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Özay B, Tükel EY, Ayna Duran G, Kiraz Y. Identification of potential inhibitors for drug resistance in acute lymphoblastic leukemia through differentially expressed gene analysis and in silico screening. Anal Biochem 2024; 694:115619. [PMID: 39025197 DOI: 10.1016/j.ab.2024.115619] [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: 05/13/2024] [Revised: 07/11/2024] [Accepted: 07/13/2024] [Indexed: 07/20/2024]
Abstract
Acute lymphoblastic leukemia (ALL) is a disease of lymphocyte origin predominantly diagnosed in children. While its 5-year survival rate is high, resistance to chemotherapy drugs is still an obstacle. Our aim is to determine differentially expressed genes (DEGs) related to Asparaginase, Daunorubicin, Prednisolone, and Vincristine resistance and identify potential inhibitors via docking. Three datasets were accessed from the Gene Expression Omnibus database; GSE635, GSE19143, and GSE22529. The microarray data was analyzed using R4.2.0 and Bioconductor packages, and pathway and protein-protein interaction analysis were performed. We identified 1294 upregulated DEGs, with 12 genes consistently upregulated in all four resistant groups. KEGG analysis revealed an association with the PI3K-Akt pathway. Among DEGs, 33 hub genes including MDM2 and USP7 were pinpointed. Within common genes, CLDN9 and HS3ST3A1 were subjected to molecular docking against 3556 molecules. Following ADMET analysis, three drugs emerged as potential inhibitors: Flunarizine, Talniflumate, and Eltrombopag. Molecular dynamics analysis for HS3ST3A1 indicated all candidates had the potential to overcome drug resistance, Eltrombopag displaying particularly promising results. This study promotes a further understanding of drug resistance in ALL, introducing novel genes for consideration in diagnostic screening. It also presents potential inhibitor candidates to tackle drug resistance through repurposing.
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Affiliation(s)
- Başak Özay
- İzmir University of Economics, Faculty of Engineering, Department of Genetics and Bioengineering, 35330, Balçova, Izmir, Turkey
| | - Ezgi Yağmur Tükel
- İzmir University of Economics, Faculty of Engineering, Department of Genetics and Bioengineering, 35330, Balçova, Izmir, Turkey
| | - Gizem Ayna Duran
- İzmir University of Economics, Faculty of Engineering, Department of Biomedical Engineering, 35330, Balçova, Izmir, Turkey
| | - Yağmur Kiraz
- İzmir University of Economics, Faculty of Engineering, Department of Genetics and Bioengineering, 35330, Balçova, Izmir, Turkey.
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2
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Wahyuni DK, Junairiah J, Rosyanti C, Kharisma VD, Syukriya AJ, Rahmawati CT, Purkan P, Subramaniam S, Prasongsuk S, Purnobasuki H. Computational and in vitro analyses of the antibacterial effect of the ethanolic extract of Pluchea indica L. leaves. Biomed Rep 2024; 21:137. [PMID: 39129835 PMCID: PMC11310492 DOI: 10.3892/br.2024.1825] [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: 03/21/2024] [Accepted: 06/19/2024] [Indexed: 08/13/2024] Open
Abstract
The most common gram-negative, Escherichia coli, and gram-positive bacteria, Bacillus spp., have evolved different mechanisms that have caused the emergence of multi-drug resistance. As a result, drugs that block the bacterial growth cycle are needed. Here, in silico and in vitro studies were performed to assess compounds in the Pluchea indica leaf extract, a medicinal plant, that can inhibit bacterial proteins. Briefly, P. indica leaves were extracted using ethanol. The crude extract was then subjected to gas chromatography-mass spectrometry for metabolite screening. Molecular docking simulations with rhomboid protease (Rpro) (Protein data bank ID number: 3ZMI from E. coli and filamenting temperature-sensitive mutant Z (FtsZ) protein data bank ID number: 2VAM from Bacillus subtilis were performed. Moreover, the well diffusion method was used to confirm the antibacterial activity of P. indica leaf extract. A total of 10 compounds were identified in the P. indica extract and used for computational analysis. Based on drug-likeness prediction, P. indica compounds may be drug-like molecules. Binding affinity tests indicated that 10,10-Dimethyl-2,6-dimethylenebicyclo(7.2.0)undecan-5.β.-ol and 11,11-Dimethyl-4,8-dimethylenebicyclo(7.2.0)undecan-3-ol had the most negative values. Accordingly, these compounds may be potential ligands that bind to bacterial proteins. The root mean square fluctuation values was <2 Å, indicating stable fluctuation binding for the ligand-protein complex. According to in vitro antibacterial assays, a high concentration (50%) of the P. indica extract markedly inhibited E. coli and B. subtilis, with inhibitory zone diameters of 31.86±1.63 and 21.09±0.09 mm, respectively. Overall, the compounds in the P. indica leaf extract were identified as functional inhibitors of E. coli and B. subtilis proteins via in silico analysis. This may facilitate development of antibacterial agents.
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Affiliation(s)
- Dwi Kusuma Wahyuni
- Department of Biology, Faculty of Science and Technology, Universitas Airlangga, Surabaya, East Java 60115, Indonesia
- Center of Excellence in Plant Biodiversity and Biotechnology, Department of Biology, Faculty of Science and Technology, Universitas Airlangga, Surabaya, East Java 60115, Indonesia
| | - Junairiah Junairiah
- Department of Biology, Faculty of Science and Technology, Universitas Airlangga, Surabaya, East Java 60115, Indonesia
- Center of Excellence in Plant Biodiversity and Biotechnology, Department of Biology, Faculty of Science and Technology, Universitas Airlangga, Surabaya, East Java 60115, Indonesia
| | - Chery Rosyanti
- Department of Biology, Faculty of Science and Technology, Universitas Airlangga, Surabaya, East Java 60115, Indonesia
| | - Viol Dhea Kharisma
- Department of Biology, Faculty of Science and Technology, Universitas Airlangga, Surabaya, East Java 60115, Indonesia
| | - Alvi Jauharotus Syukriya
- Department of Biology, Faculty of Science and Technology, Universitas Airlangga, Surabaya, East Java 60115, Indonesia
| | - Cici Tya Rahmawati
- Department of Biology, Faculty of Science and Technology, Universitas Airlangga, Surabaya, East Java 60115, Indonesia
| | - Purkan Purkan
- Department of Chemistry, Faculty of Science and Technology, Universitas Airlangga, Surabaya, East Java 60115, Indonesia
| | - Sreeramanan Subramaniam
- Department of Biology, Faculty of Science and Technology, Universitas Airlangga, Surabaya, East Java 60115, Indonesia
- School of Biological Science, Universiti Sains Malaysia, Georgetown 11800, Malaysia
- Centre for Chemical Biology, Universiti Sains Malaysia (USM), Bayan Lepas, 11900, Penang, Malaysia
| | - Sehanat Prasongsuk
- Plant Biomass Utilization Research Unit, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Hery Purnobasuki
- Department of Biology, Faculty of Science and Technology, Universitas Airlangga, Surabaya, East Java 60115, Indonesia
- Center of Excellence in Plant Biodiversity and Biotechnology, Department of Biology, Faculty of Science and Technology, Universitas Airlangga, Surabaya, East Java 60115, Indonesia
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3
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Ahmad F, Gupta A, Marzook H, Woodgett JR, Saleh MA, Qaisar R. Natural compound screening predicts novel GSK-3 isoform-specific inhibitors. Biochimie 2024; 225:68-80. [PMID: 38723940 DOI: 10.1016/j.biochi.2024.05.002] [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: 02/11/2024] [Revised: 04/21/2024] [Accepted: 05/02/2024] [Indexed: 05/24/2024]
Abstract
Glycogen synthase kinase-3 (GSK-3) plays important roles in the pathogenesis of cardiovascular, metabolic, neurological disorders and cancer. Isoform-specific loss of either GSK-3α or GSK-3β often provides cytoprotective effects under such clinical conditions. However, available synthetic small molecule inhibitors are relatively non-specific, and their chronic use may lead to adverse effects. Therefore, screening for natural compound inhibitors to identify the isoform-specific inhibitors may provide improved clinical utility. Here, we screened 70 natural compounds to identify novel natural GSK-3 inhibitors employing comprehensive in silico and biochemical approaches. Molecular docking and pharmacokinetics analysis identified two natural compounds Psoralidin and Rosmarinic acid as potential GSK-3 inhibitors. Specifically, Psoralidin and Rosmarinic acid exhibited the highest binding affinities for GSK-3α and GSK-3β, respectively. Consistent with in silico findings, the kinase assay-driven IC50 revealed superior inhibitory effects of Psoralidin against GSK-3α (IC50 = 2.26 μM) vs. GSK-3β (IC50 = 4.23 μM) while Rosmarinic acid was found to be more potent against GSK-3β (IC50 = 2.24 μM) than GSK-3α (IC50 = 5.14 μM). Taken together, these studies show that the identified natural compounds may serve as GSK-3 inhibitors with Psoralidin serving as a better inhibitor for GSK-3α and Rosmarinic for GSK-3β isoform, respectively. Further characterization employing in vitro and preclinical models will be required to test the utility of these compounds as GSK-3 inhibitors for cardiometabolic and neurological disorders and cancers.
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Affiliation(s)
- Firdos Ahmad
- Department of Basic Medical Sciences, College of Medicine, University of Sharjah, Sharjah, 27272, United Arab Emirates; Cardiovascular Research Group, Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, 27272, United Arab Emirates; Space Medicine Research Group, Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, 27272, United Arab Emirates.
| | - Anamika Gupta
- Cardiovascular Research Group, Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Hezlin Marzook
- Cardiovascular Research Group, Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - James R Woodgett
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - Mohamed A Saleh
- Cardiovascular Research Group, Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, 27272, United Arab Emirates; Department of Pharmacology and Toxicology, Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt; Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Rizwan Qaisar
- Department of Basic Medical Sciences, College of Medicine, University of Sharjah, Sharjah, 27272, United Arab Emirates; Cardiovascular Research Group, Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, 27272, United Arab Emirates; Space Medicine Research Group, Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, 27272, United Arab Emirates
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Mohammed EZ, El-Dydamony NM, Taha EA, Taha MN, Mehany ABM, Abdel Aziz HA, Abd El-Aleam RH. Design, synthesis, and molecular dynamic simulations of some novel benzo[d]thiazoles with anti-virulence activity against Pseudomonas aeruginosa. Eur J Med Chem 2024; 279:116880. [PMID: 39303517 DOI: 10.1016/j.ejmech.2024.116880] [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: 07/17/2024] [Revised: 09/02/2024] [Accepted: 09/12/2024] [Indexed: 09/22/2024]
Abstract
Inhibition of quorum sensing (QS) is an impending approach for targeting bacterial infection. Fourteen benzo[d]thiazole and 2-pyrazolo[1,5-a]pyrimidin-3-yl)benzo[d]thiazoles analogues were designed and synthesized as promising LasR antagonists with QS inhibition activity. Among the investigated compounds, compounds 3c, 3e, and 8d exhibited the highest percentage inhibition in biofilm formation (77 %, 63.9 %, 69.4 %), pyocyanin production (74.6 %, 64.9, 69.4 %), and rhamnolipids production (58.5 %, 51 %, 54.3 %) in P. aeruginosa, respectively. Additionally, compounds 3c, 3e and 8d achieved IC50 values against Las R equal 1.37 ± 0.35, 1.55 ± 0.24, 1.1 ± 0.15 μM respectively. Also, molecular docking of the target compounds into the LasR binding site co-crystalized "odDHL" revealed their binding with the essential residues for protein inhibition. Additionally, molecular dynamics simulation (MDS) experiments over 200 ns of compound 3c showed its ability to interact with the LasR binding site with dissociation of the protein's dimer confirming its action as a LasR antagonist. The obtained findings inspire further investigation for benzo[d]thiazole and 2-pyrazolo[1,5-a]pyrimidin-3-yl)benzo[d]thiazoles aiming to design and synthesize more potential QS inhibitors.
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Affiliation(s)
- Esraa Z Mohammed
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, October 6 University, Giza, 12585, Egypt.
| | - Nehad M El-Dydamony
- Pharmaceutical Chemistry Department, College of Pharmaceutical Sciences and Drug Manufacturing, Misr University for Science and Technology, 6th of October City, Egypt
| | - Enas A Taha
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, October 6 University, Giza, 12585, Egypt
| | - Mostafa N Taha
- Microbiology and Immunology Department, Faculty of Pharmacy, Nahda University, Beni-Suef, Egypt
| | - Ahmed B M Mehany
- Zoology Department, Faculty of Science, Al-Azhar University, Cairo, Egypt
| | - Hatem A Abdel Aziz
- Applied Organic Chemistry Department, National Research Centre, Dokki, Giza, P.O.Box 12622, Egypt; Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Pharos University in Alexandria, Canal El Mahmoudia St., Alexandria, 21648, Egypt.
| | - Rehab H Abd El-Aleam
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Modern University for Technology and Information MTI, Cairo, 11571, Egypt
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5
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Batool Z, Ullah S, Khan A, Siddique F, Nadeem S, Alshammari A, Albekairi NA, Talib R, Al-Harrasi A, Shafiq Z. Design, synthesis, and in vitro and in silico study of 1-benzyl-indole hybrid thiosemicarbazones as competitive tyrosinase inhibitors. RSC Adv 2024; 14:28524-28542. [PMID: 39247501 PMCID: PMC11378339 DOI: 10.1039/d4ra05015k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2024] [Accepted: 08/30/2024] [Indexed: 09/10/2024] Open
Abstract
Developing new anti-tyrosinase drugs seems crucial for the medical and industrial fields since irregular melanin synthesis is linked to the resurgence of several skin conditions, including melanoma, and the browning of fruits and vegetables. A novel series of N-1 and C-3 substituted indole-based thiosemicarbazones 5(a-r) are synthesized and further analyzed for their inhibition potential against tyrosinase enzyme through in vitro assays. The synthesized compounds displayed very good to moderate inhibition with half maximal inhibitory concentration in the range of 12.40 ± 0.26 μM to 47.24 ± 1.27 μM. Among all the derivatives 5k displayed the highest inhibitory activity. According to SAR analysis, the derivatives with 4-substitution at the benzyl or phenyl ring of the thiosemicarbazones exhibited better inhibitory potential against tyrosinase. In silico analysis (including ADMET prediction and molecular docking) was conducted and compared with the standard drug (kojic acid). These findings may help the hunt for new melanogenesis inhibitors that the food and cosmetics industries may find valuable.
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Affiliation(s)
- Zahra Batool
- Institute of Chemical Sciences, Bahauddin Zakariya University Multan-60800 Pakistan
| | - Saeed Ullah
- Natural and Medical Sciences Research Centre, University of Nizwa P.O. Box 33, PC 616, Birkat Al Mauz Nizwa Sultanate of Oman
| | - Ajmal Khan
- Natural and Medical Sciences Research Centre, University of Nizwa P.O. Box 33, PC 616, Birkat Al Mauz Nizwa Sultanate of Oman
- Department of Chemical and Biological Engineering, College of Engineering, Korea University 145 Anam-ro, Seongbuk-gu Seoul 02841 Republic of Korea
| | - Farhan Siddique
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Bahauddin Zakariya University Multan-60800 Pakistan
| | - Sumaira Nadeem
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Bahauddin Zakariya University Multan-60800 Pakistan
- Department of Pharmacy, The Women University Multan 60000 Pakistan
| | - Abdulrahman Alshammari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University Post bezBox 2455 Riyadh 11451 Saudi Arabia
| | - Norah A Albekairi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University Post bezBox 2455 Riyadh 11451 Saudi Arabia
| | - Rimsha Talib
- Institute of Chemical Sciences, Bahauddin Zakariya University Multan-60800 Pakistan
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Centre, University of Nizwa P.O. Box 33, PC 616, Birkat Al Mauz Nizwa Sultanate of Oman
| | - Zahid Shafiq
- Institute of Chemical Sciences, Bahauddin Zakariya University Multan-60800 Pakistan
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Khan MKA, Alouffi S, Ahmad S. Identifying potential inhibitors of C-X-C motif chemokine ligand10 against vitiligo: structure-based virtual screening, molecular dynamics simulation, and principal component analysis. J Biomol Struct Dyn 2024; 42:8045-8062. [PMID: 37565326 DOI: 10.1080/07391102.2023.2242952] [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: 09/09/2022] [Accepted: 07/26/2023] [Indexed: 08/12/2023]
Abstract
The research aims to envisage small molecule inhibitors targeting the C-X-C motif chemokine ligand 10 (CXCL10) of the JAK/STAT pathway. CXCL10 plays a significant role in inducing auto-immunity in vitiligo through JAK/STAT pathway. To accomplish the aim, structure-based virtual screening with fundamental search limits, e.g., molecular weight (MW ≤ 500 Da), hydrogen bond donor (HBD ≤ 5), hydrogen bond acceptor (HBA ≤ 10), and lipophilicity (logP ≤ 5) was used to screen investigational molecules from MCULE database. The SBVS-ligand hits were sifted through toxicity profiling followed by filtration through the Brain or IntestinaL EstimateD-Egg model to check the human intestinal abortion and blood-brain barrier permeation based on two physicochemical properties, including topological surface area and WLOGP. The BOILED-Egg filtered compounds were passed through drug-likeness features other than Pfizer's Lipinski rule of five, viz., Ghose filters, Muegge filters, Egan parameters, and Veber filters, followed by medicinal chemistry's pan assay interference structure and Brenk alert investigation. Chemical compounds that comply with the above ADME descriptors were docked with target protein CXCL10 via AutoDock Vina. The stability of the top two ligand hits was assessed through dynamics simulations of 100 ns and principal component analysis and compared with the reference drugs Baicalein and EGCG. Based on the findings of Gibbs free energy of binding, ADME profiling, medicinal chemistry attributes depiction, root-mean-square deviation, root-mean-square fluctuation, solvent accessible surface area, the free energy of solvation, the radius of gyration, and PCA, MCULE2726078782-0-2 was found better than potential reference drug Baicalein.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Sultan Alouffi
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, University of Hail, Hail, Saudi Arabia
| | - Saheem Ahmad
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, University of Hail, Hail, Saudi Arabia
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Dil KV, Palchykov VA. O,S,Se-containing Biginelli products based on cyclic β-ketosulfone and their postfunctionalization. Beilstein J Org Chem 2024; 20:2143-2151. [PMID: 39224228 PMCID: PMC11368051 DOI: 10.3762/bjoc.20.184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Accepted: 08/13/2024] [Indexed: 09/04/2024] Open
Abstract
A one-pot three-component Biginelli synthesis of dihydropyrimidinones/thiones/selenones via acetic acid or solvent-free Yb(OTf)3-catalyzed tandem reaction of β-ketosulfone (dihydro-2H-thiopyran-3(4H)-one-1,1-dioxide), an appropriate urea, and arylaldehyde has been developed. The reaction proceeds with high chemo- and regioselectivity to give diverse DHPMs in reasonable yields up to 95%. Moreover, an SO2-containing analogue of anticancer drug-candidate enastron (SO2 vs C=O) was obtained by using the here reported method in gram scale. We also demonstrate the reactivity of the Biginelli product in various directions - synthesis of condensed thiazoles and tetrazoles. In silico assessment of ADMET parameters shows that most compounds meet the lead-likeness requirements. The biological profiles of new compounds demonstrate high probability levels of activity against the following pathogens/diseases: Candida albicans, Alphis gossypii, Tripomastigote Chagas, Tcruzi amastigota, Tcruzi epimastigota, Leishmania amazonensis, and Dengue larvicida.
