the withanolides as an immune booster and anti-viral agents against the coronavirus-19. Withanolides from Withania somnifera were retrieved from the open-source database, their targets were predicted using DIGEP-Pred, and the protein-protein interaction was evaluated. The drug-likeness score and intestinal absorptivity of each compound were also predicted. The network of compounds, proteins, and modulated pathways was constructed using Cytoscape, and docking was performed using autodock4.0, and selected protein-ligand complexes were subjected to 100 ns Molecular Dynamics simulations. The molecular dynamics trajectories were subjected to free energy calculation by the MM-GBSA method. Withanolide_Q was predicted to modulate the highest number of proteins, showed human intestinal absorption, and was predicted for the highest drug-likeness score. Similarly, combined network interaction identified Withanolide_Q to target the highest number of proteins; RAC1 was majorly targeted, and fluid shear stress and atherosclerosis associated pathway were chiefly regulated. Similarly, Withanolide_D and Withanolide_G were predicted to have a better binding affinity with PLpro, Withanolide_M with 3CLpro, and Withanolide_M with spike protein based on binding energy and number of hydrogen bond interactions. MD studies suggested Withanoside_I with the highest binding free energy (ΔGbind-31.56 kcal/mol) as the most promising inhibitor. Among multiple withanolides from W. somnifera, Withanolide_D, Withanolide_G, Withanolide_M, and Withanolide_Q were predicted as the lead hits based on drug-likeness score, modulated proteins, and docking score to boost the immune system and inhibit the COVID-19 infection, which could primarily act against COVID-19. HighlightsWithanolides are immunity boosters.Withanolides are a group of bio-actives with potential anti-viral properties.Withanolide_G, Withanolide_I, and Withanolide_M from Withania somnifera showed the highest binding affinity with PLpro, 3CLpro, and spike protein, respectively.Withanolides from Withania somnifera holds promising anti-viral efficacy against COVID-19.Communicated by Vsevolod Makeev.
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Affiliation(s)
- Pukar Khanal
- Department of Pharmacology and Toxicology, KLE College of Pharmacy Belagavi, KLE Academy of Higher Education and Research (KAHER), Belagavi, India
| | | | - Yadu Nandan Dey
- School of Pharmaceutical Technology, Adamas University, Kolkata, West Bengal, India
| | - Ismail Pasha
- Department of Pharmacology, Orotta College of Medicine and Health Sciences, Asmara University, Asmara, Eritrea
| | - Sharad Chand
- Department of Pharmacy Practice, NGSM Institute of Pharmaceutical Sciences, NITTE (Deemed to be University), Deralakatte, Karnataka, India
| | - Nilambari Gurav
- PES's Rajaram and Tarabai Bandekar College of Pharmacy, Ponda, Goa University, Goa, India
| | - Muniappan Ayyanar
- Department of Botany, A. Veeriya Vandayar Memorial Sri Pushpam College (Autonomous), Affiliated to Bharathidasan University, Thanjavur, India
| | - B M Patil
- Department of Pharmacology and Toxicology, KLE College of Pharmacy Belagavi, KLE Academy of Higher Education and Research (KAHER), Belagavi, India
| | - Shailendra Gurav
- Goa College of Pharmacy, Department of Pharmacognosy, Panaji, Goa University, Goa, India
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Patil R, Chikhale R, Khanal P, Gurav N, Ayyanar M, Sinha S, Prasad S, Dey YN, Wanjari M, Gurav SS. Computational and network pharmacology analysis of bioflavonoids as possible natural antiviral compounds in COVID-19. INFORMATICS IN MEDICINE UNLOCKED 2020; 22:100504. [PMID: 33363251 PMCID: PMC7756171 DOI: 10.1016/j.imu.2020.100504] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 12/15/2020] [Accepted: 12/15/2020] [Indexed: 12/17/2022] Open
Abstract
Bioflavonoids are the largest group of plant-derived polyphenolic compounds with diverse biological potential and have also been proven efficacious in the treatment of Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS). The present investigation validates molecular docking, simulation, and MM-PBSA studies of fifteen bioactive bioflavonoids derived from plants as a plausible potential antiviral in the treatment of COVID-19. Molecular docking studies for 15 flavonoids on the three SARS CoV-2 proteins, non-structural protein-15 Endoribonuclease (NSP15), the receptor-binding domain of spike protein (RBD of S protein), and main protease (Mpro/3CLpro) were performed and selected protein-ligand complexes were subjected to Molecular Dynamics simulations. The molecular dynamics trajectories were subjected to free energy calculation by the MM-PBSA method. All flavonoids were further assessed for their effectiveness as adjuvant therapy by network pharmacology analysis on the target proteins. The network pharmacology analysis suggests the involvement of selected bioflavonoids in the modulation of multiple signaling pathways like p53, FoxO, MAPK, Wnt, Rap1, TNF, adipocytokine, and leukocyte transendothelial migration which plays a significant role in immunomodulation, minimizing the oxidative stress and inflammation. Molecular docking and molecular dynamics simulation studies illustrated the potential of glycyrrhizic acid, amentoflavone, and mulberroside in inhibiting key SARS-CoV-2 proteins and these results could be exploited further in designing future ligands from natural sources.