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Affiliation(s)
- Kateryna V Dil
- Research Institute of Chemistry and Geology, Oles Honchar Dnipro National University, Nauky Av. 72, Dnipro, 49045, Ukraine
- Enamine Ltd. (www.enamine.net), Winston Churchill Str. 78, Kyiv, 02094, Ukraine
| | - Vitalii A Palchykov
- Research Institute of Chemistry and Geology, Oles Honchar Dnipro National University, Nauky Av. 72, Dnipro, 49045, Ukraine
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Stefanes NM, de Oliveira Silva L, Walter LO, Steimbach JV, Markendorf E, Ribeiro AAB, Feuser PE, Cordeiro AP, Santos-Silva MC. Sodium diethyldithiocarbamate trihydrate: an effective and selective compound for hematological malignancies. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024:10.1007/s00210-024-03399-8. [PMID: 39186189 DOI: 10.1007/s00210-024-03399-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Accepted: 08/18/2024] [Indexed: 08/27/2024]
Abstract
Myeloid leukemias and lymphomas are among the most common and well-studied hematological malignancies. However, due to the aggressiveness and rapid progression of certain subtypes, treating these diseases remains a challenge. Considering the promising results of diethyldithiocarbamates in preclinical and clinical oncology trials, this study aimed to investigate the potential of sodium diethyldithiocarbamate trihydrate (DETC) as a prototype for developing new drugs to treat hematological malignancies. In silico analysis using SwissADME was conducted to evaluate the physicochemical characteristics and pharmacokinetic properties of DETC. An in vitro investigation utilizing the MTT assay assessed the cytotoxic effects of DETC on neoplastic and non-neoplastic cell lines. Selectivity was determined using a selectivity index and a hemolysis assay, while the mechanism of cell death in neoplastic cell lines was examined through flow cytometry analysis of pro-apoptotic and anti-apoptotic protein levels. The results demonstrated that the physicochemical characteristics of DETC are suitable for oral administration. Furthermore, the compound showed promising cytotoxic activity against human myeloid leukemia (K562) and Burkitt's lymphoma (Daudi) cell lines, with high selectivity for neoplastic cells over non-neoplastic cells of the bone marrow microenvironment (HS-5 cell line). Moreover, hemolysis was observed only at very high concentrations. The cytotoxicity mechanism of DETC against both neoplastic cell lines involved cell cycle arrest and the production of reactive oxygen species. In K562 cells, cell death was induced via apoptosis. Additional experiments are needed to confirm the exact mechanism of cell death in Daudi Burkitt's lymphoma cells.
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Affiliation(s)
- Natália Marcéli Stefanes
- Experimental Oncology and Hemopathies Laboratory, Department of Clinical Analysis, Health Sciences Center, Federal University of Santa Catarina, Florianópolis, 88040-900, SC, Brazil
- Graduate Program in Pharmacy, Health Sciences Center, Federal University of Santa Catarina, Florianópolis, 88040-900, SC, Brazil
| | - Lisandra de Oliveira Silva
- Experimental Oncology and Hemopathies Laboratory, Department of Clinical Analysis, Health Sciences Center, Federal University of Santa Catarina, Florianópolis, 88040-900, SC, Brazil
- Graduate Program in Pharmacy, Health Sciences Center, Federal University of Santa Catarina, Florianópolis, 88040-900, SC, Brazil
| | - Laura Otto Walter
- Experimental Oncology and Hemopathies Laboratory, Department of Clinical Analysis, Health Sciences Center, Federal University of Santa Catarina, Florianópolis, 88040-900, SC, Brazil
- Graduate Program in Pharmacy, Health Sciences Center, Federal University of Santa Catarina, Florianópolis, 88040-900, SC, Brazil
| | - João Vitor Steimbach
- Experimental Oncology and Hemopathies Laboratory, Department of Clinical Analysis, Health Sciences Center, Federal University of Santa Catarina, Florianópolis, 88040-900, SC, Brazil
- Graduate Program in Pharmacy, Health Sciences Center, Federal University of Santa Catarina, Florianópolis, 88040-900, SC, Brazil
| | - Emanueli Markendorf
- Experimental Oncology and Hemopathies Laboratory, Department of Clinical Analysis, Health Sciences Center, Federal University of Santa Catarina, Florianópolis, 88040-900, SC, Brazil
| | - Amanda Abdalla Biasi Ribeiro
- Experimental Oncology and Hemopathies Laboratory, Department of Clinical Analysis, Health Sciences Center, Federal University of Santa Catarina, Florianópolis, 88040-900, SC, Brazil
- Graduate Program in Pharmacy, Health Sciences Center, Federal University of Santa Catarina, Florianópolis, 88040-900, SC, Brazil
| | - Paulo Emílio Feuser
- Graduate Program in Chemical Engineering, Technological Center, Federal University of Santa Catarina, Florianópolis, 88040-900, SC, Brazil
| | - Arthur Poester Cordeiro
- Graduate Program in Chemical Engineering, Technological Center, Federal University of Santa Catarina, Florianópolis, 88040-900, SC, Brazil
| | - Maria Cláudia Santos-Silva
- Experimental Oncology and Hemopathies Laboratory, Department of Clinical Analysis, Health Sciences Center, Federal University of Santa Catarina, Florianópolis, 88040-900, SC, Brazil.
- Graduate Program in Pharmacy, Health Sciences Center, Federal University of Santa Catarina, Florianópolis, 88040-900, SC, Brazil.
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Kalasin S, Surareungchai W. Artificial intelligence-aiding lab-on-a-chip workforce designed oral [3.1.0] bi and [4.2.0] tricyclic catalytic interceptors inhibiting multiple SARS-CoV-2 protomers assisted by double-shell deep learning. RSC Adv 2024; 14:26897-26910. [PMID: 39193274 PMCID: PMC11347926 DOI: 10.1039/d4ra03965c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Accepted: 08/20/2024] [Indexed: 08/29/2024] Open
Abstract
While each massive pandemic has claimed the lives of millions of vulnerable populations over the centuries, one limitation exists: that the Edisonian approach (human-directed with trial errors) relies on repurposing pharmaceuticals, designing drugs, and herbal remedies with the violation of Lipinski's rule of five druglikeness. It may lead to adverse health effects with long-term health multimorbidity. Nevertheless, declining birth rates and aging populations will likely cause a shift in society due to a shortage of a scientific workforce to defend against the next pandemic incursion. The challenge of combating the ongoing post-COVID-19 pandemic has been exacerbated by the lack of gold standard drugs to deactivate multiple SARS-CoV-2 protein targets. Meanwhile, there are three FDA-approved antivirals, Remdesivir, Molnupiravir, and Paxlovid, with moderate clinical efficacy and drug resistance. There is a pressing need for additional antivirals and prepared omics technology to combat the current and future devastating coronavirus pandemics. While there is a limitation of existing contemporary inhibitors to deactivate viral RNA replication with minimal rotational bonds, one strategy is to create Lipinski inhibitors with less than 10 rotational bonds and precise halogen bond placement to destabilize multiple viral protomers. This work describes the efforts to design gold-standard oral inhibitors of bi- and tri-cyclic catalytic interceptors with electrophilic heads using double-shell deep learning. Here, KS1 with and KS2 compounds designed by lab-on-a-chip technology attain 5-fold novel filtered-Lipinski, GHOSE, VEBER, EGAN, and MUEGGE druglikeness. The graph neural network (GNN) relies on module-initiation, expansion, relabeling atom index, and termination (METORITE) iterations, while the deep neural network (DNN) engages pinning, extraction, convolution, pooling, and flattening (PROOF) operations. The cyclic compound's specific halogen atom location enhances the nitrile catalytic head, which deactivates several viral protein targets. Initiating this lab-on-a-chip that is not susceptible to the aging process for creating clinical compounds can leverage a new path to many valuable drugs with speedy oral drug discovery, especially to defend the loss of vulnerable population and prevent multimorbidity that is susceptible to hidden viral persistence in the continuing aging times.
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Affiliation(s)
- Surachate Kalasin
- Faculty of Science and Nanoscience & Nanotechnology Graduate Program, King Mongkut's University of Technology Thonburi 10140 Thailand
| | - Werasak Surareungchai
- Faculty of Science and Nanoscience & Nanotechnology Graduate Program, King Mongkut's University of Technology Thonburi 10140 Thailand
- Pilot Plant Research and Development Laboratory, King Mongkut's University of Technology Thonburi 10150 Bangkok Thailand
- School of Bioresource and Technology, King Mongkut's University of Technology Thonburi 10150 Bangkok Thailand
- Analytical Sciences and National Doping Test Institute, Mahidol University Bangkok 10400 Thailand
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10
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Soni S, Teli S, Teli P, Manhas A, Jha PC, Agarwal S. Highly efficient synthesis of isoxazolones and pyrazolones using g-C 3N 4·OH nanocomposite with their in silico molecular docking, pharmacokinetics and simulation studies. Sci Rep 2024; 14:19123. [PMID: 39155360 PMCID: PMC11330972 DOI: 10.1038/s41598-024-70071-9] [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: 04/15/2024] [Accepted: 08/12/2024] [Indexed: 08/20/2024] Open
Abstract
An environmentally friendly, versatile multicomponent reaction for synthesizing isoxazol-5-one and pyrazol-3-one derivatives has been developed, utilizing a freshly prepared g-C3N4·OH nanocomposite as a highly efficient catalyst at room temperature in aqueous environment. This innovative approach yielded all the desired products with exceptionally high yields and concise reaction durations. The catalyst was well characterized by FT-IR, XRD, SEM, EDAX, and TGA/DTA studies. Notably, the catalyst demonstrated outstanding recyclability, maintaining its catalytic efficacy over six consecutive cycles without any loss. The sustainability of this methodology was assessed through various eco-friendly parameters, including E-factor and eco-score, confirming its viability as a green synthetic route in organic chemistry. Additionally, the gram-scale synthesis verifies its potential for industrial applications. The ten synthesized compounds were also analyzed via a PASS online tool to check their several pharmacological activities. The study is complemented by in silico molecular docking, pharmacokinetics, and molecular dynamics simulation studies. These studies discover 5D as a potential candidate for drug development, supported by its favorable drug-like properties, ADMET studies, docking interaction, and stable behavior in the protein binding cavity.
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Affiliation(s)
- Shivani Soni
- Synthetic Organic Chemistry Laboratory, Department of Chemistry, MLSU, Udaipur, Rajasthan, 313001, India
| | - Sunita Teli
- Synthetic Organic Chemistry Laboratory, Department of Chemistry, MLSU, Udaipur, Rajasthan, 313001, India
| | - Pankaj Teli
- Synthetic Organic Chemistry Laboratory, Department of Chemistry, MLSU, Udaipur, Rajasthan, 313001, India
| | - Anu Manhas
- Department of Chemistry, School of Energy Technology, Pandit Deendayal Energy University, Gandhinagar, 382426, India
| | - Prakash C Jha
- School of Applied Material Sciences, Central University of Gujarat, Gandhinagar, 382030, India
| | - Shikha Agarwal
- Synthetic Organic Chemistry Laboratory, Department of Chemistry, MLSU, Udaipur, Rajasthan, 313001, India.
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11
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Osman EO, Khalil NA, Magdy A, El-Dash Y. New pyrazole-pyridazine hybrids as selective COX-2 inhibitors: design, synthesis, molecular docking, in silico studies and investigation of their anti-inflammatory potential by evaluation of TNF-α, IL-6, PGE-2 and NO in LPS-induced RAW264.7 macrophages. RSC Med Chem 2024; 15:2692-2708. [PMID: 39149111 PMCID: PMC11324043 DOI: 10.1039/d4md00135d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 05/14/2024] [Indexed: 08/17/2024] Open
Abstract
Hybrid-based design has gained significant interest in the development of novel active substances with anti-inflammatory properties. In this study, two series of new pyrazole-pyridazine-based hybrids, 5a-f and 6a-f, were designed and synthesized. Molecules containing pyrazole and pyridazine pharmacophores in a single molecule, each with a unique mechanism of action and different pharmacological characteristics, are believed to exert higher biological activity. The cell viability of all compounds was evaluated using MTT assay in LPS-induced RAW264.7 macrophages. In vitro COX-1 and COX-2 inhibition assays were performed for the investigation of the anti-inflammatory activity of target compounds. Trimethoxy derivatives 5f and 6f were the most active candidates, demonstrating higher COX-2 inhibitory action than celecoxib, with IC50 values of 1.50 and 1.15 μM, respectively. Bromo derivative 6e demonstrated a COX-2 inhibitory activity comparable to celecoxib. Further, the ability of compounds 5f, 6e, and 6f to inhibit the generation of specific pro-inflammatory cytokines and mediators, including nitric oxide (NO), tumor necrosis factor-α (TNF-α), interleukin-6 (IL-6) and prostaglandin-E2 (PGE-2), in RAW264.7 macrophages stimulated by LPS was also estimated. Compounds 5f and 6f demonstrated the most potent activity. Morover, according to the investigation using molecular modeling studies, derivatives 5f and 6f showed respectable binding affinity towards the COX-2 active site compared to the reference ligand. Moreover, the ADME parameters, physicochemical characteristics, pharmacokinetic characteristics, and l of the most potent compounds were also computed.
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Affiliation(s)
- Eman O Osman
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Cairo University 33 Kasr El-Aini Street Cairo 11562 Egypt +20 2023635140 +20 2023639307
| | - Nadia A Khalil
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Cairo University 33 Kasr El-Aini Street Cairo 11562 Egypt +20 2023635140 +20 2023639307
| | - Alaa Magdy
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Cairo University 33 Kasr El-Aini Street Cairo 11562 Egypt +20 2023635140 +20 2023639307
| | - Yara El-Dash
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Cairo University 33 Kasr El-Aini Street Cairo 11562 Egypt +20 2023635140 +20 2023639307
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12
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Delogu GL, Bengala M, Matos MJ, Crucitti D, Sogos V, Era B, Fais A. A New Class of Benzo[ b]thiophene-chalcones as Cholinesterase Inhibitors: Synthesis, Biological Evaluation, Molecular Docking and ADME Studies. Molecules 2024; 29:3748. [PMID: 39202830 PMCID: PMC11356821 DOI: 10.3390/molecules29163748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Revised: 08/01/2024] [Accepted: 08/03/2024] [Indexed: 09/03/2024] Open
Abstract
In this study, heterocyclic compounds containing a benzothiophene scaffold were designed and synthetized, and their inhibitory activity against cholinesterases (ChE) and the viability of SH-SY5Y cells have been evaluated. Benzothiophenes 4a-4i and benzothiophene-chalcone hybrids 5a-5i were tested against both acetylcholinesterase (AChE) and butyrylcholinesterase (BChE), revealing interesting structure-activity relationships. In general, benzothiophene-chalcone hybrids from series 5 proved to be better inhibitors of both enzymes, with compound 5f being the best AChE inhibitor (IC50 = 62.10 μM) and compound 5h being the best BChE inhibitor (IC50 = 24.35 μM), the last one having an IC50 similar to that of galantamine (IC50 = 28.08 μM), the reference compound. The in silico ADME profile of the compounds was also studied. Molecular docking calculations were carried out to analyze the best binding scores and to elucidate enzyme-inhibitors' interactions.