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Key Words
- 2019-nCoV, 2019 Novel Coronavirus
- Amentoflavone
- Bioflavonoids
- COVID-19, Coronavirus Disease-2019
- CoV, Corona Virus
- Glycyrrhizic acid
- In-silico study
- MD, Molecular Dynamics
- MM-PBSA, Molecular Mechanics Poisson-Boltzmann Surface Area
- Mulberroside
- NSP, Non-structural Protein
- Novel Coronavirus-2
- OPLS, Optimized Potentials for Liquid Simulations
- ORF, Open Reading Frame
- RBD, Receptor Binding Domain
- RMSD, Root Mean Square Deviation
- SARS, Severe Acute Respiratory syndrome
- SARS-CoV-2, Severe Acute Respiratory syndrome Coronavirus-2
- SDF, Structure Data File
- WHO, World Health Organization
- Å, Angstrom
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Affiliation(s)
- Rajesh Patil
- Sinhgad Technical Education Society's, Smt. Kashibai Navale College of Pharmacy, Pune, Maharashtra, India
| | - Rupesh Chikhale
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Pukar Khanal
- Department of Pharmacology and Toxicology, KLE College of Pharmacy Belagavi, KLE Academy of Higher Education and Research (KAHER), Belagavi, 590010, India
| | - Nilambari Gurav
- PES's Rajaram and Tarabai Bandekar College of Pharmacy, Ponda, Goa University, Goa, 403401, India
| | - Muniappan Ayyanar
- Department of Botany, A. Veeriya Vandayar Memorial Sri Pushpam College (Autonomous), Affiliated to Bharathidasan University, Poondi, Thanjavur, 613 503, India
| | - Saurabh Sinha
- Department of Pharmaceutical Sciences, Mohanlal Shukhadia University, Udaipur, Rajasthan, 313 001, India
| | - Satyendra Prasad
- Department of Pharmaceutical Sciences, R.T.M. University, Nagpur, Maharashtra, 440033, India
| | - Yadu Nandan Dey
- School of Pharmaceutical Technology, Adamas University, Kolkata, 700126, West Bengal, India
| | - Manish Wanjari
- Regional Ayurveda Research Institute for Drug Development, Gwalior, 474009, Madhya Pradesh, India
| | - Shailendra S Gurav
- Department of Pharmacognosy and Phytochemistry, Goa College of Pharmacy, Panaji, Goa University, Goa, 403 001, India
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Li S, Ding Y, Chen M, Chen Y, Kirchmair J, Zhu Z, Wu S, Xia J. HDAC3i-Finder: A Machine Learning-based Computational Tool to Screen for HDAC3 Inhibitors. Mol Inform 2020; 40:e2000105. [PMID: 33067876 DOI: 10.1002/minf.202000105] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 10/16/2020] [Indexed: 11/10/2022]
Abstract
Histone deacetylase 3 (HDAC3) is a potential drug target for treatment of human diseases such as cancer, chronic inflammation, neurodegenerative diseases and diabetes. Machine learning (ML) as an essential cheminformatics approach has been widely used for QSAR modeling. However, none of them has been applied to HDAC3. To this end, we carefully compiled a set of 1098 compounds from the ChEMBL database that have been assayed against HDAC3 and calculated three different sets of molecular features for each compound, i. e. two-dimensional Mordred descriptors, MACCS keys (166 bits) and Morgan2 fingerprints (1024 bits). Five ML classifiers, i. e. k-Nearest Neighbour (KNN), Support Vector Machine (SVM), Random forest (RF), eXtreme Gradient Boosting (XGBoost) and Deep Neural Network (DNN) were trained on each feature set and optimized for classification. A total of 15 models were generated and carefully compared, among which the best-performing one was the XGBoost model based on the Morgan2 fingerprints, i. e. XGBoost_morgan2. Evaluated on a well-curated benchmarking set named MUBD-HDAC3, this model achieved a high early ROC enrichment (ROCE0.5 %: 41.02). A further retrospective screening of an annotated chemical library in PubChem demonstrated that the best model could identify 8 novel-scaffold HDAC3 inhibitors while assaying only 1 % of the compounds. To make this model accessible for the scientific community, we developed a python GUI application named HDAC3i-Finder to facilitate prospective screening for HDAC3 inhibitors. The source code of HDAC3i-Finder is available at https://github.com/jwxia2014/HDAC3i-Finder.
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Affiliation(s)
- Shan Li
- College of Economics and Management, Nanjing University of Aeronautics and Astronautics, Nanjing, 211106, China
| | - Yu Ding
- College of Economics and Management, Nanjing University of Aeronautics and Astronautics, Nanjing, 211106, China
| | - Miaomiao Chen
- College of Economics and Management, Nanjing University of Aeronautics and Astronautics, Nanjing, 211106, China
| | - Ya Chen
- Center for Bioinformatics (ZBH), Department of Computer Science, Faculty of Mathematics, Informatics and Natural Sciences, Universität Hamburg, Hamburg, Germany
| | - Johannes Kirchmair
- Center for Bioinformatics (ZBH), Department of Computer Science, Faculty of Mathematics, Informatics and Natural Sciences, Universität Hamburg, Hamburg, Germany.,Department of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Zihao Zhu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Song Wu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Jie Xia
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
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Khan MF, Kader FB, Arman M, Ahmed S, Lyzu C, Sakib SA, Tanzil SM, Zim AFMIU, Imran MAS, Venneri T, Romano B, Haque MA, Capasso R. Pharmacological insights and prediction of lead bioactive isolates of Dita bark through experimental and computer-aided mechanism. Biomed Pharmacother 2020; 131:110774. [PMID: 33152933 DOI: 10.1016/j.biopha.2020.110774] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 09/15/2020] [Accepted: 09/18/2020] [Indexed: 12/18/2022] Open
Abstract
Dita bark (Alstonia scholaris (L.) R. Br.) is an ethnomedicine used for the management of various ailments. This study aimed to investigate the biological properties of methanol extract of A. scholaris bark (MEAS), through in vivo, in vitro and in silico approaches alongside its phytochemical profiling. Identification and nature of the bioactive secondary metabolites were studied by the established qualitative tests and GC-MS analysis. The antidepressant activity was determined by forced swimming test (FST) and tail suspension test (TST) in mice. The anti-inflammatory and thrombolytic effect was evaluated using inhibition of protein denaturation technique and clot lysis technique, respectively. Besides, computational studies of the isolated compounds and ADME/T analysis were performed by Schrödinger-Maestro (v11.1) software, and PASS prediction was conducted through PASS online tools. The GC-MS analysis revealed the presence of several secondary metabolites in MEAS. Treatment with MEAS revealed a significant reduction of immobility time in a dose-dependent manner in FST and TST. Besides, MEAS showed substantial anti-inflammatory effects at the higher dose (400 μg/mL) as well as revealed notable clot lysis effect as compared to control. In the case of computer-aided investigation, all compounds meet the condition of Lipinski's rule of five. PASS study also predicted for all compounds, and among these safe compound furazan-3-amine showed the most spontaneous binding energy for both antidepressant and thrombolytic activities, as well as 5-dimethylamino-6 azauracil, found promising for anti-inflammatory activity. Taken together, the investigation concludes that MEAS can be a potent source of antidepressant, anti-inflammatory, and thrombolytic agents.
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Affiliation(s)
- Mohammad Forhad Khan
- Department of Pharmacy, International Islamic University Chittagong, Chittagong, 4318, Bangladesh
| | - Faisal Bin Kader
- Department of Pharmacy, International Islamic University Chittagong, Chittagong, 4318, Bangladesh
| | - Mohammad Arman
- Department of Pharmacy, International Islamic University Chittagong, Chittagong, 4318, Bangladesh
| | - Suhel Ahmed
- Department of Pharmacy, International Islamic University Chittagong, Chittagong, 4318, Bangladesh
| | - Chadni Lyzu
- Biomedical and Toxicological Research Institute, Bangladesh Council of Scientific and Industrial Research, Dhaka, 1205, Bangladesh
| | - Shahenur Alam Sakib
- Department of Pharmacy, International Islamic University Chittagong, Chittagong, 4318, Bangladesh
| | - Shaifullah Mansur Tanzil
- Department of Pharmacy, International Islamic University Chittagong, Chittagong, 4318, Bangladesh
| | - A F M Irfan Uddin Zim
- Department of Applied Food Science and Nutrition, Chittagong Veterinary and Animal Sciences University, Chittagong, 4225, Bangladesh
| | - Md Abdus Shukur Imran
- Department of Pharmaceuticals and Industrial Biotechnology, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
| | - Tommaso Venneri
- Department of Pharmacy, University of Napoli Federico II, Naples, Italy
| | - Barbara Romano
- Department of Pharmacy, University of Napoli Federico II, Naples, Italy
| | - Md Areeful Haque
- Department of Pharmacy, International Islamic University Chittagong, Chittagong, 4318, Bangladesh; Drug and Herbal Research Centre, Faculty of Pharmacy, Universiti Kebangsaan Malaysia, 50300 Kuala Lumpur, Malaysia.
| | - Raffaele Capasso
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy.
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Deciphering potential inhibitors targeting THI4 of Fusarium solani sp. to combat fungal keratitis: An integrative computational approach. Comput Biol Chem 2020; 88:107350. [DOI: 10.1016/j.compbiolchem.2020.107350] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 07/23/2020] [Accepted: 07/28/2020] [Indexed: 12/27/2022]
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Khanal P, Patil BM, Chand J, Naaz Y. Anthraquinone Derivatives as an Immune Booster and their Therapeutic Option Against COVID-19. NATURAL PRODUCTS AND BIOPROSPECTING 2020; 10:325-335. [PMID: 32772313 PMCID: PMC7414902 DOI: 10.1007/s13659-020-00260-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 08/01/2020] [Indexed: 05/05/2023]
Abstract
Anthraquinone derivatives are identified for their immune-boosting, anti-inflammatory, and anti-viral efficacy. Hence, the present study aimed to investigate the reported anthraquinone derivatives as immune booster molecules in COVID-19 infection and evaluate their binding affinity with three reported targets of novel coronavirus i.e. 3C-like protease, papain-like protease, and spike protein. The reported anthraquinone derivatives were retrieved from an open-source database and filtered based on a positive druglikeness score. Compounds with positive druglikeness scores were predicted for their targets using DIGEP-Pred and the interaction among modulated proteins was evaluated using STRING. Further, the associated pathways were recorded concerning the Kyoto Encyclopedia of Genes and Genomes pathway database. Finally, the docking was performed using autodock4 to identify the binding efficacy of anthraquinone derivatives with 3C-like protease, papain-like protease, and spike protein. After docking the pose of ligand scoring minimum binding energy was chosen to visualize the ligand-protein interaction. Among 101 bioactives, 36 scored positive druglikeness score and regulated multiple pathways concerned with immune modulation and (non-) infectious diseases. Similarly, docking study revealed torososide B to possess the highest binding affinity with papain-like protease and 3C-like protease and 1,3,6-trihydroxy-2-methyl-9,10-anthraquinone-3-O-(6'-O-acetyl)-β-D-xylopyranosyl-(1 → 2)-β-D-glucopyranoside with spike protein.