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Affiliation(s)
- Giovanna Lucia Delogu
- Department of Live and Environmental Sciences, University of Cagliari, Cittadella Universitaria, SS 554, Km 4.5, 09042 Monserrato, Italy; (M.B.); (B.E.); (A.F.)
| | - Michela Bengala
- Department of Live and Environmental Sciences, University of Cagliari, Cittadella Universitaria, SS 554, Km 4.5, 09042 Monserrato, Italy; (M.B.); (B.E.); (A.F.)
| | - Maria João Matos
- Departamento de Química Orgánica, Facultad de Farmacia, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Davide Crucitti
- Group of Computational Genomics and Hematology (GreCoXen), Health Research Institute of Santiago de Compostela (IDIS), 15782 Santiago de Compostela, Spain;
- Departamento de Farmacología, Farmacia y Tecnología Farmacéutica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Valeria Sogos
- Department of Biomediacal Science, University of Cagliari, Cittadella Universitaria, SS 554, Km 4.5, 09042 Monserrato, Italy;
| | - Benedetta Era
- Department of Live and Environmental Sciences, University of Cagliari, Cittadella Universitaria, SS 554, Km 4.5, 09042 Monserrato, Italy; (M.B.); (B.E.); (A.F.)
| | - Antonella Fais
- Department of Live and Environmental Sciences, University of Cagliari, Cittadella Universitaria, SS 554, Km 4.5, 09042 Monserrato, Italy; (M.B.); (B.E.); (A.F.)
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13
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Hashim HO, Al-Shuhaib JMB, Mohammed MK, Al-Shuhaib MBS. Targeting Monkeypox Virus Methyltransferase: Virtual Screening of Natural Compounds from Middle-Eastern Medicinal Plants. Mol Biotechnol 2024:10.1007/s12033-024-01246-y. [PMID: 39097539 DOI: 10.1007/s12033-024-01246-y] [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: 01/18/2024] [Accepted: 07/01/2024] [Indexed: 08/05/2024]
Abstract
Monkeypox is an infectious disease resulting from the monkeypox virus, and its fatality rate varies depending on the virus clade and the location of the outbreak. In monkeypox virus, methyltransferase (MTase) plays a crucial role in modifying the cap structure of viral mRNA. This alteration assists the virus in evading the host's immune system, enhances viral protein synthesis, and ultimately enables successful infection and replication within host cells. Given the significance of MTase in viral infection and spread within the host, our study aimed to identify a natural inhibitor for this enzyme using docking and molecular dynamic (MD) simulations. We collected a total of 12,971 natural compounds from 200 medicinal plants in the Middle East. After eliminating duplicate compounds, we had 5,749 unique ligand conformers, which we then subjected to high-throughput virtual screening against MTase. The most promising hits were further evaluated using the extra-precision (XP) tool. The affinity of these hits was also assessed by Prime-Molecular Mechanics/Generalized Born Surface Area (MMGBSA) tool. The analysis revealed that two standard controls (sinefungin and TO1119) and two Middle-Eastern compounds (folic acid and 1,2,4,6-tetragalloylglucose) exhibited the best XP docking scores. According to Prime MMGBSA calculations, the Middle-Eastern compounds showed higher affinities, with values of - 60.61 kcal/mol for 1,2,4,6-tetragalloylglucose and - 51.87 kcal/mol for folic acid, surpassing the controls (TO1119 at - 35.71 kcal/mol and sinefungin at - 31.51 kcal/mol). In the majority of Molecular dynamic (MD) simulations, folic acid exhibited demonstrated greater stability than sinefungin. Further investigation revealed that folic acid occupied a critical position in the active site of MTase, which reduced its interaction with the mRNA substrate. Based on these findings, it can be concluded that folic acid is a highly promising natural compound for potential use in the cost-effective treatment of monkeypox virus. The identification of folic acid as a potential antiviral agent highlights the importance of nature in providing new therapeutic uses that have significant implications for global health, particularly in regions where monkeypox viral outbreaks are prevalent. However, it is essential to note that further wet-lab validations are necessary to confirm its efficacy for treatment in a medical context.
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Affiliation(s)
- Hayder O Hashim
- Department of Clinical Laboratory Sciences, College of Pharmacy, University of Babylon, Babil, 51001, Iraq
| | | | - Mudher K Mohammed
- Department of Pharmacy, Al-Manara College of Medical Science, Amarah, Iraq
| | - Mohammed Baqur S Al-Shuhaib
- Department of Animal Production, College of Agriculture, Al-Qasim Green University, Al-Qasim, 51013, Babil, Iraq.
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14
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Ghafoor NA, Kırboğa KK, Baysal Ö, Süzek BE, Silme RS. Data mining and molecular dynamics analysis to detect HIV-1 reverse transcriptase RNase H activity inhibitor. Mol Divers 2024; 28:1869-1888. [PMID: 37561229 DOI: 10.1007/s11030-023-10707-6] [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: 05/30/2023] [Accepted: 07/26/2023] [Indexed: 08/11/2023]
Abstract
HIV-1 is a deadly virus that affects millions of people worldwide. In this study, we aimed to inhibit viral replication by targeting one of the HIV-1 proteins and identifying a new drug candidate. We used data mining and molecular dynamics methods on HIV-1 genomes. Based on MAUVE analysis, we selected the RNase H activity of the reverse transcriptase (R.T) enzyme as a potential target due to its low mutation rate and high conservation level. We screened about 94,000 small molecule inhibitors by virtual screening. We validated the hit compounds' stability and binding free energy through molecular dynamics simulations and MM/PBSA. Phomoarcherin B, known for its anticancer properties, emerged as the best candidate and showed potential as an HIV-1 reverse transcriptase RNase H activity inhibitor. This study presents a new target and drug candidate for HIV-1 treatment. However, in vitro and in vivo tests are required. Also, the effect of RNase H activity on viral replication and the interaction of Phomoarcherin B with other HIV-1 proteins should be investigated.
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Affiliation(s)
- Naeem Abdul Ghafoor
- Department of Molecular Biology and Genetics, Faculty of Science, Muğla Sıtkı Koçman University, Kötekli, 48121, Muğla, Turkey
| | - Kevser Kübra Kırboğa
- Bioengineering Department, Bilecik Seyh Edebali University, 11230, Bilecik, Turkey
- Informatics Institute, Istanbul Technical University, Maslak, 34469, Istanbul, Turkey
| | - Ömür Baysal
- Molecular Microbiology Unit, Department of Molecular Biology and Genetics, Faculty of Science, Muğla Sıtkı Koçman University, Kötekli, 48121, Muğla, Turkey.
| | - Barış Ethem Süzek
- Department of Computer Engineering, Faculty of Engineering, Muğla Sıtkı Koçman University, Kötekli, 48000, Muğla, Turkey
| | - Ragıp Soner Silme
- Center for Research and Practice in Biotechnology and Genetic Engineering, Istanbul University, Vezneciler, Fatih, 34119, Istanbul, Turkey
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15
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Kaya MO, Kerimak-Öner MN, Demirci T, Musatat AB, Özdemir O, Kaya Y, Arslan M. Rational Design, Synthesis, and Computational Investigation of Dihydropyridine [2,3-d] Pyrimidines as Polyphenol Oxidase Inhibitors with Improved Potency. Protein J 2024; 43:869-887. [PMID: 39097848 DOI: 10.1007/s10930-024-10220-1] [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] [Accepted: 06/28/2024] [Indexed: 08/05/2024]
Abstract
Polyphenol oxidase (PPO) is an industrially important enzyme associated with browning reactions. In the present study, a set of ten new dihydropyridine [2,3-d] pyrimidines (TD-Hid-1-10) were synthesized and was found to be proven characteristically by 1H NMR, 13C NMR, IR, elemental analysis, and assessed as possible PPO inhibitors. PPO was purified from banana using three-phase partitioning, achieving an 18.65-fold purification and 136.47% activity recovery. Enzyme kinetics revealed that the compounds TD-Hid-6 and TD-Hid-7 are to be the most potent inhibitors, exhibiting mixed-type inhibition profile with IC50 values of 1.14 µM, 5.29 µM respectively against purified PPO enzyme. Electronic structure calculations at the B3LYP/PBE0 level of theories using def-2 SVP, def2-TZVP basis sets with various molecular descriptors characterized the electronic behavior of studied derivatives TD-Hid-1-10. Molecular electrostatic potential (MEP) and reduced density gradient analyses of RDG-NCI provided insights into charge distributions and weak intermolecular interactions. Docking study simulations predicted binding poses within crucial amino acid sequence in the 2y9x enzyme's active site, which is typically similar in sequence to the PPO form is not allowed. Ligands were analysed in terms of binding energies, inhibitor concentrations (mM) and various molecular interactions such as H-bonds, H-carbon, π-carbon, π-sigma, π-sigma, π-π T-shaped, π-π stacked, π-alkyl, Van der Waals and Cu interactions. The lowest binding energy (-7.83 kcal/mol) and the highest inhibitory effect (1.83 mM) were shown by the ligand Td-Hid-6, which forms H-bonds with Met280 and Asn260, exhibits π-sigma interactions with His61 and π-alkyl interactions with Val283. Other ligands also showed different interactions with various amino acids; for example, the Td-Hid-1 ligand formed H-bonds with His244 and showed π-sigma interactions with His244 and Val283.
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Affiliation(s)
- Mustafa Oğuzhan Kaya
- Department of Chemistry, Faculty of Arts and Science, Kocaeli University, Kocaeli, 41001, Turkey
| | - Mine Nazan Kerimak-Öner
- Department of Medicinal and Aromatic Plants, İzmit Vocational High School, Kocaeli University, Kocaeli, 41285, Turkey
| | - Tuna Demirci
- Scientific and Technological Research Laboratory, Düzce University, Düzce, 81620, Turkey
| | | | - Oğuzhan Özdemir
- Department of Veterinary Science, Technical Sciences Vocational School, Batman University, Batman, 72000, Turkey
| | - Yeşim Kaya
- Department of Chemistry, Faculty of Arts and Science, Kocaeli University, Kocaeli, 41001, Turkey
| | - Mustafa Arslan
- Department of Chemistry, Faculty of Sciences, Sakarya University, Sakarya, 54050, Turkey
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16
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Alrumaihi F. Identification of novel chemical scaffolds against kinase domain of cancer causing human epidermal growth factor receptor 2: a systemic chemoinformatic approach. J Biomol Struct Dyn 2024; 42:6269-6279. [PMID: 37424103 DOI: 10.1080/07391102.2023.2233618] [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: 02/12/2023] [Accepted: 07/01/2023] [Indexed: 07/11/2023]
Abstract
The Human epidermal growth factor receptor 2 (HER2) is expressed in high magnitude in several cancers. Designing new drug molecules that target kinase domain of the HER2 enzyme might provide an appealing platform. Considering this, herein, a multi-phase bioinformatic approach is applied to screen diverse natural and chemical scaffolds to identify compounds that fit best at the kinase domain of HER2. By doing so, three compounds; LAS_51187157, LAC_51217113, LAC_51390233 were pointed with docking score of -11.4 kcal/mol, -11.3 kcal/mol and -11.2 kcal/mol, respectively. In molecular dynamic simulation, the complexes behaved in a stable dynamic with no major local/global structural variations. The intermolecular binding free energies were further estimated that concluded LAC_51390233 complex was the most stable and has less entropy energy. The good docked affinity of LAC_51390233 with HER2 was confirmed by WaterSwap absolute binding free energy. The entropy energy demonstrated that LAC_51390233 has less freedom energy compared to others. Similarly, all three compounds revealed very favorable druglike properties and pharmacokinetics. All the selected three compounds were also non-carcinogenic, non-immunotoxicity, non-mutagenicity, and non-cytotoxic. In a nutshell, the compounds are interesting scaffolds and might be subjected to extensive experimental testing to reveal their real biological potency.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Faris Alrumaihi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
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17
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Abdizadeh T. Identification of novel potential inhibitors of monkeypox virus thymidine kinase using molecular docking, molecular dynamics simulation and MM/PBSA methods. Mol Divers 2024; 28:2513-2546. [PMID: 37462851 DOI: 10.1007/s11030-023-10692-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 07/03/2023] [Indexed: 10/05/2024]
Abstract
The monkeypox spread has been announced a public health emergency of international concern (PHEIC) by the World Health Organization (WHO). Both monkeypox and smallpox viruses are placed in the genus Orthopoxvirus. Despite recommendations for the administration of smallpox drugs versus monkeypox, no specific drug for monkeypox has yet been introduced. A reliable and effective method against this outbreak can be the use of natural products. This study aimed for identification of natural flavonoid derivatives as potential thymidine kinase inhibitors, the main drug target of monkeypox virus. Thymidine kinase protein structure was predicted by homology modeling and the quality of generated model was evaluated. Then, the interaction between natural flavonoids and the modeled thymidine kinase was explored by molecular docking. Based on docking results, more than half of the flavonoids with higher docking scores compared to reference drug (ganciclovir) were exhibited better binding affinities toward the protein. In addition, stability of the top flavonoids including eupatorin, fisetin, rhamnetin and scutellarein, was confirmed by MD simulations and binding free energy calculations using MM/PBSA analysis. These selected compounds were also shown acceptable results for drug likeness and ADMET analysis. Therefore, the results of the study showed that these flavonoids could be considered as potential thymidine kinase inhibitors for use against monkeypox virus.
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Affiliation(s)
- Tooba Abdizadeh
- Clinical Biochemistry Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran.
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18
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Kaya MO, Demirci T, Musatat AB, Özdemir O, Sönmez F, Kaya Y, Arslan M. Rabbit muscle pyruvate kinase activators: Synthesis, molecular docking and theoretical studies of N-substituted sulfonamide derivatives. Int J Biol Macromol 2024; 274:133184. [PMID: 38925176 DOI: 10.1016/j.ijbiomac.2024.133184] [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: 02/15/2024] [Revised: 06/01/2024] [Accepted: 06/13/2024] [Indexed: 06/28/2024]
Abstract
Pyruvate kinase (PK) activators have potential therapeutic applications in diseases such as sickle cell anemia. In this study, N-Substituted sulfonamide derivatives of 1,4-dihydropyridines were synthesized and evaluated as PK activators in vitro and using molecular docking studies. The compounds were synthesized by reacting dicarbonyl compounds with ammonium acetate, 5-nitrobenzaldehyde, and alumina sulfuric acid (ASA), followed by reduction and sulfonylation. The structures of the compounds were analyzed using spectroscopic techniques. DFT calculations provided insights into the electronic properties. Molecular docking of the compounds into the active site of PK showed favorable binding interactions. ADME evaluation indicated suitable solubility, BBB permeation, and lack of CYP450 inhibition. Overall, this study demonstrates the potential of new hybrid 1,4-dihydropyridine substituted sulfonamides as PK activators for further development. According to AC50 values, the compound (DTSF7, 0.97μM) is about 100-fold higher affective than the clinically used sulfonamide compound (AC50 = 90μM) for PK.
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Affiliation(s)
- Mustafa Oğuzhan Kaya
- Chemistry, Faculty of Arts and Science, Kocaeli University, 41001 Kocaeli, Turkey.
| | - Tuna Demirci
- Scientific and Technological Research Laboratory, Düzce University, 81620 Düzce, Turkey
| | | | - Oğuzhan Özdemir
- Veterinary Science Department, Technical Sciences Vocational School, Batman University, 72000 Batman, Turkey
| | - Fatih Sönmez
- Pharmacy Services Department, Pamukova Vocational School, Sakarya University of Applied Sciences, 54900 Sakarya, Turkey
| | - Yeşim Kaya
- Chemistry, Faculty of Arts and Science, Kocaeli University, 41001 Kocaeli, Turkey
| | - Mustafa Arslan
- Chemistry, Faculty of Sciences, Sakarya University, 54050, Sakarya, Turkey
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19
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Mukhtar M, Khan HA, Ibisanmi TA, Faleti AI, Zaidi NUSS. Computational Exploration of Berberis lycium Royle: A Hidden Treasure Trove for Antiviral Development. Bioinform Biol Insights 2024; 18:11779322241264144. [PMID: 39072259 PMCID: PMC11283669 DOI: 10.1177/11779322241264144] [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: 11/05/2023] [Accepted: 06/06/2024] [Indexed: 07/30/2024] Open
Abstract
Viral infections and associated illnesses account for approximately 3.5 million global fatalities and public health problems. Medicinal plants, with their wide therapeutic range and minimal side effects, have gained limelight particularly in response to growing concerns about drug resistance and sluggish development of antiviral drugs. This study computationally assessed 11 chemical compounds from Berberis lycium along with two antiviral drugs to inhibit SARS CoV 2 (coronavirus disease 2019 [COVID-19]) RNA-dependent RNA polymerase (RdRP), influenza virus RdRP, and two crucial dengue virus (DENV) enzymes (NS2B/NS3 protease and NS5 polymerase). Berberine and oxyberberine passed all pharmacokinetics analysis filters including Lipinski rule, blood-brain barrier permeant, and cytochrome suppression and demonstrated drug-likeness, bioavailability, and a non-toxic profile. Docking of phytochemicals from B lycium returned promising results with selected viral proteins, ie, DENV NS2BNS3 (punjabine -10.9 kcal/mol), DENV NS5 (punjabine -10.4 kcal/mol), COVID-19 RdRP (oxyacanthine -9.5 kcal/mol), and influenza RdRP (punjabine -10.4 kcal/mol). The optimal pharmacokinetics of berberine exhibited good binding energies with NS2BNS3 (-8.0 kcal/mol), NS5 (-8.3 kcal/mol), COVID RdRP (-7.7 kcal/mol), and influenza RdRP (-8.3 kcal/mol), while molecular dynamics simulation of a 50-ns time scale by GROMACS software package provided insights into the flexibility and stability of the complexes. A hidden treasure trove for antiviral research, berberine, berbamine, berbamunine, oxyberberine, oxyacanthine, baluchistanamine, and sindamine has showed encouraging findings as possible lead compounds. Pharmacological analyses provide credence for the proposed study; nevertheless, as the antiviral mechanisms of action of these phytochemicals are not well understood, additional research and clinical trials are required to demonstrate both their efficacy and toxicity through in vitro and in vivo studies.