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Affiliation(s)
- Pukar Khanal
- Department of Pharmacology and Toxicology, KLE College of Pharmacy, Belagavi, KLE Academy of Higher Education and Research (KAHER), Belagavi, 590010, India.
| | - B M Patil
- Department of Pharmacology and Toxicology, KLE College of Pharmacy, Belagavi, KLE Academy of Higher Education and Research (KAHER), Belagavi, 590010, India.
| | - Jagdish Chand
- Department of Pharmaceutical Chemistry, KLE College of Pharmacy, Belagavi, KLE Academy of Higher Education and Research (KAHER), Belagavi, 590010, India
| | - Yasmin Naaz
- Department of Pharmaceutical Chemistry, KLE College of Pharmacy, Belagavi, KLE Academy of Higher Education and Research (KAHER), Belagavi, 590010, India
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Khanal P, Patil BM. Gene ontology enrichment analysis of α-amylase inhibitors from Duranta repens in diabetes mellitus. J Diabetes Metab Disord 2020; 19:735-747. [PMID: 33520800 DOI: 10.1007/s40200-020-00554-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 05/05/2020] [Accepted: 05/21/2020] [Indexed: 12/13/2022]
Abstract
Background Although α-amylase is the choice of target to manage postprandial hyperglycemia, inhibitors of this enzyme may get absorbed into the systemic circulation and modulate proteins involved in the pathogenesis of diabetes mellitus. Hence, the present study aimed to identify α-amylase inhibitors from Duranta repens via in silico and in vitro and predict their role in the modulation of multiple pathways involved in diabetes mellitus. Methods α-amylase inhibitory activity of hydroalcoholic extract/fractions (s) and pure compounds from D. repens was performed using in vitro enzyme inhibitory assay. Multiple open-source databases and published literature were used to retrieve reported phytoconstituents present in D. repens and their targets. The network was constructed between α-amylase inhibitors, modulated proteins, and expressed pathways. Further, hit molecules were also confirmed for their potency to inhibit α-amylase using in silico molecular docking and in vitro enzyme inhibitory assay. The glucose uptake assay was performed to assess the effect of hydrolcoholic extract/fraction(s) using rat hemidiaphragm. Results Fraction rich in flavonoids showed the highest α-amylase inhibitory activity with a IC50 of 644.29 ± 4.36 µg/ml compared to other fractions. PI3K-Akt signaling pathway and p53 signaling pathway were predicted to be primarily modulated in the compound-protein-pathway network. Similarly, scutellarein was predicted as lead hit based on α-amylase inhibitory action, binding affinity, and regulated pathways. Further, α-amylase inhibitors were also predicted to modulate the pathways involved in diabetes complications like AGE-RAGE and FoxO signaling pathway. Fraction rich in flavonoids showed the highest glucose uptake in rat hemidiaphragm with an effective concentration of 534.73 ± 0.79 µg/ml. Conclusions The α-amylase inhibitors from D. repens may not be limited within the gastrointestinal tract to inhibit α-amylase but may get absorbed into the systemic circulation and modulate multiple pathways involved in the pathogenesis of diabetes mellitus to produce synergistic/additive effect.
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Affiliation(s)
- Pukar Khanal
- Department of Pharmacology and Toxicology, KLE College of Pharmacy, Belagavi, KLE Academy of Higher Education and Research (KAHER), Belagavi, 590010 India
| | - B M Patil
- Department of Pharmacology and Toxicology, KLE College of Pharmacy, Belagavi, KLE Academy of Higher Education and Research (KAHER), Belagavi, 590010 India
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Citral Induced Apoptosis through Modulation of Key Genes Involved in Fatty Acid Biosynthesis in Human Prostate Cancer Cells: In Silico and In Vitro Study. BIOMED RESEARCH INTERNATIONAL 2020; 2020:6040727. [PMID: 32258129 PMCID: PMC7103989 DOI: 10.1155/2020/6040727] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 08/31/2019] [Accepted: 11/21/2019] [Indexed: 12/14/2022]
Abstract
The isomers of citral (cis-citral and trans-citral) were isolated from the Cymbopogon citratus (DC.) Stapf oil demonstrates many therapeutic properties including anticancer properties. However, the effects of citral on suppressing human prostate cancer and its underlying molecular mechanism have yet to be elucidated. The citral was isolated from lemongrass oil using various spectroscopic analyses, such as electron ionized mass spectrometry (EI-MS) and nuclear magnetic resonance (NMR) spectroscopy respectively. We carried out 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) assay to evaluate the cell viability of citral in prostate cancer cells (PC-3 and PC3M). Furthermore, to confirm that PC3 undergoes apoptosis by inhibiting lipogenesis, we used several detection methods including flow cytometry, DNA fragmentation, Hoechst staining, PI staining, oil staining, qPCR, and Western blotting. Citral impaired the clonogenic property of the cancer cells and altered the morphology of cancer cells. Molecular interaction studies and the PASS biological program predicted that citral isomers tend to interact with proteins involved in lipogenesis and the apoptosis pathway. Furthermore, citral suppressed lipogenesis of prostate cancer cells through the activation of AMPK phosphorylation and downregulation of fatty acid synthase (FASN), acetyl coA carboxylase (ACC), 3-hydroxy-3-methylglutaryl-coenzyme A reductase (HMGR), and sterol regulatory element-binding protein (SREBP1) and apoptosis of PC3 cells by upregulating BAX and downregulating Bcl-2 expression. In addition, in silico studies such as ADMET predicted that citral can be used as a safe potent drug for the treatment of prostate cancer. Our results indicate that citral may serve as a potential candidate against human prostate cancer and warrants in vivo studies.