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Affiliation(s)
- Mamuna Mukhtar
- Department of Industrial Biotechnology, Atta ur Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Haris Ahmed Khan
- Department of Industrial Biotechnology, Atta ur Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
- Department of Biotechnology, University of Mianwali, Mianwali, Pakistan
| | - Tope Abraham Ibisanmi
- Department of Microbiology, School of Life Sciences, The Federal University of Technology Akure, Akure, Nigeria
| | - Ayodele Ifeoluwa Faleti
- Department of Chemistry, School of Physical Sciences, The Federal University of Technology Akure, Akure, Nigeria
| | - Najam us Sahar Sadaf Zaidi
- Department of Industrial Biotechnology, Atta ur Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
- Department of Biological and Health Sciences, Pak-Austria Fachhochschule: Institute of Applied Sciences and Technology, Mang, Haripur-KPK, Pakistan
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20
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Masarkar N, Pal M, Roy M, Yadav AK, Pandya B, Lokhande S, Kanwar JR, Ray SK, Mukherjee S. In-silico screening of bioactive compounds of Moringa oleifera as potential inhibitors targeting HIF-1α/VEGF/GLUT-1 pathway against Breast Cancer. JOURNAL OF COMPLEMENTARY & INTEGRATIVE MEDICINE 2024; 0:jcim-2024-0176. [PMID: 39024644 DOI: 10.1515/jcim-2024-0176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2024] [Accepted: 06/24/2024] [Indexed: 07/20/2024]
Abstract
OBJECTIVES Breast cancer is among the most heterogeneous and aggressive diseases and a foremost cause of death in women globally. Hypoxic activation of HIF-1α in breast cancers triggers the transcription of a battery of genes encoding proteins that facilitate tumor growth and metastasis and is correlated with a poor prognosis. Based on the reported cytotoxic and anti-cancer properties of Moringa oleifera (Mo), this study explores the inhibitory effect of bioactive compounds from M. oleifera and breast cancer target proteins HIF-1α, VEGF, and GLUT-1 in silico. METHODS The X-ray crystallographic structures of HIF-1α, VEGF, and GLUT1 were sourced from the Protein Data Bank (PDB) and docked with 70 3D PubChem structures of bioactive compounds of M. oleifera using AutoDock Vina, and binding modes were analyzed using Discovery Studio. Five compounds with the highest binding energies were selected and further drug-likeness, oral bioavailability, ADME, and toxicity profiles were analyzed using SwissADME, ADMETSaR, and ADMETlab 3.0 web server. RESULTS Out of the screened 70 bioactive compounds, the top five compounds with the best binding energies were identified namely Apigenin, Ellagic Acid, Isorhamnetin, Luteolin, and Myricetin with each receptor. Molecular docking results indicated that the ligands interact strongly with the target HIF-1α, VEGF, and GLUT-1 receptors through hydrogen bonds and hydrophobic interactions. These compounds showed favorable drug-like and pharmacokinetic properties, possessed no substantial toxicity, and were fairly bioavailable. CONCLUSIONS Results suggested that the compounds possess strong potential in developing putative lead compounds targeting HIF-1α that are safe natural plant-based drugs against breast cancer.
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Affiliation(s)
- Neha Masarkar
- Department of Biochemistry, 390706 All India Institute of Medical Sciences (AIIMS) Bhopal , Bhopal, Madhya Pradesh, India
| | - Maynak Pal
- Department of Chemistry, National Institute of Technology Manipur, Imphal, India
| | - Mithun Roy
- Department of Chemistry, National Institute of Technology Manipur, Imphal, India
| | - Ashish K Yadav
- Department of Biochemistry, 390706 All India Institute of Medical Sciences (AIIMS) Bhopal , Bhopal, Madhya Pradesh, India
| | - Bharati Pandya
- Department of General Surgery, All India Institute of Medical Sciences (AIIMS) Bhopal, Bhopal, India
| | - Suryabhan Lokhande
- Department of Biochemistry, 390706 All India Institute of Medical Sciences (AIIMS) Bhopal , Bhopal, Madhya Pradesh, India
| | - Jagat R Kanwar
- Department of Biochemistry, 390706 All India Institute of Medical Sciences (AIIMS) Bhopal , Bhopal, Madhya Pradesh, India
| | | | - Sukhes Mukherjee
- Department of Biochemistry, 390706 All India Institute of Medical Sciences (AIIMS) Bhopal , Bhopal, Madhya Pradesh, India
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21
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Cordero AMF, Gonzales AA. Using Multiscale Molecular Modeling to Analyze Possible NS2b-NS3 Protease Inhibitors from Philippine Medicinal Plants. Curr Issues Mol Biol 2024; 46:7592-7618. [PMID: 39057092 PMCID: PMC11275823 DOI: 10.3390/cimb46070451] [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: 06/05/2024] [Revised: 07/15/2024] [Accepted: 07/16/2024] [Indexed: 07/28/2024] Open
Abstract
Within the field of Philippine folkloric medicine, the utilization of indigenous plants like Euphorbia hirta (tawa-tawa), Carica papaya (papaya), and Psidium guajava (guava) as potential dengue remedies has gained attention. Yet, limited research exists on their comprehensive effects, particularly their anti-dengue activity. This study screened 2944 phytochemicals from various Philippine plants for anti-dengue activity. Absorption, distribution, metabolism, excretion, and toxicity (ADMET) profiling provided 1265 compounds demonstrating pharmacokinetic profiles suitable for human use. Molecular docking targeting the dengue virus NS2b-NS3 protease's catalytic triad (Asp 75, Ser 135, and His 51) identified ten ligands with higher docking scores than reference compounds idelalisib and nintedanib. Molecular dynamics simulations confirmed the stability of eight of these ligand-protease complexes. Molecular Mechanics/Poisson-Boltzmann Surface Area (MM/PBSA) analysis highlighted six ligands, including veramiline (-80.682 kJ/mol), cyclobranol (-70.943 kJ/mol), chlorogenin (-63.279 kJ/mol), 25beta-Hydroxyverazine (-61.951 kJ/mol), etiolin (-59.923 kJ/mol), and ecliptalbine (-56.932 kJ/mol) with favorable binding energies, high oral bioavailability, and drug-like properties. This integration of traditional medical knowledge with advanced computational drug discovery methods paves new pathways for the development of treatments for dengue.
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Affiliation(s)
| | - Arthur A. Gonzales
- Department of Chemical Engineering, University of the Philippines Diliman, Quezon City 1101, Philippines;
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22
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Oudah KH, Najm MAA, Barghash RF, Kutkat O, GabAllah M, Albohy A, Abouzid KAM. Drug repurposing of pyrazolotriazine derivatives as potential anti-SARS-CoV-2 agents: in vitro and in silico studies. BMC Chem 2024; 18:132. [PMID: 39014447 PMCID: PMC11253567 DOI: 10.1186/s13065-024-01233-z] [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: 09/25/2023] [Accepted: 06/25/2024] [Indexed: 07/18/2024] Open
Abstract
The search for new molecules targeting SARS-CoV-2 has been a priority since 2020. The continuous evolution of new mutants increases the need for more research in the area. One way to find new leads is to repurpose existing drugs and molecules against the required target. Here, we present the in vitro and in silico screening of ten previously synthesized and reported compounds as anti-COVID 19 agents. The compounds were screened in vitro against VERO-E6 cells to find their Cytotoxic Concentration (CC50) and their Inhibitory Concentration (IC50). Compounds 1, 2, and 5 revealed a promising anti-SARS-CoV-2 of (IC50 = 2.4, 11.2 and 2.8 µM), respectively while compounds 3 and 7 showed moderate activity of (IC50 = 17.8 and 26.1 µM) compared to Chloroquine which showed an IC50 of 24.9 µM. Among tested compounds, 1 showed the highest selectivity (CC50/IC50) of 192.8. Docking, molecular dynamics and ADME studies were done to investigate potential interactions between compounds and SARS-CoV-2 targets as well as to study the possibility of using them as lead compounds.
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Affiliation(s)
- Khulood H Oudah
- Department of Pharmacy, Mazaya University Collage, Nasiriyah, Thi-Qar, Iraq
| | - Mazin A A Najm
- Department of Pharmacy, Mazaya University Collage, Nasiriyah, Thi-Qar, Iraq
| | - Reham F Barghash
- Institute of Chemical Industries Research, National Research Centre, Dokki, Giza, 12622, Egypt
- Faculty of Biotechnology, October University for Modern Science and Arts (MSA University), Giza, Egypt
| | - Omnia Kutkat
- Center of Scientifc Excellence for Infuenza Viruses, National Research Centre, Dokki, Giza, 12622, Egypt
- Department of microbiology, Faculty of pharmacy, Ahram Canadian University, 6 th of October, Giza, 12566, Egypt
| | - Mohamed GabAllah
- Center of Scientifc Excellence for Infuenza Viruses, National Research Centre, Dokki, Giza, 12622, Egypt
| | - Amgad Albohy
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, The British University in Egypt, El-Sherouk City, 11837, Cairo, Egypt.
| | - Khaled A M Abouzid
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Ain Shams University, Abbassia, 11566, Cairo, Egypt.
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23
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Castillo F, Ramírez D, Ramos MC, Martinez-Arribas B, Domingo-Contreras E, Mackenzie TA, Peña-Varas C, Lindemann S, Montero F, Annang F, Vicente F, Genilloud O, González-Pacanowska D, Fernandez-Godino R. Repurposing the Open Global Health Library for the discovery of novel Mpro destabilizers with scope as broad-spectrum antivirals. Front Pharmacol 2024; 15:1390705. [PMID: 39050758 PMCID: PMC11267763 DOI: 10.3389/fphar.2024.1390705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 05/29/2024] [Indexed: 07/27/2024] Open
Abstract
The SARS coronavirus 2 (SARS-CoV-2) epidemic remains globally active. The emergence of new variants of interest and variants of concern (VoCs), which are potentially more vaccine-resistant and less sensitive to existing treatments, is evident due to their high prevalence. The prospective spread of such variants and other coronaviruses with epidemic potential demands preparedness that can be met by developing fast-track workflows to find new candidates that target viral proteins with a clear in vitro and in vivo phenotype. Mpro (or 3CLpro) is directly involved in the viral replication cycle and the production and function of viral polyproteins, which makes it an ideal target. The biological relevance of Mpro is highly conserved among betacoronaviruses like HCoV-OC43 and SARS-CoV-2, which makes the identification of new chemical scaffolds targeting them a good starting point for designing broad-spectrum antivirals. We report an optimized methodology based on orthogonal cell-free assays to identify small molecules that inhibit the binding pockets of both SARS-CoV-2-Mpro and HCoV-OC43-Mpro; this blockade correlates with antiviral activities in HCoV-OC43 cellular models. By using such a fast-tracking approach against the Open Global Health Library (Merck KGaA), we have found evidence of the antiviral activity of compound OGHL98. In silico studies dissecting intermolecular interactions between OGHL98 and both proteases and comprising docking and molecular dynamics simulations (MDSs) concluded that the binding mode was primarily governed by conserved H-bonds with their C-terminal amino acids and that the rational design of OGHL98 has potential against VoCs proteases resistant to current therapeutics.
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Affiliation(s)
| | - David Ramírez
- Departamento de Farmacología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | | | - Blanca Martinez-Arribas
- Instituto de Parasitología y Biomedicina Lopez-Neyra, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | | | | | - Carlos Peña-Varas
- Departamento de Farmacología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
- Doctorado en Biotecnología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Sven Lindemann
- Strategic Innovation, Merck Healthcare KGaA, Darmstadt, Germany
| | - Fernando Montero
- Fundación MEDINA, Granada, Spain
- Department of Physical Chemistry and Institute of Biotechnology, Universidad de Granada, Granada, Spain
| | | | | | | | - Dolores González-Pacanowska
- Instituto de Parasitología y Biomedicina Lopez-Neyra, Consejo Superior de Investigaciones Científicas, Granada, Spain
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24
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Tükel EY, Ateş O, Kiraz Y. In Silico Drug Repurposing Against PSMB8 as a Potential Target for Acute Myeloid Leukemia Treatment. Mol Biotechnol 2024:10.1007/s12033-024-01224-4. [PMID: 38954355 DOI: 10.1007/s12033-024-01224-4] [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: 10/03/2023] [Accepted: 06/21/2024] [Indexed: 07/04/2024]
Abstract
PSMB8 emerges as a prominent gene associated with cancer survival, yet its potential therapeutic role in acute myeloid leukemia (AML) remains unexplored within the existing literature. The principal aim of this study is to systematically screen an expansive library of molecular entities, curated from various databases to identify the prospective inhibitory agents with an affinity for PSMB8. A comprehensive assortment of molecular compounds obtained from the ZINC15 database was subjected to molecular docking simulations with PSMB8 by using the AutoDock tool in PyRx (version 0.9.9) to elucidate binding affinities. Following the docking simulations, a select subset of molecules underwent further investigation through comprehensive ADMET (absorption, distribution, metabolism, excretion, and toxicity) analysis employing AdmetSar and SwissADME tools. Finally, RMSD, RMSF, Rg, and H bond analyses were conducted via GROMACS to determine the best conformationally dynamic molecule that represents the candidate agent for the study. Following rigorous evaluation, Adozelesin, Fiduxosin, and Rimegepant have been singled out based on considerations encompassing bioavailability scores, compliance with filter criteria, and acute oral toxicity levels. Additionally, ligand interaction analysis indicates that Adozelesin and Fiduxosin exhibit an augmented propensity for hydrogen bond formation, a factor recognized for its facilitative role in protein-ligand interactions. After final analyses, we report that Fiduxosin may offer a treatment possibility by reversing the low survival rates caused by PSMB8 high activation in AML. This study represents a strategic attempt to repurpose readily available pharmaceutical agents, potentially obviating the need for de novo drug development, and thereby offering promising avenues for therapeutic intervention in specific diseases.
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Affiliation(s)
- Ezgi Yağmur Tükel
- Department of Genetics and Bioengineering, Faculty of Engineering, İzmir University of Economics, Sakarya st. No:156, 35330, Balçova, İzmir, Turkey
| | - Onur Ateş
- Department of Genetics and Bioengineering, Faculty of Engineering, İzmir University of Economics, Sakarya st. No:156, 35330, Balçova, İzmir, Turkey
| | - Yağmur Kiraz
- Department of Genetics and Bioengineering, Faculty of Engineering, İzmir University of Economics, Sakarya st. No:156, 35330, Balçova, İzmir, Turkey.
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25
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Arif B, Yasir S, Saeed M, Fatmi MQ. Natural products can be potential inhibitors of metalloproteinase II from Bacteroides fragilis to intervene colorectal cancer. Heliyon 2024; 10:e32838. [PMID: 39005891 PMCID: PMC11239599 DOI: 10.1016/j.heliyon.2024.e32838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 05/03/2024] [Accepted: 06/10/2024] [Indexed: 07/16/2024] Open
Abstract
Bacteroides fragilis, a gram negative and obligate anaerobe bacterium, is a member of normal gut microbiota and facilitates many essential roles being performed in human body in normal circumstances specifically in Gastrointestinal or GI tract. Sometimes, due to genetics, epigenetics, and environmental factors, Bacteroides fragilis and their protein(s) start interacting with intestinal epithelium thus damaging the lining leading to colorectal cancers (CRC). To identify these protein(s), we incorporated a novel subtractive proteomics approach in the study. Metalloproteinase II (MPII), a Bacteroides fragilis toxin (bft), was investigated for its virulence and unique pathways to demonstrate its specificity and uniqueness in pathogenicity followed by molecular docking against a set of small drug-like natural molecules to discover potential inhibitors against the toxin. All these identified inhibitor-like molecules were analyzed for their ADMET calculations and detailed physiochemical properties to predict their druggability, GI absorption, blood brain barrier and skin permeation, and others. Resultantly, a total of ten compounds with the least binding energies were obtained and were subjected to protein-compound interaction analysis. Interaction analysis revealed the most common ligand-interacting residues in MPII are His 345, Glu 346, His 339, Gly 310, Tyr 341, Pro 340, Asp 187, Phe 309, Lys 307, Ile 185, Thr 308, and Pro 184. Therefore, top three compounds complexed with MPII having best binding energies were selected in order to analyze their trajectories. RMSD, RMSF, Rg and MMPBSA analysis revealed that all compounds showed good binding and keeping the complex stable and compact throughout the simulation time in addition to all properties and qualities of being a potential inhibitor against MPII.