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Moraes ES, Reis GF, Cruz J, Cozzolino K, Neto AFG, Andrade-Filho T, Neto AMJC. Thermodynamics study of biokerosene from coconut and palm kernel oils and JP-8 aircraft fuels in the gas phase by the DFT method. J Mol Model 2020; 26:79. [DOI: 10.1007/s00894-020-4327-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 02/23/2020] [Indexed: 11/25/2022]
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Kolotyeva NA, Gilmiyarova FN. [The role of small molecules in metabolism regulation (review).]. Klin Lab Diagn 2020; 64:716-722. [PMID: 32040894 DOI: 10.18821/0869-2084-2019-64-12-716-722] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 10/30/2019] [Indexed: 11/17/2022]
Abstract
The paper focuses on intermolecular interactions, particularly interactions between proteins and natural intermediates (small molecules). Molecules with a molecular weight of up to 1000 Da are free in cytoplasmic solution and form a pool of intermediates. Methods of computer modeling for prediction of protein-proteinaceous, protein-ligand, protein - a small molecule of interactions are presented. The program for modeling predicted biological activity in silico is Prediction of Activity Spectrum for Substances (PASS). In the Search Tool for Interacting Chemicals (STITCH) system, it is possible to identify potential protein interaction partners for small molecules. A review of the literature presents modern data on small molecules - metabolic switches, such as α-glycerophosphatedihydroxyacetone phosphate, pyruvate-lactate, oxaloacetate-malate. The molecules we study have different and multiple effects on metabolism and on intercellular interaction systems. Natural intermediates are at the intersection of metabolic pathways of metabolism of proteins, carbohydrates, lipids; they are signal molecules, participate in regulation of protein function, gene expression, enzyme activity. An increasing interest in deciphering protein-small molecule/metabolite interactions at the systemic level will lay a conceptual foundation that provides insight into complex epigenetic regulation under various environmental influences. A complete interplay, including a protein-small molecule interaction, will be crucial to eventually unraveling the complex relationships between the genotype and phenotype and to provide a deeper understanding of health and disease.
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Affiliation(s)
- N A Kolotyeva
- Samara State Medical University, 43099, Samara, Russia
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Computer-aided prediction of biological activity spectra for organic compounds: the possibilities and limitations. Russ Chem Bull 2020. [DOI: 10.1007/s11172-019-2683-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Joshi SV, Patel EP, Vyas BA, Lodha SR, Kalyankar GG. Repurposing of Iloperidone: Antihypertensive and ocular hypotensive activity in animals. Eur J Pharm Sci 2019; 143:105173. [PMID: 31809906 DOI: 10.1016/j.ejps.2019.105173] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 11/29/2019] [Accepted: 12/02/2019] [Indexed: 12/14/2022]
Abstract
PURPOSE Iloperidone, second generation antipsychotic drug, reported in clinical trial to produce orthostatic hypotension as side effect. It was claimed to be antagonistic at alpha adrenergic receptor in central nervous system. We evaluated effect of Iloperidone on peripheral alpha 1 adrenoreceptor by in silico and in vitro methods while in vivo hypotensive, antihypertensive and ocular hypotensive activity was evaluated in animals. METHODS Pharmacological activity prediction of Iloperidone was done using PASSOnline and SwissTargetPrediction softwares and molecular docking with Alpha 1A adrenoreceptor using AutoDock Vina. Hypotensive activity in normotensive and antihypertensive activity against DOCA-salt induced hypertension in rats were evaluated at doses 0.03 mg/Kg and 0.1 mg/Kg, i.p of Iloperidone. Blood pressure was measured by invasive blood pressure measurement technique using PowerLab 4/30 and intraocular pressure was measured using digital tonometer. RESULTS Iloperidone (0.1 mg/Kg) showed significant decrease in blood pressure (38.96 ± 1.1%) in normotensive rats, while in DOCA salt induced hypertensive rats, systolic blood pressure was found to be decreased by 29.04 ± 1.45% and 31.43 ± 1.21% in 0.03 mg/Kg and 0.1 mg/Kg treated rats respectively. Iloperidone prevented rise in systolic BP with adrenaline. Intraocular pressure was found to be decreased by 36.66 ± 3.15% in rabbits after 1 h of instillation of 0.1% Iloperidone. CONCLUSION Iloperidone exerted hypotensive and/or anti-hypertensive activity in rats and ocular hypotensive activity in rabbits.
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Affiliation(s)
- Shrikant V Joshi
- Maliba Pharmacy College, Uka Tarsadia University, Maliba Campus, Bardoli-Mahuva Road, Tarsadi. Distt. Surat, Gujarat, 394 350 India.