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Affiliation(s)
- Bushra Arif
- Department of Biosciences, COMSATS University Islamabad, Islamabad Campus, Pakistan
| | - Saba Yasir
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Muhammad Saeed
- Department of Biosciences, COMSATS University Islamabad, Islamabad Campus, Pakistan
| | - M. Qaiser Fatmi
- Department of Biosciences, COMSATS University Islamabad, Islamabad Campus, Pakistan
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26
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Al-Wahaibi L, El-Emam AA, S. M. Abdelbaky M, Garcia-Granda S, Maurya A, Pal M, Siddiqui Z, Shukla R, Pathak SK, Srivastava R, Shukla VK, Prasad O, Sinha L. Structural Characterization, Spectroscopic Profile, Molecular Docking, ADMET Properties, Molecular Dynamics Simulation Studies, and Molecular Mechanics Generalized Born Surface Area Analysis of 5-(Adamantan-1-yl)-4-butyl-2,4-dihydro-3 H-1,2,4-triazole-3-thione as a Potential COX Inhibitor. ACS OMEGA 2024; 9:26651-26672. [PMID: 38911725 PMCID: PMC11191079 DOI: 10.1021/acsomega.4c03512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 05/22/2024] [Accepted: 05/24/2024] [Indexed: 06/25/2024]
Abstract
Employing a synergistic combination of theoretical density functional theory (DFT) and experimental techniques, we conducted a comprehensive analysis elucidating the structural and pharmacological attributes of 5-(adamantan-1-yl)-4-butyl-2,4-dihydro-3H-1,2,4-triazole-3-thione (5A4BT) as a potent COX inhibitor. The X-ray crystallographic data of 5A4BT showed the pivotal role played by weak interactions, notably π-π and C-H-π interactions, alongside hydrogen bonding, in orchestrating the intricate supramolecular architectures within the crystalline lattice. A quantitative analysis of the arrangement of the crystal structure, as well as both inter- and intramolecular interactions, was conducted using Hirshfeld surfaces and 2D fingerprint plots. Additionally, a comprehensive examination of the IR spectra was undertaken, employing both experimental methods and theoretical DFT techniques, to elucidate the vibrational characteristics of the compound. The strength of intermolecular N-H···S hydrogen bonding and charge transfer within the system was assessed through natural bonding orbital analysis. Moreover, Bader's atoms in molecules theory was employed to estimate the strength of intermolecular hydrogen bonds, revealing strong interactions within the 5A4BT dimer. The title compound exhibited binding affinities of -6.4 and -6.5 kcal/mol for COX1 (PDB 3KK6) and COX2 (1CX2) target proteins, respectively. For the first time, predictions regarding ADMET properties, drug-likeness, and toxicity, including favorable bioavailability, along with 100 ns molecular dynamics simulations, binding free energy, and energy decomposition per residue in the binding cavity of the protein from molecular mechanics generalized born surface area approach, collectively indicate the potential of 5A4BT as a nonselective COX inhibitor.
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Affiliation(s)
- Lamya
H. Al-Wahaibi
- Department
of Chemistry, College of Sciences, Princess
Nourah bint Abdulrahman University, Riyadh 11671, Saudi Arabia
| | - Ali A. El-Emam
- Department
of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Mohammed S. M. Abdelbaky
- Department
of Physical and Analytical Chemistry, Faculty of Chemistry, Oviedo University-CINN, Oviedo 33006, Spain
| | - Santiago Garcia-Granda
- Department
of Physical and Analytical Chemistry, Faculty of Chemistry, Oviedo University-CINN, Oviedo 33006, Spain
| | - Anushree Maurya
- Department
of Physics, University of Lucknow, Lucknow 226007, Uttar Pradesh, India
| | - Mamta Pal
- Department
of Physics, University of Lucknow, Lucknow 226007, Uttar Pradesh, India
| | - Zohra Siddiqui
- Department
of Physics, University of Lucknow, Lucknow 226007, Uttar Pradesh, India
| | - Raj Shukla
- Department
of Physics, University of Lucknow, Lucknow 226007, Uttar Pradesh, India
| | - Shilendra K. Pathak
- Department
of Physics, M. M. M. P. G. College, Deoria 274502, Uttar Pradesh, India
| | - Ruchi Srivastava
- Department
of Physics, University of Lucknow, Lucknow 226007, Uttar Pradesh, India
| | - Vikas K. Shukla
- Department
of Physics, Maharishi University of Information
Technology, Lucknow 226013, Uttar Pradesh, India
| | - Onkar Prasad
- Department
of Physics, University of Lucknow, Lucknow 226007, Uttar Pradesh, India
| | - Leena Sinha
- Department
of Physics, University of Lucknow, Lucknow 226007, Uttar Pradesh, India
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27
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Muthukrishnan S, Sekar S, Raman C, Pandiyan J, Ponnaiah J. Phytochemical analysis, physicochemical, pharmacokinetic properties and molecular docking studies of bioactive compounds in Ottelia alismoides (L.) pers. Against breast cancer proteins. In Silico Pharmacol 2024; 12:53. [PMID: 38860144 PMCID: PMC11162403 DOI: 10.1007/s40203-024-00227-y] [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: 10/26/2023] [Accepted: 05/28/2024] [Indexed: 06/12/2024] Open
Abstract
Plants provide compounds that can be used to treat diseases, and in silico methods help to expedite drug discovery while reducing costs. This study explored the phytochemical profile of methanol extract of O. alismoides using GC-MS to identify potential bioactive compounds. Autodock 4.2.6. was employed for molecular docking evaluation of the efficacy of these identified compounds against Estrogen Receptor Alpha (ERα), Human Epidermal Growth Factor Receptor 2 (HER2), and Epidermal Growth Factor Receptor (EGFR), proteins. Additionally, the ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) properties of the compounds were predicted using the SwissADME online tool. The preliminary phytochemical analysis revealed the presence of alkaloids, carbohydrates, glycosides, and steroids. During the GC-MS analysis, seven compounds were identified, and drug-likeness prediction of these compounds showed good pharmacokinetic properties having high gastrointestinal absorption, and orally bioavailable. The molecular docking studies exhibited promising binding affinities of bioactive compounds against all target proteins. Specifically, the compounds Tricyclo[5.2.1.0(2,6)]decan-10-ol and 2,2,6-Trichloro-7-oxabicyclo[4.1.0]heptane-1-carboxamide demonstrated the highest binding affinities with the ERα (-6.3 and - 6.0 k/cal), HER2 (-5.6 and - 6.1 k/cal), and EGFR (-5.4 and - 5.4 k/cal), respectively. These findings suggest the potential of O. alismoides as a source for developing new cancer therapeutics. The study highlights the effectiveness of in silico approaches for accelerating drug discovery from natural sources and paves the way for further exploration of these promising compounds. Supplementary Information The online version contains supplementary material available at 10.1007/s40203-024-00227-y.
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Affiliation(s)
- Sathish Muthukrishnan
- Department of Microbiology, JJ College of Arts and Science (Autonomous), (Affiliated to Bharathidasan University, Tiruchirappalli, Pudukkottai, Tamil Nadu 622 422 India
| | - Suriya Sekar
- Department of Microbiology, JJ College of Arts and Science (Autonomous), (Affiliated to Bharathidasan University, Tiruchirappalli, Pudukkottai, Tamil Nadu 622 422 India
| | - Chamundeeswari Raman
- Department of Microbiology, JJ College of Arts and Science (Autonomous), (Affiliated to Bharathidasan University, Tiruchirappalli, Pudukkottai, Tamil Nadu 622 422 India
| | - Jeevan Pandiyan
- Department of Microbiology, JJ College of Arts and Science (Autonomous), (Affiliated to Bharathidasan University, Tiruchirappalli, Pudukkottai, Tamil Nadu 622 422 India
| | - Jansirani Ponnaiah
- Department of Botany, The Madura College (Autonomous), Madurai Kamarajar University, Madurai, Tamil Nadu India
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28
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Cristovão-Silva AC, Brelaz-de-Castro MCA, Dionisio da Silva E, Leite ACL, Santiago LBAA, Conceição JMD, da Silva Tiburcio R, de Santana DP, Bedor DCG, de Carvalho BÍV, Ferreira LFGR, de Freitas E Silva R, Alves Pereira VR, Hernandes MZ. Trypanosoma cruzi killing and immune response boosting by novel phenoxyhydrazine-thiazole against Chagas disease. Exp Parasitol 2024; 261:108749. [PMID: 38593864 DOI: 10.1016/j.exppara.2024.108749] [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: 10/04/2023] [Revised: 03/23/2024] [Accepted: 04/06/2024] [Indexed: 04/11/2024]
Abstract
Trypanosoma cruzi (T. cruzi) causes Chagas, which is a neglected tropical disease (NTD). WHO estimates that 6 to 7 million people are infected worldwide. Current treatment is done with benznidazole (BZN), which is very toxic and effective only in the acute phase of the disease. In this work, we designed, synthesized, and characterized thirteen new phenoxyhydrazine-thiazole compounds and applied molecular docking and in vitro methods to investigate cell cytotoxicity, trypanocide activity, nitric oxide (NO) production, cell death, and immunomodulation. We observed a higher predicted affinity of the compounds for the squalene synthase and 14-alpha demethylase enzymes of T. cruzi. Moreover, the compounds displayed a higher predicted affinity for human TLR2 and TLR4, were mildly toxic in vitro for most mammalian cell types tested, and LIZ531 (IC50 2.8 μM) was highly toxic for epimastigotes, LIZ311 (IC50 8.6 μM) for trypomastigotes, and LIZ331 (IC50 1.9 μM) for amastigotes. We observed that LIZ311 (IC50 2.5 μM), LIZ431 (IC50 4.1 μM) and LIZ531 (IC50 5 μM) induced 200 μg/mL of NO and JM14 induced NO production in three different concentrations tested. The compound LIZ331 induced the production of TNF and IL-6. LIZ311 induced the secretion of TNF, IFNγ, IL-2, IL-4, IL-10, and IL-17, cell death by apoptosis, decreased acidic compartment formation, and induced changes in the mitochondrial membrane potential. Taken together, LIZ311 is a promising anti-T. cruzi compound is not toxic to mammalian cells and has increased antiparasitic activity and immunomodulatory properties.
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Affiliation(s)
- Ana Catarina Cristovão-Silva
- Laboratory of Immunopathology and Molecular Biology, Aggeu Magalhães Institute, Oswaldo Cruz Foundation, 50670-42, Recife, Pernambuco, Brazil
| | - Maria Carolina Accioly Brelaz-de-Castro
- Laboratory of Immunopathology and Molecular Biology, Aggeu Magalhães Institute, Oswaldo Cruz Foundation, 50670-42, Recife, Pernambuco, Brazil; Laboratory of Parasitology, Vitória Academic Center, Federal University of Pernambuco, 55608-680, Vitória de Santo Antão, Pernambuco, Brazil
| | - Elis Dionisio da Silva
- Laboratory of Immunopathology and Molecular Biology, Aggeu Magalhães Institute, Oswaldo Cruz Foundation, 50670-42, Recife, Pernambuco, Brazil
| | - Ana Cristina Lima Leite
- Laboratory of Planning and Synthesis in Medicinal Chemistry, Pharmaceutical Sciences Department, Federal University of Pernambuco, 50740-520, Recife, Pernambuco, Brazil
| | - Lizandra Beatriz Amorim Alves Santiago
- Laboratory of Planning and Synthesis in Medicinal Chemistry, Pharmaceutical Sciences Department, Federal University of Pernambuco, 50740-520, Recife, Pernambuco, Brazil
| | - Juliana Maria da Conceição
- Laboratory of Planning and Synthesis in Medicinal Chemistry, Pharmaceutical Sciences Department, Federal University of Pernambuco, 50740-520, Recife, Pernambuco, Brazil
| | - Robert da Silva Tiburcio
- Laboratory of Planning and Synthesis in Medicinal Chemistry, Pharmaceutical Sciences Department, Federal University of Pernambuco, 50740-520, Recife, Pernambuco, Brazil
| | - Davi Pereira de Santana
- Pharmaceutical and Cosmetic Development Center (NUDFAC), Department of Pharmaceutical Science, Federal University of Pernambuco, Recife, PE, Brazil
| | - Danilo Cesar Galindo Bedor
- Pharmaceutical and Cosmetic Development Center (NUDFAC), Department of Pharmaceutical Science, Federal University of Pernambuco, Recife, PE, Brazil
| | - Breno Ítalo Valença de Carvalho
- Pharmaceutical and Cosmetic Development Center (NUDFAC), Department of Pharmaceutical Science, Federal University of Pernambuco, Recife, PE, Brazil
| | - Luiz Felipe Gomes Rebello Ferreira
- Laboratory of Theoretical and Medicinal Chemistry, Pharmaceutical Sciences Department, Federal University of Pernambuco, 50740-520, Recife, Pernambuco, Brazil
| | - Rafael de Freitas E Silva
- Laboratory of Immunopathology and Molecular Biology, Aggeu Magalhães Institute, Oswaldo Cruz Foundation, 50670-42, Recife, Pernambuco, Brazil.
| | - Valéria Rêgo Alves Pereira
- Laboratory of Immunopathology and Molecular Biology, Aggeu Magalhães Institute, Oswaldo Cruz Foundation, 50670-42, Recife, Pernambuco, Brazil.
| | - Marcelo Zaldini Hernandes
- Laboratory of Theoretical and Medicinal Chemistry, Pharmaceutical Sciences Department, Federal University of Pernambuco, 50740-520, Recife, Pernambuco, Brazil.
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Mili A, Birangal S, Nandakumar K, Lobo R. A computational study to identify Sesamol derivatives as NRF2 activator for protection against drug-induced liver injury (DILI). Mol Divers 2024; 28:1709-1731. [PMID: 37392347 PMCID: PMC11269468 DOI: 10.1007/s11030-023-10686-8] [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: 01/07/2023] [Accepted: 06/23/2023] [Indexed: 07/03/2023]
Abstract
Drug-induced liver injury can be caused by any drugs, their metabolites, or natural products due to the inefficient functioning of drug-metabolizing enzymes, resulting in reactive oxygen species generation and leading to oxidative stress-induced cell death. For protection against oxidative stress, our cell has various defense mechanisms. One of the mechanisms is NRF2 pathway, when activated, protects the cell against oxidative stress. Natural antioxidants such as Sesamol have reported pharmacological activity (hepatoprotective & cardioprotective) and signaling pathways (NRF2 & CREM) altering potential. A Computational analysis was done using molecular docking, IFD, ADMET, MM-GBSA, and Molecular dynamic simulation of the Schrödinger suite. A total of 63,345 Sesamol derivatives were downloaded for the PubChem database. The protein structure of KEAP1-NRF2 (PDB: 4L7D) was downloaded from the RCSB protein database. The molecular docking technique was used to screen compounds that can form an interaction similar to the co-crystalized ligand (1VX). Based on MM-GBSA, docking score, and interactions, ten compounds were selected for ADMET profiling and IFD. After IFD, five compounds (66867225, 46148111, 12444939, 123892179, & 94817569) were selected for molecular dynamics simulation (MDS). Protein-ligand complex stability was assessed during MDS. The selected compounds (66867225, 46148111, 12444939, 123892179, & 94817569) complex with KEAP1 protein shows good stability and bond retentions. In our study, we observed that the selected compounds show good interaction, PCA, Rg, binding free energy, and ADMET profile. We can conclude that the selected compounds can act as NRF2 activators, which should be validated using proper in-vivo/in-vitro models.
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Affiliation(s)
- Ajay Mili
- Department of Pharmacognosy, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Sumit Birangal
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Krishnadas Nandakumar
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Richard Lobo
- Department of Pharmacognosy, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India.
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Pandiyan S, Wang L. In-silico design of novel potential HDAC inhibitors from indazole derivatives targeting breast cancer through QSAR, molecular docking and pharmacokinetics studies. Comput Biol Chem 2024; 110:108035. [PMID: 38460437 DOI: 10.1016/j.compbiolchem.2024.108035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 02/19/2024] [Accepted: 02/20/2024] [Indexed: 03/11/2024]
Abstract
Latest studies confirmed that abnormal function of histone deacetylase (HDAC) plays a pivotal role in formation of tumors and is a potential therapeutic target for treating breast cancer. In this research, in-silico drug discovery approaches via quantitative structure activity relationship (QSAR) and molecular docking simulations were adapted to 43 compounds of indazole derivatives with HDAC inhibition for anticancer activity against breast cancer. The QSAR models were built from multiple linear regression (MLR), and models predictability was cross-validated by leave-one-out (LOO) method. Based on these results, compounds C32, C26 and C31 from model 3 showed superior inhibitory activity with pIC50 of 9.30103, 9.1549 and 9.1549. We designed 10 novel compounds with molecular docking scores ranging from -7.9 to -9.3 kcal/mol. The molecular docking simulation results reveal that amino acid residues ILE1122 and PRO1123 play a significant role in bonding with 6CE6 protein. Furthermore, newly designed compounds P5, P2 and P7 with high docking scores of -9.3 kcal/mol, -8.9 kcal/mol and -8.8 kcal/mol than FDA-approved drug Raloxifene (-8.5 kcal/mol) and aid in establishment of potential drug candidate for HDAC inhibitors. The in-silico ADME functionality is used in the final phase to evaluate newly designed inhibitors as potential drug candidates. The results suggest that newly designed compounds P5, P2 and P7 can be used as a potential anti-breast cancer drug candidate.