| | - Ekta P Patel
- Maliba Pharmacy College, Uka Tarsadia University, Maliba Campus, Bardoli-Mahuva Road, Tarsadi. Distt. Surat, Gujarat, 394 350 India
| | - Bhavin A Vyas
- Maliba Pharmacy College, Uka Tarsadia University, Maliba Campus, Bardoli-Mahuva Road, Tarsadi. Distt. Surat, Gujarat, 394 350 India
| | - Sandesh R Lodha
- Maliba Pharmacy College, Uka Tarsadia University, Maliba Campus, Bardoli-Mahuva Road, Tarsadi. Distt. Surat, Gujarat, 394 350 India
| | - Gajanan G Kalyankar
- Maliba Pharmacy College, Uka Tarsadia University, Maliba Campus, Bardoli-Mahuva Road, Tarsadi. Distt. Surat, Gujarat, 394 350 India
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Geronikaki A, Petrou A, Kartsev V, Eleftheriou P, Boga R, Bartolo B, Crespan E, Franco G, Maga G. Molecular docking, design, synthesis and biological evaluation of novel 2,3-aryl-thiazolidin-4-ones as potent NNRTIs. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2019; 30:697-714. [PMID: 31542957 DOI: 10.1080/1062936x.2019.1653364] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 08/05/2019] [Indexed: 06/10/2023]
Abstract
Nonnucleoside reverse transcriptase inhibitors (NNRTIs) remain the most promising anti-AIDS agents that target the HIV-1 reverse transcriptase enzyme (RT). However, the efficiency of approved NNRTI drugs has decreased by the appearance of drug-resistant viruses and side effects upon long-term usage. Thus, there is an urgent need for developing new, potent NNRTIs with broad spectrum against HIV-1 virus and with improved properties. In this study, a series of thiazolidinone derivatives was designed based on a butterfly mimicking scaffold consisting of a substituted benzothiazolyl moiety connected with a substituted phenyl ring via a thiazolidinone moiety. The most promising derivatives were selected using molecular docking analysis and PASS prediction program, synthesized and evaluated for HIV-1 RT inhibition. Five out of fifteen tested compounds exhibited good inhibitory action. It was observed that the presence of Cl or CN substituents at the position 6 of the benzothiazole ring in combination with two fluoro atoms at the ortho-positions or a hydrogen acceptor substituent at the 4-position of the phenyl ring are favourable for the HIV RT inhibitory activity.
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Affiliation(s)
- A Geronikaki
- School of Pharmacy, Aristotle University of Thessaloniki , Thessaloniki , Greece
| | - A Petrou
- School of Pharmacy, Aristotle University of Thessaloniki , Thessaloniki , Greece
| | | | - P Eleftheriou
- Department of Biomedical Sciences, School of Health Sciences, International Hellenic University , Thessaloniki , Greece
| | - R Boga
- BogaR Laboratories LLC , Suwanee , USA
| | - B Bartolo
- Faculty of Sciences, Institute of Molecular Genetics "Luigi Luca Cavalli-Sforza" IGM-CNR , Pavia , Italy
| | - E Crespan
- Faculty of Sciences, Institute of Molecular Genetics "Luigi Luca Cavalli-Sforza" IGM-CNR , Pavia , Italy
| | - G Franco
- Faculty of Sciences, Institute of Molecular Genetics "Luigi Luca Cavalli-Sforza" IGM-CNR , Pavia , Italy
| | - G Maga
- Faculty of Sciences, Institute of Molecular Genetics "Luigi Luca Cavalli-Sforza" IGM-CNR , Pavia , Italy
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Anti-arthritic activity of ferulic acid in complete Freund's adjuvant (CFA)-induced arthritis in rats: JAK2 inhibition. Inflammopharmacology 2019; 28:463-473. [PMID: 31562605 DOI: 10.1007/s10787-019-00642-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 09/09/2019] [Indexed: 12/28/2022]
Abstract
Ferulic acid (FA), a hydroxycinnamic acid, is an organic compound found in several plant species. Previous studies have shown that FA contains anti-inflammatory and anti-arthritic properties. This study aimed to investigate the anti-arthritic activity and possible mechanism(s) of action of FA in complete Freund's adjuvant (CFA)-induced arthritis. The progression of rheumatoid arthritis (RA) involves the activation of the Janus kinase-signal transducer and activator of transcription (JAK/STAT) pathway by proinflammatory cytokines. Molecular docking of FA showed promising Janus kinase 2 (JAK2) inhibition with a docking score of - 6.7, which is comparable with that of ruxolitinib, a standard inhibitor. However, in vitro JAK2 inhibition assay showed a half maximal inhibitory concentration (IC50) of 6.67 ± 0.88 µg/ml. Both doses of FA (25 and 50 mg/kg) significantly attenuated primary (volume of paw edema) and secondary lesions. CFA-induced arthritic rats showed a significant decrease in body weight, A/G ratio, and Hb but showed a greater arthritic index, ESR levels, and percentage of lymphocytes. These alterations were significantly reduced in rats treated with FA and prednisolone. FA also reversed changes to biochemical parameters and inflammatory markers, such as C-reactive protein (CRP) and rhematoid factor (RF). Additionally, we found CFA-induced arthritis triggered the secretion of TNF- α, increased JAK2 levels, and reduced TGF-β levels in tissue homogenates. However, in rats treated with FA, such alterations significantly improved. Thus, our results reveal that FA contains anti-arthritic activity, which is possibly mediated by the inhibition of the JAK/STAT pathway.
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Identification of New Inhibitors with Potential Antitumor Activity from Polypeptide Structures via Hierarchical Virtual Screening. Molecules 2019; 24:molecules24162943. [PMID: 31416180 PMCID: PMC6720962 DOI: 10.3390/molecules24162943] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 08/08/2019] [Accepted: 08/10/2019] [Indexed: 12/12/2022] Open
Abstract
Leukemias are neoplasms that affect hematopoietic cells, which are developed by genetic alterations (mutations) that lead to the loss of proliferation control mechanisms (maturation and/or cell death). The α4β1 integrin receptor is a therapeutic target for inflammation, autoimmune diseases and lymphoid tumors. This study was carried out to search through the antagonists-based virtual screening for α4β1 receptor. Initially, seventeen (17) structures were selected (based on the inhibitory activity values, IC50) and the structure with the best value was chosen as the pivot. The pharmacophoric pattern was determined from the online PharmaGist server and resulted in a model of score value equal to 97.940 with 15 pharmacophoric characteristics that were statistically evaluated via Pearson correlations, principal component analysis (PCA) and hierarchical clustering analysis (HCA). A refined model generated four pharmacophoric hypotheses totaling 1.478 structures set of Zinc_database. After, the pharmacokinetic, toxicological and biological activity predictions were realized comparing with pivot structure that resulted in five (ZINC72088291, ZINC68842860, ZINC14365931, ZINC09588345 and ZINC91247798) structures with optimal in silico predictions. Therefore, future studies are needed to confirm antitumor potential activity of molecules selected this work with in vitro and in vivo assays.
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Desai TH, Joshi SV. In silico evaluation of apoptogenic potential and toxicological profile of triterpenoids. Indian J Pharmacol 2019; 51:181-207. [PMID: 31391686 PMCID: PMC6644186 DOI: 10.4103/ijp.ijp_90_18] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
AIM: Caspases-3 and 8 are key mediators of intrinsic and extrinsic pathway of apoptosis, respectively. Triterpenoids of natural and synthetic origin reported as anticancer agents with apoptotic potential and hence may prove to be good candidates for in silico testing against caspases-3 and 8. MATERIALS AND METHODS: Various naturally-occurring and synthetic triterpenoids were subjected to activity prediction using PASS Online software, and among them, 67 compounds were selected for further processing. Protein structure of caspase-3 (3DEI) and caspase-8 (3KJQ) was obtained from the protein data bank and docked with selected triterpenoids using AutoDock Tools and AutoDock Vina. Toxicological profile was predicted based on clinical manifestations using PASS online software. RESULTS: The high docking score of -10.0, -9.9, -9.8, and -9.5 were shown by friedelin, tingenone, albiziasaponin A, and albiziasaponin C, respectively, for caspase-3, and -11.0, -9.6, -9.6, and -9.4 by β-boswellic acid, bryonolic acid, canophyllic acid, and CDDO, respectively, for caspase-8. Possible adverse events were predicted with varying degree of probability and major relevant effects were reported. Hydrostatic interactions along with formation of hydrogen bonds with specific amino acids in the binding pocket were identified with each triterpenoid. CONCLUSION: Lead molecules identified through this in silico study such as friedelin, tingenone, albiziasaponin, bryonolic acid, and canophyllic acid may be utilized for further in vitro/in vivo studies as apoptotic agents targeting caspases-3 and 8.
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Shaikh IU, Patel RK, Mevada VA, Gupta VK, Jadeja RN. Binary and Ternary Zinc(II) Complexes of Acyl Pyrazolones: Synthesis, Spectroscopic Analysis, Crystal Structure and Antimalarial Activity. ChemistrySelect 2019. [DOI: 10.1002/slct.201901058] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Irfan U. Shaikh
- Department of ChemistryFaculty of ScienceThe M.S. University of Baroda, Vadodara 390 002 India
| | - Rajesh K. Patel
- Department of BioscienceVeer Narmad South Gujarat University Surat- 395007 India
| | - Vishal A. Mevada
- Super Computing FacilityVeer Narmad South Gujarat University Surat- 395007 India
| | - Vivek K. Gupta
- Post-Graduate Department of Physics & ElectronicsUniversity of Jammu Jammu Tawi 180 006 India
| | - Rajendrasinh N. Jadeja
- Department of ChemistryFaculty of ScienceThe M.S. University of Baroda, Vadodara 390 002 India
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Olugbodi JO, Tincho MB, Oguntibeju OO, Olaleye MT, Akinmoladun AC. Glyphaea brevis - In vitro antioxidant and in silico biological activity of major constituents and molecular docking analyses. Toxicol In Vitro 2019; 59:187-196. [PMID: 30998971 DOI: 10.1016/j.tiv.2019.04.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 04/12/2019] [Accepted: 04/12/2019] [Indexed: 11/26/2022]
Abstract
Previous studies have revealed that leaf extracts of Glyphaea brevis possess antioxidant activity but the bioactivity and mechanisms of action of its major constituents remain unknown. This study evaluated in vitro antioxidant and free radical scavenging activities of Glyphaea brevis twigs and leaves, and probable toxicity profile, pharmacological activities and mechanisms of action of major phytoconstituents in silico. Phytochemical screening detected saponins, tannins, steroids, anthraquinones, flavonoids, terpenoids and phenolics in the extracts. HPLC fingerprinting revealed major compounds as ferulic, catechuic and coumaric acids. Twig extract contained more flavanols compared to the leaf extract while the leaf extract had more flavonol content. Extract of the twigs demonstrated higher ORAC, TEAC and FRAP compared to the leaf extract. In silico analyses predicted low acute toxicity risk and pharmacological activities which are in agreement with traditional use of the plant in the management of diseases such as dyspepsia, ulcers, chest pains, diarrhea, dysentery and sleeping sickness. The molecular docking studies revealed that coumaric acid and ferulic acid have the best binding for all proteins tested. In summary, Glyphaea brevis twigs possess higher antioxidant activity than the leaves and major constituents showed low toxicological potential and promising biological activities which support its ethnomedical use.