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Affiliation(s)
- Sanjeevi Pandiyan
- Research Center for Intelligent Information Technology, Nantong University, Nantong, China; School of Information Science and Technology, Nantong University, Nantong, China; Nantong Research Institute for Advanced Communication Technologies, Nantong, China.
| | - Li Wang
- Research Center for Intelligent Information Technology, Nantong University, Nantong, China; School of Information Science and Technology, Nantong University, Nantong, China; Nantong Research Institute for Advanced Communication Technologies, Nantong, China
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31
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Ranteh O, Tedasen A, Rahman MA, Ibrahim MA, Sama-Ae I. Bioactive compounds from Ocimum tenuiflorum and Poria cocos: A novel natural Compound for insomnia treatment based on A computational approach. Comput Biol Med 2024; 175:108491. [PMID: 38657467 DOI: 10.1016/j.compbiomed.2024.108491] [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: 09/05/2023] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 04/26/2024]
Abstract
Insomnia, a widespread public health issue, is associated with substantial distress and daytime functionality impairments and can predispose to depression and cardiovascular disease. Cognitive Behavioral Anti-insomnia therapies including benzodiazepines often face limitations due to patient adherence or potential adverse effects. This study focused on identifying novel bioactive compounds from medicinal plants, aiming to discover and develop new therapeutic agents with low risk-to-benefit ratios using computational drug discovery methods. Through a systematic framework involving compound library preparation, evaluation of drug-likeness and pharmacokinetics, toxicity prediction, molecular docking, and molecular dynamic simulations, two natural compounds such as 2-(4-hydroxy-3-methoxyphenyl)-8-methoxy-6-prop-2-enyl-3,4-dihydro-2H-chromen-3-ol from Ocimum tenuiflorum and 7-(2-hydroxypropan-2-yl)-1,4a-dimethyl-9-oxo-3,4,10,10a-tetrahydro-2H-phenanthrene-1-carboxylic acid from Poria cocos exhibited high binding affinity with orexin receptor type 1 (OX1R) and type 2 (OX2R), surpassing commercial drugs used in insomnia treatment. Additionally, they showed interactions with critical amino acid residues within the receptors that play crucial roles in competitive inhibitor activity, like commercial drugs such as Suvorexant, Lemborexant, and Daridorexant. Further, molecular dynamics simulations of the protein-ligand complexes under conditions that mimic the in vivo environment revealed both compounds' sustained and robust interactions with the OX1R and OX2R, reinforcing their potential as effective therapeutic candidates. Furthermore, upon evaluating both compounds' drug-likeness, pharmacokinetics, and toxicity profiles, it was discerned that they displayed considerable drug-like properties and favorable pharmacokinetics, along with diminished toxicity. The research provides a solid foundation for further exploring and validating these compounds as potential anti-insomnia therapeutics.
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Affiliation(s)
- Onggan Ranteh
- Department of Community Public Health, School of Public Health, Walailak University, Tha Sala District, Nakhon Si Thammarat, 80160, Thailand; Excellent Centre of Dengue and Community Public Health (EC for DACH), Walailak University, Tha Sala District, Nakhon Si Thammarat, 80160, Thailand.
| | - Aman Tedasen
- Department of Medical Technology, School of Allied Health Sciences, Walailak University, Tha Sala District, Nakhon Si Thammarat, 80160, Thailand; Research Excellence Center for Innovation and Health Products, Walailak University, Tha Sala, Nakhon Si Thammarat, 80161, Thailand.
| | - Md Atiar Rahman
- Department of Medical Technology, School of Allied Health Sciences, Walailak University, Tha Sala District, Nakhon Si Thammarat, 80160, Thailand; Department of Biochemistry and Molecular Biology, University of Chittagong, Chittagong-4331, Bangladesh.
| | | | - Imran Sama-Ae
- Department of Medical Technology, School of Allied Health Sciences, Walailak University, Tha Sala District, Nakhon Si Thammarat, 80160, Thailand; Center of Excellence Research for Melioidosis and Microorganisms (CERMM), Walailak University, Tha Sala District, Nakhon Si Thammarat, 80160, Thailand.
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32
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Faris A, Hadni H, Ibrahim IM, Elhallaoui M. In silico discovery of potent and selective Janus kinase 3 (JAK3) inhibitors through 3D-QSAR, covalent docking, ADMET analysis, molecular dynamics simulations, and binding free energy of pyrazolopyrimidine derivatives. J Biomol Struct Dyn 2024; 42:4817-4833. [PMID: 37338041 DOI: 10.1080/07391102.2023.2222839] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 06/02/2023] [Indexed: 06/21/2023]
Abstract
Rheumatoid arthritis is a prevalent and debilitating chronic disease worldwide. Targeting Janus kinase 3 (JAK3) has emerged as a crucial molecular strategy to treat this condition. In this study, we employed a comprehensive theoretical approach that included 3D-QSAR, covalent docking, ADMET, and molecular dynamics to propose and optimize new anti-JAK3 compounds. We investigated a series of 28 1H-pyrazolo[3.4-d]pyrimidin-4-amino inhibitors and developed a highly accurate 3D-QSAR model using comparative molecular similarity index analysis (COMSIA). The model predicted with Q2 = 0.59, R2 = 0.96, and R2(Pred) = 0.89, was validated using Y-randomization and external validation methods. Our covalent docking studies identified T3 and T5 as highly potent inhibitors of JAK3 compared to the reference ligand 17. Additionally, we evaluated the ADMET properties and drug similarity of our newly developed compounds and reference ligand, providing critical insights for further optimization of anti-JAK3 medications. Furthermore, MM-GBSA analysis showed promising results for the designed compounds. Finally, we validated our docking results using molecular dynamics simulations, which confirmed the stability of hydrogen bonding contacts with key residues required to block JAK3 activity. Our findings offer new chemical scaffolds and insights that could lead to the development of novel and effective JAK3 therapeutic targets for treating rheumatoid arthritis.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Abdelmoujoud Faris
- LIMAS, Department of Chemical Sciences, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Hanine Hadni
- LIMAS, Department of Chemical Sciences, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Ibrahim M Ibrahim
- Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt
| | - Menana Elhallaoui
- LIMAS, Department of Chemical Sciences, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
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33
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Guerfi M, Berredjem M, Dekir A, Bahadi R, Djouad SE, Sothea TO, Redjemia R, Belhani B, Boussaker M. Anticancer activity, DFT study, ADMET prediction, and molecular docking of novel α-sulfamidophosphonates. Mol Divers 2024; 28:1023-1038. [PMID: 37010709 DOI: 10.1007/s11030-023-10630-w] [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: 01/22/2023] [Accepted: 03/09/2023] [Indexed: 04/04/2023]
Abstract
A series of novel α-sulfamidophosphonate derivatives (3a-3 g) were synthesized and evaluated for anticancer activity against different human cancer cell lines (PRI, K562, and JURKAT). The antitumor activity of all compounds using the MTT test remains moderate compared to the standard drug chlorambucil. Compounds 3c and 3 g were found to be more active anticancer agent against PRI and K562 cells with IC50 value 0.056-0.097 and 0.182-0.133 mM, respectively. Molecular docking study related to binding affinity and binding mode analysis showed that synthesized compounds had potential to inhibit glutamate carboxypeptidase II (GCPII). Furthermore, computational analysis was performed through Density Functional Theory (DFT) utilizing the B3LYP 6-31 G (d, p) basis set and the theoretical results were correlated with experimental data. The ADME/toxicity analyses carried out by Swiss ADME and OSIRIS software show that all synthesized molecules exhibited good pharmacokinetics, bioavailability, and had no toxicity profile.
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Affiliation(s)
- Meriem Guerfi
- Chemistry Department, Laboratory of Applied Organic Chemistry, Synthesis of Biomolecules and Molecular Modelling Group, Sciences Faculty, Badji-Mokhtar Annaba University, Box 12, 23000, Annaba, Algeria
| | - Malika Berredjem
- Chemistry Department, Laboratory of Applied Organic Chemistry, Synthesis of Biomolecules and Molecular Modelling Group, Sciences Faculty, Badji-Mokhtar Annaba University, Box 12, 23000, Annaba, Algeria.
| | - Ali Dekir
- Chemistry Department, Laboratory of Applied Organic Chemistry, Synthesis of Biomolecules and Molecular Modelling Group, Sciences Faculty, Badji-Mokhtar Annaba University, Box 12, 23000, Annaba, Algeria
| | - Rania Bahadi
- Chemistry Department, Laboratory of Applied Organic Chemistry, Synthesis of Biomolecules and Molecular Modelling Group, Sciences Faculty, Badji-Mokhtar Annaba University, Box 12, 23000, Annaba, Algeria
| | - Seif-Eddine Djouad
- Chemistry Department, Laboratory of Applied Organic Chemistry, Synthesis of Biomolecules and Molecular Modelling Group, Sciences Faculty, Badji-Mokhtar Annaba University, Box 12, 23000, Annaba, Algeria
- Laboratory of Therapeutic Chemistry of Hospitalo-University Center Benflis Touhami, Batna, Algeria
| | - Tan Ouk Sothea
- Laboratoire Peirene, EA7500 Université de Limoges, 123 Avenue Albert Thomas, 87000, Limoges Cedex, France
| | - Rayenne Redjemia
- Chemistry Department, Laboratory of Applied Organic Chemistry, Synthesis of Biomolecules and Molecular Modelling Group, Sciences Faculty, Badji-Mokhtar Annaba University, Box 12, 23000, Annaba, Algeria
| | - Billel Belhani
- Chemistry Department, Laboratory of Applied Organic Chemistry, Synthesis of Biomolecules and Molecular Modelling Group, Sciences Faculty, Badji-Mokhtar Annaba University, Box 12, 23000, Annaba, Algeria
| | - Meriem Boussaker
- Chemistry Department, Laboratory of Applied Organic Chemistry, Synthesis of Biomolecules and Molecular Modelling Group, Sciences Faculty, Badji-Mokhtar Annaba University, Box 12, 23000, Annaba, Algeria
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34
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Batista JEDS, Rodrigues MB, Bristot IJ, Silva V, Bernardy S, Rodrigues OED, Dornelles L, Carvalho FB, de Sousa FJF, Fernandes MDC, Zanatta G, Soares FAA, Klamt F. Systematic screening of synthetic organochalcogen compounds with anticancer activity using human lung adenocarcinoma spheroids. Chem Biol Interact 2024; 396:111047. [PMID: 38735454 DOI: 10.1016/j.cbi.2024.111047] [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: 03/15/2024] [Revised: 05/06/2024] [Accepted: 05/10/2024] [Indexed: 05/14/2024]
Abstract
Lung adenocarcinoma stands as a leading global cause of cancer-related fatalities, with current therapeutic approaches remaining unsatisfactory. Given the association between elevated oxidative markers and the aggressive nature of cancer cells (including multidrug resistance and metastatic potential) that can predict poor outcome of lung adenocarcinoma patients, any compounds that interfere with their aberrant redox biology should be rationally explored as innovative intervention strategies. This study was designed to screen potential anticancer activities within nine newly synthesized organochalcogen - compounds characterized by the presence of oxygen, sulfur, or selenium elements in their structure and exhibiting antioxidant activity - and systematically evaluated their performance against cisplatin, the cornerstone therapeutic agent for lung adenocarcinoma. Our methodology involved the establishment of optimal conditions for generating single tumor spheroids using A549 human lung adenocarcinoma cell line. The initiation interval for spheroid formation was determined to be four days in vitro (DIV), and these single spheroids demonstrated sustained growth over a period of 20 DIV. Toxic dose-response curves were subsequently performed for each compound after 24 and 48 h of incubation at the 12th DIV. Our findings reveal that at least two of the synthetic organochalcogen compounds exhibited noteworthy anticancer activity, surpassing cisplatin in key parameters such as lower LD (Lethal Dose) 50, larger drug activity area, and maximum amplitude of effect, and are promising drugs for futures studies in the treatment of lung adenocarcinomas. Physicochemical descriptors and prediction ADME (absorption, distribution, metabolism, and excretion) parameters of selected compounds were obtained using SwissADME computational tool; Molinspiration server was used to calculate a biological activity score, and possible molecule targets were evaluated by prediction with the SwissTargetPrediction server. This research not only sheds light on novel avenues for therapeutic exploration but also underscores the potential of synthetic organochalcogen compounds as agents with superior efficacy compared to established treatments.
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Affiliation(s)
- Jéssica Eduarda Dos Santos Batista
- Department of Biochemistry and Molecular Biology, Federal University of Santa Maria (UFSM), Santa Maria, RS, 97105-900, Brazil; Laboratory of Cellular Biochemistry, Department of Biochemistry, Institute of Basic Health Sciences (ICBS), Federal University of Rio Grande Do Sul (UFRGS), Porto Alegre, RS, 90035-003, Brazil; National Institutes of Science and Technology-Translational Medicine (INCT-TM), Brazil
| | | | - Ivi Juliana Bristot
- Laboratory of Cellular Biochemistry, Department of Biochemistry, Institute of Basic Health Sciences (ICBS), Federal University of Rio Grande Do Sul (UFRGS), Porto Alegre, RS, 90035-003, Brazil; National Institutes of Science and Technology-Translational Medicine (INCT-TM), Brazil
| | - Valquíria Silva
- Laboratory of Cellular Biochemistry, Department of Biochemistry, Institute of Basic Health Sciences (ICBS), Federal University of Rio Grande Do Sul (UFRGS), Porto Alegre, RS, 90035-003, Brazil; National Institutes of Science and Technology-Translational Medicine (INCT-TM), Brazil
| | - Silvia Bernardy
- Department of Chemistry, Federal University of Santa Maria (UFSM), Santa Maria, RS, 97105-900, Brazil
| | | | - Luciano Dornelles
- Department of Chemistry, Federal University of Santa Maria (UFSM), Santa Maria, RS, 97105-900, Brazil
| | - Fabiano Barbosa Carvalho
- Pathology Laboratory, Federal University of Health Sciences of Porto Alegre (UFCSPA), Porto Alegre, RS, 90050-170, Brazil
| | | | - Marilda da Cruz Fernandes
- Pathology Laboratory, Federal University of Health Sciences of Porto Alegre (UFCSPA), Porto Alegre, RS, 90050-170, Brazil
| | - Geancarlo Zanatta
- Department of Biophysics, UFRGS, Porto Alegre, RS, 91501-970, Brazil
| | - Félix Alexandre Antunes Soares
- Department of Biochemistry and Molecular Biology, Federal University of Santa Maria (UFSM), Santa Maria, RS, 97105-900, Brazil
| | - Fábio Klamt
- Laboratory of Cellular Biochemistry, Department of Biochemistry, Institute of Basic Health Sciences (ICBS), Federal University of Rio Grande Do Sul (UFRGS), Porto Alegre, RS, 90035-003, Brazil; National Institutes of Science and Technology-Translational Medicine (INCT-TM), Brazil.
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35
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Raduly FM, Raditoiu V, Raditoiu A, Nicolae CA, Grapin M, Stan MS, Voinea IC, Vlasceanu RI, Nitu CD, Mihailescu DF, Avram S, Mernea M. Half-Curcuminoids Encapsulated in Alginate-Glucosamine Hydrogel Matrices as Bioactive Delivery Systems. Gels 2024; 10:376. [PMID: 38920923 PMCID: PMC11203298 DOI: 10.3390/gels10060376] [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: 04/20/2024] [Revised: 05/14/2024] [Accepted: 05/28/2024] [Indexed: 06/27/2024] Open
Abstract
The therapeutic effects of curcumin and its derivatives, based on research in recent years, are limited by their low bioavailability. To improve bioavailability and develop the medical field of application, different delivery systems have been developed that are adapted to certain environments or the proposed target type. This study presents some half-curcuminoids prepared by the condensation of acetylacetone with 4-hydroxybenzaldehyde (C1), 4-hydroxy-3-methoxybenzaldehyde (C2), 4-acetamidobenzaldehyde (C3), or 4-diethylaminobenzaldehyde (C4), at microwaves as a simple, solvent-free, and eco-friendly method. The four compounds obtained were characterized in terms of morphostructural and photophysical properties. Following the predictions of theoretical studies on the biological activities related to the molecular structure, in vitro tests were performed for compounds C1-C3 to evaluate the antitumor properties and for C4's possible applications in the treatment of neurological diseases. The four compounds were encapsulated in two types of hydrogel matrices. First, the alginate-glucosamine network was generated and then the curcumin analogs were loaded (G1, G3, G5-G7, and G9). The second type of hydrogels was obtained by loading the active compound together with the generation of the hydrogel carrier matrices, by simply dissolving (G4 and G10) or by chemically binding half-curcuminoid derivatives to glucosamine (G2 and G8). Thus, two types of curcumin analog delivery systems were obtained, which could be applied in various types of medical treatments.
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Affiliation(s)
- Florentina Monica Raduly
- National Research and Development Institute for Chemistry and Petrochemistry—ICECHIM, 202 Splaiul Independentei, 060021 Bucharest, Romania; (F.M.R.); (A.R.); (C.A.N.); (M.G.)
| | - Valentin Raditoiu
- National Research and Development Institute for Chemistry and Petrochemistry—ICECHIM, 202 Splaiul Independentei, 060021 Bucharest, Romania; (F.M.R.); (A.R.); (C.A.N.); (M.G.)
| | - Alina Raditoiu
- National Research and Development Institute for Chemistry and Petrochemistry—ICECHIM, 202 Splaiul Independentei, 060021 Bucharest, Romania; (F.M.R.); (A.R.); (C.A.N.); (M.G.)
| | - Cristian Andi Nicolae
- National Research and Development Institute for Chemistry and Petrochemistry—ICECHIM, 202 Splaiul Independentei, 060021 Bucharest, Romania; (F.M.R.); (A.R.); (C.A.N.); (M.G.)
| | - Maria Grapin
- National Research and Development Institute for Chemistry and Petrochemistry—ICECHIM, 202 Splaiul Independentei, 060021 Bucharest, Romania; (F.M.R.); (A.R.); (C.A.N.); (M.G.)
| | - Miruna Silvia Stan
- Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Bucharest, 91-95 Splaiul Independentei, 050095 Bucharest, Romania; (I.C.V.); (R.-I.V.)
| | - Ionela Cristina Voinea
- Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Bucharest, 91-95 Splaiul Independentei, 050095 Bucharest, Romania; (I.C.V.); (R.-I.V.)
| | - Raluca-Ioana Vlasceanu
- Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Bucharest, 91-95 Splaiul Independentei, 050095 Bucharest, Romania; (I.C.V.); (R.-I.V.)
| | - Cristina Doina Nitu
- Department of Anatomy, Animal Physiology and Biophysics, Faculty of Biology, University of Bucharest, 91-95 Splaiul Independentei, 050095 Bucharest, Romania; (C.D.N.); (D.F.M.); (S.A.); (M.M.)
- Institute of Oncology “Prof. dr. Al. Trestioreanu”, 252, Fundeni, 022328 Bucharest, Romania
| | - Dan F. Mihailescu
- Department of Anatomy, Animal Physiology and Biophysics, Faculty of Biology, University of Bucharest, 91-95 Splaiul Independentei, 050095 Bucharest, Romania; (C.D.N.); (D.F.M.); (S.A.); (M.M.)
| | - Speranta Avram
- Department of Anatomy, Animal Physiology and Biophysics, Faculty of Biology, University of Bucharest, 91-95 Splaiul Independentei, 050095 Bucharest, Romania; (C.D.N.); (D.F.M.); (S.A.); (M.M.)
| | - Maria Mernea
- Department of Anatomy, Animal Physiology and Biophysics, Faculty of Biology, University of Bucharest, 91-95 Splaiul Independentei, 050095 Bucharest, Romania; (C.D.N.); (D.F.M.); (S.A.); (M.M.)
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36
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Lim H. Development of scoring-assisted generative exploration (SAGE) and its application to dual inhibitor design for acetylcholinesterase and monoamine oxidase B. J Cheminform 2024; 16:59. [PMID: 38790018 PMCID: PMC11127438 DOI: 10.1186/s13321-024-00845-w] [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: 07/18/2023] [Accepted: 04/26/2024] [Indexed: 05/26/2024] Open
Abstract
De novo molecular design is the process of searching chemical space for drug-like molecules with desired properties, and deep learning has been recognized as a promising solution. In this study, I developed an effective computational method called Scoring-Assisted Generative Exploration (SAGE) to enhance chemical diversity and property optimization through virtual synthesis simulation, the generation of bridged bicyclic rings, and multiple scoring models for drug-likeness. In six protein targets, SAGE generated molecules with high scores within reasonable numbers of steps by optimizing target specificity without a constraint and even with multiple constraints such as synthetic accessibility, solubility, and metabolic stability. Furthermore, I suggested a top-ranked molecule with SAGE as dual inhibitors of acetylcholinesterase and monoamine oxidase B through multiple desired property optimization. Therefore, SAGE can generate molecules with desired properties by optimizing multiple properties simultaneously, indicating the importance of de novo design strategies in the future of drug discovery and development. SCIENTIFIC CONTRIBUTION: The scientific contribution of this study lies in the development of the Scoring-Assisted Generative Exploration (SAGE) method, a novel computational approach that significantly enhances de novo molecular design. SAGE uniquely integrates virtual synthesis simulation, the generation of complex bridged bicyclic rings, and multiple scoring models to optimize drug-like properties comprehensively. By efficiently generating molecules that meet a broad spectrum of pharmacological criteria-including target specificity, synthetic accessibility, solubility, and metabolic stability-within a reasonable number of steps, SAGE represents a substantial advancement over traditional methods. Additionally, the application of SAGE to discover dual inhibitors for acetylcholinesterase and monoamine oxidase B not only demonstrates its potential to streamline and enhance the drug development process but also highlights its capacity to create more effective and precisely targeted therapies. This study emphasizes the critical and evolving role of de novo design strategies in reshaping the future of drug discovery and development, providing promising avenues for innovative therapeutic discoveries.
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Affiliation(s)
- Hocheol Lim
- Bioinformatics and Molecular Design Research Center (BMDRC), Incheon, Republic of Korea.
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Ranjbar S, Sadeghian P, Khademian S, Emami M, Jahromi ZP, Mirmajidi SH, Zare F, Negahdaripour M, Ghasemi Y, Khoshneviszadeh M. 5-Oxo-dihydropyranopyran derivatives as anti-proliferative agents; synthesis, biological evaluation, molecular docking, MD simulation, DFT, and in-silico pharmacokinetic studies. Heliyon 2024; 10:e29850. [PMID: 38707385 PMCID: PMC11066326 DOI: 10.1016/j.heliyon.2024.e29850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 04/14/2024] [Accepted: 04/16/2024] [Indexed: 05/07/2024] Open
Abstract
A series of ethyl 2-amino-7-methyl-5-oxo-4-phenyl-4,5-dihydropyrano[4,3-b]pyran-3-carboxylate derivatives (4a-j) bearing different substitutions on the C4-phenyl ring was synthesized. The anti-proliferative activity of all the synthesized compounds was assessed against two human cancer-cell lines, including SW-480 and MCF-7, by using MTT method. Derivatives 4g, 4i, and 4j, possessing 4-NO2, 4-Cl, and 3,4,5-(OCH3)3 substitutions, were found to be the most potent compounds against both cell lines. The obtained IC50 values for 4g, 4i, and 4j were 34.6, 35.9, and 38.6 μM against SW-480 cells and 42.6, 34.2, and 26.6 μM against MCF-7 cells, respectively. Evaluation of the free radical scavenging potential of the compounds against DPPH radicals showed the highest result for compound 4j with an EC50 value of 580 μM. Molecular docking studies revealed the compounds were well accommodated within the binding site of cyclin-dependent kinase-2 (CDK2) with binding energies comparable to those of DTQ (the co-crystallized inhibitor) and BMS-265246 (a well-known CDK2 inhibitor). Molecular dynamics simulation studies confirmed the interactions and stability of the 4g-CDK2 complex. All derivatives, except 4g, were predicted to comply with the drug-likeness rules. Compound 4j may be proposed as an anti-cancer lead candidate for further studies due to the promising findings from in-silico pharmacokinetic studies, such as high GI absorption, not being a P-gp substrate, and being a P-gp inhibitor. Density functional theory (DFT) analysis was performed at the B3LYP/6-311++G (d,p) level of theory to examine the reactivity or stability descriptors of 4d, 4g, 4i, and 4j derivatives. The highest value of energy gap between HOMO and LUMO and thermochemical parameters were obtained for 4i and 4j.
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Affiliation(s)
- Sara Ranjbar
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
- Computational Vaccine and Drug Design Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Paria Sadeghian
- Department of Medicinal Chemistry, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Sara Khademian
- Department of Medicinal Chemistry, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mina Emami
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zahra Pakrouh Jahromi
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Seyedeh Habibeh Mirmajidi
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Fateme Zare
- Department of Medicinal Chemistry, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Manica Negahdaripour
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
- Computational Vaccine and Drug Design Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Younes Ghasemi
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mehdi Khoshneviszadeh
- Computational Vaccine and Drug Design Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Medicinal Chemistry, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
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Ismail TI, El-Khazragy N, Azzam RA. In the pursuit of novel therapeutic agents: synthesis, anticancer evaluation, and physicochemical insights of novel pyrimidine-based 2-aminobenzothiazole derivatives. RSC Adv 2024; 14:16332-16348. [PMID: 38769969 PMCID: PMC11103668 DOI: 10.1039/d4ra01874e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 05/13/2024] [Indexed: 05/22/2024] Open
Abstract
Cancer remains a worldwide healthcare undertaking, demanding continual innovation in anticancer drug development due to frequent drug resistance and adverse effects associated with existing therapies. The benzothiazole compounds, particularly 2-aminobenzothiazole derivatives, have attracted interest for their versatility in generating novel anticancer agents. This study explores the synthesis, and anticancer evaluation of new pyrimidine-based 2-aminobenzothiazole derivatives. A range of synthetic methods have been developed based on the reaction of 2-benzothaizolyl guanidine with various reagents such as α,β-unsaturated carbonyl, 2-cyano-three-(dimethylamino)-N-acrylamide, β-diketones, β-keto esters, and S,S ketene dithioacetals. Human tumour cell lines such as HepG2, HCT116, and MCF7 were used in in vitro cytotoxicity studies, and the results showed that several of the synthesized compounds were more potent than the standard drug, 5-fluorouracil, in terms of cell viability% with low IC50. Furthermore, the computed drug likeness and ADMET properties of the most potent synthesized compounds suggest their potential as promising candidates for further development, with favorable bioavailability and pharmacokinetic profiles.
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Affiliation(s)
- Toka I Ismail
- Chemistry Department, Faculty of Science, Helwan University Cairo 11795 Egypt
| | - Nashwa El-Khazragy
- Department of Clinical Pathology-Hematology, Ain Shams Medical Research Institute (MASRI), Faculty of Medicine, Ain Shams University Cairo 11566 Egypt
- Department of Genetics and Molecular Biology, Egypt Center for Research and Regenerative Medicine (ECRRM) Cairo 11599 Egypt
| | - Rasha A Azzam
- Chemistry Department, Faculty of Science, Helwan University Cairo 11795 Egypt
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Tanvir R, Ijaz S, Sajid I, Hasnain S. Multifunctional in vitro, in silico and DFT analyses on antimicrobial BagremycinA biosynthesized by Micromonospora chokoriensis CR3 from Hieracium canadense. Sci Rep 2024; 14:10976. [PMID: 38745055 PMCID: PMC11093986 DOI: 10.1038/s41598-024-61490-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 05/06/2024] [Indexed: 05/16/2024] Open
Abstract
Among the actinomycetes in the rare genera, Micromonospora is of great interest since it has been shown to produce novel therapeutic compounds. Particular emphasis is now on its isolation from plants since its population from soil has been extensively explored. The strain CR3 was isolated as an endophyte from the roots of Hieracium canadense, and it was identified as Micromonospora chokoriensis through 16S gene sequencing and phylogenetic analysis. The in-vitro analysis of its extract revealed it to be active against the clinical isolates of methicillin-resistant Staphylococcus aureus (MRSA) and Candida tropicalis (15 mm). No bioactivity was observed against Gram-negative bacteria, Escherichia coli ATCC 25922, and Klebsiella pneumoniae ATCC 706003. The Micromonospora chokoriensis CR3 extract was also analyzed through the HPLC-DAD-UV-VIS resident database, and it gave a maximum match factor of 997.334 with the specialized metabolite BagremycinA (BagA). The in-silico analysis indicated that BagA strongly interacted with the active site residues of the sterol 14-α demethylase and thymidylate kinase enzymes, with the lowest binding energies of - 9.7 and - 8.3 kcal/mol, respectively. Furthermore, the normal mode analysis indicated that the interaction between these proteins and BagA was stable. The DFT quantum chemical properties depicted BagA to be reasonably reactive with a HOMO-LUMO gap of (ΔE) of 4.390 eV. BagA also passed the drug-likeness test with a synthetic accessibility score of 2.06, whereas Protox-II classified it as a class V toxicity compound with high LD50 of 2644 mg/kg. The current study reports an endophytic actinomycete, M. chokoriensis, associated with H. canadense producing the bioactive metabolite BagA with promising antimicrobial activity, which can be further modified and developed into a safe antimicrobial drug.
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Affiliation(s)
- Rabia Tanvir
- Institute of Microbiology (IOM), University of Veterinary and Animal Sciences (UVAS), Lahore, 54000, Punjab, Pakistan.
| | - Saadia Ijaz
- Department of Microbiology and Molecular Genetics, The Women University, Multan, 66000, Punjab, Pakistan
| | - Imran Sajid
- Institute of Microbiology and Molecular Genetics (IMMG), University of the Punjab, Quaid-e-Azam Campus, Lahore, 54590, Punjab, Pakistan
| | - Shahida Hasnain
- Institute of Microbiology and Molecular Genetics (IMMG), University of the Punjab, Quaid-e-Azam Campus, Lahore, 54590, Punjab, Pakistan
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Faris M, Bostancı HE, Özcan İ, Öztürk M, Koçyiğit ÜM, Erdoğan T, Tahtaci H. Imidazole-Derived Alkyl and Aryl Ethers: Synthesis, Characterization, In Vitro Anticancer and Antioxidant Activities, Carbonic Anhydrase I-II Inhibition Properties, and In Silico Studies. ACS OMEGA 2024; 9:20937-20956. [PMID: 38764643 PMCID: PMC11097166 DOI: 10.1021/acsomega.4c00028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 04/16/2024] [Accepted: 04/23/2024] [Indexed: 05/21/2024]
Abstract
Imidazole derivatives display extensive applications in pharmaceutical chemistry and have been investigated as bioactive compounds for medicinal chemistry. In this study, besides the starting materials (3a-c and 4a-c), synthesis, characterization, and biological activity studies were conducted on a total of 18 compounds, nine of which are known and the other nine are original. The compounds investigated in the study are a series of alkyl (7-15) and aryl (16-24) ether derivatives bearing substituted phenyl and imidazole rings, which were characterized using various methods including 1H NMR, 13C NMR, FT-IR analysis, elemental analysis, and mass spectroscopy. Computer-aided drug design studies have been carried out to predict the biological activities of compounds. Besides DFT calculations, the binding affinities of the compounds to EGFR, VEGFR2, FGFR1, HSP90, hCA I, and hCA II were investigated. Additionally, drug-likeness and ADME analyses were performed on the compounds. Anticancer, antioxidant, and enzyme inhibition activity tests were performed in biological activity studies on the synthesized compounds. Among the synthesized compounds, compounds 17 and 19-24 generally exhibited inhibition profiles against the widespread cytosolic hCA I isozyme with IC50 values ranging from 4.13 to 15.67 nM and cytosolic hCA II isozyme with IC50 values ranging from 5.65 to 14.84 nM. L929 (mouse fibroblast cell line) was used as the control healthy cell line, and MCF7 (breast cancer), C6 (rat glioblastoma), and HT-29 (colon cancer) cells were used in cell culture studies as cancer cell lines. Before the study on cancer cells, all compounds were examined on healthy cells, and their cytotoxicity was determined. As a result of these data, studies continued with six compounds determined to be nontoxic. On cancerous cells, it was determined that compounds 3a, 3b, 4a, 4b, 4c, and 7 had cytotoxic effects on both colon cancer and brain tumors. It was found that compound 3b had a more toxic effect than cisplatin on the glioma cell line with an IC50 value of 10.721 ± 0.38 μM, and compound 3a had a more toxic effect on the colon cancer cell line with an IC50 value of 20.88 ± 1.02 μM. However, it was determined that the same compounds did not have a statistically significant effect on breast cancer. Flow cytometry studies also showed that when the IC50 dose of compound 3b was applied to the C6 cell line, the cells tended to early and late apoptosis. Additionally, it has been shown by flow cytometry that the cell cycle stops in the G0/G1 phase. A similar effect was observed in the colon cancer cell line with compound 3a. Compound 3b caused early and late apoptosis of the colon cancer cell line with the applied IC50 dose and stopped the cell cycle in the G0/G1 phase. Finally, the FRAP method studied all synthesized compounds' antioxidant effects. According to the measured antioxidant power results, it was determined that no compound had a more effective reducing power than vitamin E.
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Affiliation(s)
- Mays Faris
- Department
of Chemistry, Faculty of Science, Karabuk
University, 78050 Karabuk, Türkiye
| | - Hayrani Eren Bostancı
- Department
of Biochemistry Sivas, Faculty of Pharmacy, Sivas Cumhuriyet University, 58010 Sivas, Türkiye
| | - İbrahim Özcan
- Department
of Chemistry, Faculty of Science, Karabuk
University, 78050 Karabuk, Türkiye
| | - Mustafa Öztürk
- Sivas
Vocational School of Technical Sciences, Sivas Cumhuriyet University, 58010 Sivas, Türkiye
| | - Ümit Muhammed Koçyiğit
- Department
of Biochemistry Sivas, Faculty of Pharmacy, Sivas Cumhuriyet University, 58010 Sivas, Türkiye
| | - Taner Erdoğan
- Kocaeli
Vocational School, Department of Chemistry and Chemical Processing
Technologies, Kocaeli University, 41140 Kocaeli, Türkiye
| | - Hakan Tahtaci
- Department
of Chemistry, Faculty of Science, Karabuk
University, 78050 Karabuk, Türkiye
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Allam RM, El Kerdawy AM, Gouda AE, Ahmed KA, Abdel-Mohsen HT. Benzimidazole-oxindole hybrids as multi-kinase inhibitors targeting melanoma. Bioorg Chem 2024; 146:107243. [PMID: 38457953 DOI: 10.1016/j.bioorg.2024.107243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 02/15/2024] [Accepted: 02/24/2024] [Indexed: 03/10/2024]
Abstract
In the current study, a series of benzimidazole-oxindole conjugates 8a-t were designed and synthesized as type II multi-kinase inhibitors. They exhibited moderate to potent inhibitory activity against BRAFWT up to 99.61 % at 10 µM. Notably, compounds 8e, 8k, 8n and 8s demonstrated the most promising activity, with 99.44 to 99.61 % inhibition. Further evaluation revealed that 8e, 8k, 8n and 8s exhibit moderate to potent inhibitory effects on the kinases BRAFV600E, VEGFR-2, and FGFR-1. Additionally, compounds 8a-t were screened for their cytotoxicity by the NCI, and several compounds showed significant growth inhibition in diverse cancer cell lines. Compound 8e stood out with a GI50 range of 1.23 - 3.38 µM on melanoma cell lines. Encouraged by its efficacy, it was further investigated for its antitumor activity and mechanism of action, using sorafenib as a reference standard. The hybrid compound 8e exhibited potent cellular-level suppression of BRAFWT, VEGFR-2, and FGFR-1 in A375 cell line, surpassing the effects of sorafenib. In vivo studies demonstrate that 8e significantly inhibits the growth of B16F10 tumors in mice, leading to increased survival rates and histopathological tumor regression. Furthermore, 8e reduces angiogenesis markers, mRNA expression levels of VEGFR-2 and FGFR-1, and production of growth factors. It also downregulated Notch1 protein expression and decreased TGF-β1 production. Molecular docking simulations suggest that 8e binds as a promising type II kinase inhibitor in the target kinases interacting with the key regions in their kinase domain.