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Affiliation(s)
- Janet Olayemi Olugbodi
- Phytomedicine, Biochemical Pharmacology and Toxicology Laboratories, Department of Biochemistry, School of Sciences, PMB 704, The Federal University of Technology, Akure, Nigeria; Department of Biochemistry, Bingham University, PMB 005, Karu, Nasarawa State, Nigeria.
| | - Marius Belmondo Tincho
- Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa
| | - Oluwafemi O Oguntibeju
- Phytomedicine and Phytochemistry Group, Oxidative Stress Research Centre, Department of Biomedical Sciences, Faculty of Health & Wellness Sciences, Cape Peninsula University of Technology, P.O. Box1906, Bellville Campus, Bellville 7535, South Africa
| | - Mary Tolulope Olaleye
- Phytomedicine, Biochemical Pharmacology and Toxicology Laboratories, Department of Biochemistry, School of Sciences, PMB 704, The Federal University of Technology, Akure, Nigeria
| | - Afolabi Clement Akinmoladun
- Phytomedicine, Biochemical Pharmacology and Toxicology Laboratories, Department of Biochemistry, School of Sciences, PMB 704, The Federal University of Technology, Akure, Nigeria
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Sirakanyan SN, Spinelli D, Geronikaki A, Kartsev VG, Hakobyan EK, Hovakimyan AA. Synthesis and antimicrobial activity of new derivatives of pyrano[4'',3'':4',5']pyrido[3',2':4,5]thieno[3,2-d]pyrimidine and new heterocyclic systems. SYNTHETIC COMMUN 2019. [DOI: 10.1080/00397911.2019.1595659] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Samvel N. Sirakanyan
- Institute of Fine Organic Chemistry of A.L.Mnjoyan, Scientific Technological Center of Organic and Pharmaceutical Chemistry, National Academy of Sciences of Republic of Armenia, Yerevan, Armenia
| | - Domenico Spinelli
- Dipartimento di Chimica G. Ciamician, Alma Mater Studiorum-Università di Bologna, Bologna, Italy
| | - Athina Geronikaki
- School of Pharmacy, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | | | - Elmira K. Hakobyan
- Institute of Fine Organic Chemistry of A.L.Mnjoyan, Scientific Technological Center of Organic and Pharmaceutical Chemistry, National Academy of Sciences of Republic of Armenia, Yerevan, Armenia
| | - Anush A. Hovakimyan
- Institute of Fine Organic Chemistry of A.L.Mnjoyan, Scientific Technological Center of Organic and Pharmaceutical Chemistry, National Academy of Sciences of Republic of Armenia, Yerevan, Armenia
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Desai TH, Joshi SV. Anticancer activity of saponin isolated from Albizia lebbeck using various in vitro models. JOURNAL OF ETHNOPHARMACOLOGY 2019; 231:494-502. [PMID: 30408535 DOI: 10.1016/j.jep.2018.11.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Revised: 11/02/2018] [Accepted: 11/03/2018] [Indexed: 06/08/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Albizia lebbeck (L.) Benth. (Family: Mimosaceae) is commonly known as Sirisha in Sanskrit. The leaves and pods of A. lebbeck were claimed to be used against cancer in traditional medicine. Previous studies using bark, leaves, seeds and pods of A. lebbeck showed cytotoxic activity against hepatic, colon, larynx, cervical and breast cancer cell lines. AIM OF THE STUDY To evaluate the anticancer activity of saponin rich fraction of Albizia lebbeck by using various in vitro models. MATERIALS AND METHODS Albiziasaponins (A-E) are oleanene triterpene presents in Albizia lebbeck were used for in silico studies. In silico testing of albiziasaponins for structure based pharmacological activity prediction using PASS Online software and docking with Autodock tool and Autodock Vina revels it's anticancer and apoptogenic potential. Antiproliferative activity of saponin rich fraction of A. lebbeck was performed using MCF-7 human breast cancer cells by MTT assay methods. Anti-angiogenic property of saponin rich fraction of A. lebbeck was evaluated in in vitro shell less chick embryo cultures with different concentrations (0.1 µg/ml, 0.5 µg/ml, and 1 µg/ml) by using ImageJ software. In vitro cultured lymphocytes chromosomal aberration assay was performed to determine the physical integrity of chromosomes in cells and effect of saponin rich fraction of A. lebbeck on cell cycle. Apoptogenic potential was evaluated using Caspases-3 and Caspase-8 ELISA assay in MCF-7 cells. RESULTS Result of MTT assay showed IC50 of saponin rich fraction of A. lebbeck at 1 μg/ml in MCF-7 cells. Treatment with saponin rich fraction of A. lebbeck significantly (p < 0.05) reduced angiogenic parameters. Significant chromosomal aberrations (hypodiploid, hyperdiploid, ring, premature separation, Dicentric fragments, Acentric fragment, chromatid break, and chromosomal gap) were observed in saponin rich fraction of A. lebbeck treated groups. Treatment with saponin rich fraction of A. lebbeck increased levels of Caspases-3 (optical density of 0.24 at 450 nm) and Caspase-8 (optical density of 0.31 at 450 nm) as compared to staurosporine (optical density of 2.47 and 2.65 for caspases-3 and -8 respectively at 450 nm). CONCLUSION In our study, saponin rich fraction of A. lebbeck showed antiproliferative, antiangiogenic and apoptogenic potential using various in-vitro models. It also found to increase chromosomal aberration and thereby may affect cell cycle.
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Affiliation(s)
- Tanvi H Desai
- Maliba Pharmacy College, Bardoli, Surat, Gujarat, India.
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Abstract
Drugs modulate disease states through their actions on targets in the body. Determining these targets aids the focused development of new treatments, and helps to better characterize those already employed. One means of accomplishing this is through the deployment of in silico methodologies, harnessing computational analytical and predictive power to produce educated hypotheses for experimental verification. Here, we provide an overview of the current state of the art, describe some of the well-established methods in detail, and reflect on how they, and emerging technologies promoting the incorporation of complex and heterogeneous data-sets, can be employed to improve our understanding of (poly)pharmacology.
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Affiliation(s)
- Ryan Byrne
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Zurich, Switzerland
| | - Gisbert Schneider
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Zurich, Switzerland.
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