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Affiliation(s)
- Rasha M Allam
- Department of Pharmacology, Medical and Clinical Research Institute, National Research Centre, El-Buhouth St., Dokki, P.O. Box 12622, Cairo, Egypt
| | - Ahmed M El Kerdawy
- School of Pharmacy, College of Health and Science, University of Lincoln, Joseph Banks Laboratories, Green Lane, Lincoln, United Kingdom; Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Cairo University, Kasr El-Aini Street, P.O. Box 11562, Cairo, Egypt
| | - Ahmed E Gouda
- Pharmaceutical Research Department, Nawah Scientific, Cairo, Egypt
| | - Kawkab A Ahmed
- Pathology Department, Faculty of Veterinary Medicine, Cairo University, Giza, 12211, Egypt
| | - Heba T Abdel-Mohsen
- Chemistry of Natural and Microbial Products Department, Pharmaceutical and Drug Industries Research Institute, National Research Centre, El-Buhouth St., Dokki, P.O. Box 12622, Cairo, Egypt.
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Al Khoury C, Tokajian S, Nemer N, Nemer G, Rahy K, Thoumi S, Al Samra L, Sinno A. Computational Applications: Beauvericin from a Mycotoxin into a Humanized Drug. Metabolites 2024; 14:232. [PMID: 38668360 PMCID: PMC11051850 DOI: 10.3390/metabo14040232] [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: 03/15/2024] [Revised: 04/09/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
Drug discovery was initially attributed to coincidence or experimental research. Historically, the traditional approaches were complex, lengthy, and expensive, entailing costly random screening of synthesized compounds or natural products coupled with in vivo validation largely depending on the availability of appropriate animal models. Currently, in silico modeling has become a vital tool for drug discovery and repurposing. Molecular docking and dynamic simulations are being used to find the best match between a ligand and a molecule, an approach that could help predict the biomolecular interactions between the drug and the target host. Beauvericin (BEA) is an emerging mycotoxin produced by the entomopathogenic fungus Beauveria bassiana, being originally studied for its potential use as a pesticide. BEA is now considered a molecule of interest for its possible use in diverse biotechnological applications in the pharmaceutical industry and medicine. In this manuscript, we provide an overview of the repurposing of BEA as a potential therapeutic agent for multiple diseases. Furthermore, considerable emphasis is given to the fundamental role of in silico techniques to (i) further investigate the activity spectrum of BEA, a secondary metabolite, and (ii) elucidate its mode of action.
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Affiliation(s)
- Charbel Al Khoury
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Beirut Campus, P.O. Box 13-5053, Chouran, Beirut 1102 2801, Lebanon
| | - Sima Tokajian
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Byblos Campus, Byblos P.O. Box 36, Lebanon
| | - Nabil Nemer
- Department of Agriculture and Food Engineering, Holy Spirit University of Kaslik, Jounieh P.O. Box 446, Lebanon
| | - Georges Nemer
- Division of Genomics and Translational Biomedicine, College of Health and Life Sciences, Hamad Bin Khalifa University, Doha P.O. Box 34110, Qatar
| | - Kelven Rahy
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Byblos P.O. Box 36, Lebanon
| | - Sergio Thoumi
- Department of Computer Science and Mathematics, Lebanese American University, Beirut P.O. Box 13-5053, Lebanon
| | - Lynn Al Samra
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Beirut Campus, P.O. Box 13-5053, Chouran, Beirut 1102 2801, Lebanon
| | - Aia Sinno
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Beirut Campus, P.O. Box 13-5053, Chouran, Beirut 1102 2801, Lebanon
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Stevanović MZ, Bekić SS, Petri ET, Ćelić AS, Jakimov DS, Sakač MN, Kuzminac IZ. Synthesis, in vitro and in silico anticancer evaluation of novel pyridin-2-yl estra-1,3,5(10)-triene derivatives. Future Med Chem 2024; 16:1127-1145. [PMID: 38629440 PMCID: PMC11221553 DOI: 10.4155/fmc-2024-0039] [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: 02/01/2024] [Accepted: 03/26/2024] [Indexed: 06/26/2024] Open
Abstract
Aim: The aim of this study was the synthesis of steroid compounds with heterocyclic rings and good anticancer properties. Materials & methods: The synthesis, in silico and in vitro anticancer testing of novel pyridin-2-yl estra-1,3,5(10)-triene derivatives was performed. Results: All synthesized compounds have shown promising results for, antiproliferative activity, relative binding affinities for the ligand binding domains of estrogen receptors α, β and androgen receptor, aromatase binding potential, and inhibition of AKR1C3 enzyme. Conclusion: 3-Benzyloxy (17E)-pycolinilidene derivative 9 showed the best antitumor potential against MDA-MB-231 cell line, an activity that can be explained by its moderate inhibition of AKR1C3. Molecular docking simulation indicates that it binds to AKR1C3 in a very similar orientation and geometry as steroidal inhibitor EM1404.
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Affiliation(s)
- Milica Z Stevanović
- Department of Chemistry, Biochemistry & Environmental Protection, University of Novi Sad, Faculty of Sciences, Trg Dositeja Obradovića 3, 21000 Novi Sad, Serbia
| | - Sofija S Bekić
- Department of Chemistry, Biochemistry & Environmental Protection, University of Novi Sad, Faculty of Sciences, Trg Dositeja Obradovića 3, 21000 Novi Sad, Serbia
| | - Edward T Petri
- Department of Biology & Ecology, University of Novi Sad, Faculty of Sciences, Trg Dositeja Obradovića 2, 21000 Novi Sad, Serbia
| | - Andjelka S Ćelić
- Department of Biology & Ecology, University of Novi Sad, Faculty of Sciences, Trg Dositeja Obradovića 2, 21000 Novi Sad, Serbia
| | - Dimitar S Jakimov
- Oncology Institute of Vojvodina, Faculty of Medicine, University of Novi Sad, Put Dr Goldmana 4, 21204 Sremska Kamenica, Serbia
| | - Marija N Sakač
- Department of Chemistry, Biochemistry & Environmental Protection, University of Novi Sad, Faculty of Sciences, Trg Dositeja Obradovića 3, 21000 Novi Sad, Serbia
| | - Ivana Z Kuzminac
- Department of Chemistry, Biochemistry & Environmental Protection, University of Novi Sad, Faculty of Sciences, Trg Dositeja Obradovića 3, 21000 Novi Sad, Serbia
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Kibet S, Kimani NM, Mwanza SS, Mudalungu CM, Santos CBR, Tanga CM. Unveiling the Potential of Ent-Kaurane Diterpenoids: Multifaceted Natural Products for Drug Discovery. Pharmaceuticals (Basel) 2024; 17:510. [PMID: 38675469 PMCID: PMC11054903 DOI: 10.3390/ph17040510] [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: 03/15/2024] [Revised: 03/29/2024] [Accepted: 04/02/2024] [Indexed: 04/28/2024] Open
Abstract
Natural products hold immense potential for drug discovery, yet many remain unexplored in vast libraries and databases. In an attempt to fill this gap and meet the growing demand for effective drugs, this study delves into the promising world of ent-kaurane diterpenoids, a class of natural products with huge therapeutic potential. With a dataset of 570 ent-kaurane diterpenoids obtained from the literature, we conducted an in silico analysis, evaluating their physicochemical, pharmacokinetic, and toxicological properties with a focus on their therapeutic implications. Notably, these natural compounds exhibit drug-like properties, aligning closely with those of FDA-approved drugs, indicating a high potential for drug development. The ranges of the physicochemical parameters were as follows: molecular weights-288.47 to 626.82 g/mol; number of heavy atoms-21 to 44; the number of hydrogen bond donors and acceptors-0 to 8 and 1 to 11, respectively; the number of rotatable bonds-0 to 11; fraction Csp3-0.65 to 1; and TPSA-20.23 to 189.53 Ų. Additionally, the majority of these molecules display favorable safety profiles, with only 0.70%, 1.40%, 0.70%, and 46.49% exhibiting mutagenic, tumorigenic, reproduction-enhancing, and irritant properties, respectively. Importantly, ent-kaurane diterpenoids exhibit promising biopharmaceutical properties. Their average lipophilicity is optimal for drug absorption, while over 99% are water-soluble, facilitating delivery. Further, 96.5% and 28.20% of these molecules exhibited intestinal and brain bioavailability, expanding their therapeutic reach. The predicted pharmacological activities of these compounds encompass a diverse range, including anticancer, immunosuppressant, chemoprotective, anti-hepatic, hepatoprotectant, anti-inflammation, antihyperthyroidism, and anti-hepatitis activities. This multi-targeted profile highlights ent-kaurane diterpenoids as highly promising candidates for further drug discovery endeavors.
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Affiliation(s)
- Shadrack Kibet
- Department of Physical Sciences, University of Embu, Embu P.O. Box 6-60100, Kenya; (S.K.); (S.S.M.)
- International Centre of Insects Physiology and Ecology, Nairobi P.O. Box 30772-00100, Kenya;
| | - Njogu M. Kimani
- Department of Physical Sciences, University of Embu, Embu P.O. Box 6-60100, Kenya; (S.K.); (S.S.M.)
- Natural Product Chemistry and Computational Drug Discovery Laboratory, Embu P.O. Box 6-60100, Kenya
| | - Syombua S. Mwanza
- Department of Physical Sciences, University of Embu, Embu P.O. Box 6-60100, Kenya; (S.K.); (S.S.M.)
- International Centre of Insects Physiology and Ecology, Nairobi P.O. Box 30772-00100, Kenya;
| | - Cynthia M. Mudalungu
- International Centre of Insects Physiology and Ecology, Nairobi P.O. Box 30772-00100, Kenya;
- School of Chemistry and Material Science, The Technical University of Kenya, Nairobi P.O. Box 52428-00200, Kenya
| | - Cleydson B. R. Santos
- Graduate Program in Medicinal Chemistry and Molecular Modelling, Health Science Institute, Federal University of Pará, Belém 66075-110, Brazil;
- Laboratory of Modelling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, Brazil
| | - Chrysantus M. Tanga
- International Centre of Insects Physiology and Ecology, Nairobi P.O. Box 30772-00100, Kenya;
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Chowdhury R, Bhuia S, Rakib AI, Al Hasan S, Shill MC, El-Nashar HAS, El-Shazly M, Islam MT. Gigantol, a promising natural drug for inflammation: a literature review and computational based study. Nat Prod Res 2024:1-17. [PMID: 38623737 DOI: 10.1080/14786419.2024.2340042] [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: 10/11/2023] [Accepted: 03/26/2024] [Indexed: 04/17/2024]
Abstract
Gigantol, a bibenzyl compound extracted from various medicinal plants, has shown a number of biological activities, making it an attractive candidate for potential medical applications. This systematic review aims to shed light on gigantol's promising role in inflammation treatment and its underlying mechanisms. Gigantol exhibits potential anti-inflammatory properties in pre-clinical pharmacological test systems. It effectively reduced the levels of pro-inflammatory markers and arachidonic acid metabolites through various pathways, such as NF-κB, AKT, PI3K, and JNK/cPLA2/12-LOX. The in-silico investigations demonstrated that the MMP-13 enzyme served as the most promising target for gigantol with highest binding affinity (docking score = -8.8 kcal/mol). Encouragingly, the absorption, distribution, metabolism, excretion, and toxicity (ADMET) analysis of gigantol confirmed its compatibility with the necessary physiochemical, pharmacokinetic, and toxicity properties, bolstering its potential as a drug candidate. Gigantol, with its well-documented anti-inflammatory properties, could be a promising agent for treating inflammation in the near future.
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Affiliation(s)
- Raihan Chowdhury
- Department of Pharmacy, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Bangladesh
- Bioluster Research Center, Dhaka, Bangladesh
| | - Shimul Bhuia
- Department of Pharmacy, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Bangladesh
- Bioluster Research Center, Dhaka, Bangladesh
| | - Asraful Islam Rakib
- Department of Pharmacy, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Bangladesh
| | - Sakib Al Hasan
- Department of Pharmacy, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Bangladesh
| | - Manik Chandra Shill
- Department of Pharmaceutical Sciences, North South University, Dhaka, Bangladesh
| | - Heba A S El-Nashar
- Department of Pharmacognosy, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Mohamed El-Shazly
- Department of Pharmacognosy, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Muhammad Torequl Islam
- Department of Pharmacy, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Bangladesh
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Cheshmazar N, Hamzeh-Mivehroud M, Hemmati S, Abolhasani H, Heidari F, Charoudeh HN, Zessin M, Schutkowski M, Sippl W, Dastmalchi S. Key structural requirements of benzamide derivatives for histone deacetylase inhibition: design, synthesis and biological evaluation. Future Med Chem 2024; 16:859-872. [PMID: 38623995 PMCID: PMC11188831 DOI: 10.4155/fmc-2023-0122] [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: 04/30/2023] [Accepted: 03/18/2024] [Indexed: 04/17/2024] Open
Abstract
Background: Histone deacetylase inhibitors (HDACIs) are important as anticancer agents. Objective: This study aimed to investigate some key structural features of HDACIs via the design, synthesis and biological evaluation of novel benzamide-based derivatives. Methods: Novel structures, designed using a molecular modification approach, were synthesized and biologically evaluated. Results: The results indicated that a subset of molecules with CH3/NH2 at R2 position possess selective antiproliferative activity. However, only those with an NH2 group showed HDACI activity. Importantly, the shorter the molecule length, the stronger HDACI. Among all, 7j was the most potent HDAC1-3 inhibitor and antiproliferative compound. Conclusion: The results of the present investigation could provide valuable structural knowledge applicable for the development of the HDACIs and benzamide-based antiproliferative agents in the future.
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Affiliation(s)
- Narges Cheshmazar
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, 5165665813, Iran
| | - Maryam Hamzeh-Mivehroud
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, 5165665813, Iran
- Department of Medicinal Chemistry, School of Pharmacy, Tabriz University of Medical Sciences, Tabriz, 5166414766, Iran
| | - Salar Hemmati
- Drug applied research Center, Tabriz University of Medical Sciences, Tabriz, 5165665811, Iran
| | - Hoda Abolhasani
- Cellular & Molecular Research Center, Qom University of Medical Sciences, Qom, Iran
- Department of Pharmacology, School of Medicine, Qom University of Medical Sciences, Qom, Iran
| | - Fatemeh Heidari
- Cellular & Molecular Research Center, Qom University of Medical Sciences, Qom, Iran
| | | | - Matthes Zessin
- Department of Enzymology, Institute of Biochemistry, Martin-Luther-University Halle-Wittenberg, Halle/Saale, 06120, Germany
| | - Mike Schutkowski
- Department of Enzymology, Institute of Biochemistry, Martin-Luther-University Halle-Wittenberg, Halle/Saale, 06120, Germany
| | - Wolfgang Sippl
- Department of Medicinal Chemistry, Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, Halle/Saale, 06120, Germany
| | - Siavoush Dastmalchi
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, 5165665813, Iran
- Department of Medicinal Chemistry, School of Pharmacy, Tabriz University of Medical Sciences, Tabriz, 5166414766, Iran
- Faculty of Pharmacy, Near East University, PO Box 99138, Nicosia, North Cyprus, Mersin, 10, Turkey
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Clay WK, Buck AK, He Y, Hernández Sánchez DN, Ward NA, Lear JM, Nguyen KQ, Clark BH, Sapia RJ, Lalisse RF, Sriraman A, Cadieux CL, McElroy CA, Callam CS, Hadad CM. Treatment of Organophosphorus Poisoning with 6-Alkoxypyridin-3-ol Quinone Methide Precursors: Resurrection of Methylphosphonate-Aged Acetylcholinesterase. Chem Res Toxicol 2024; 37:643-657. [PMID: 38556765 DOI: 10.1021/acs.chemrestox.4c00024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/02/2024]
Abstract
Organophosphorus (OP) nerve agents inhibit acetylcholinesterase (AChE), creating a cholinergic crisis in which death can occur. The phosphylated serine residue spontaneously dealkylates to the OP-aged form, which current therapeutics cannot reverse. Soman's aging half-life is 4.2 min, so immediate recovery (resurrection) of OP-aged AChE is needed. In 2018, we showed pyridin-3-ol-based quinone methide precursors (QMPs) can resurrect OP-aged electric eel AChE in vitro, achieving 2% resurrection after 24 h of incubation (pH 7, 4 mM). We prepared 50 unique 6-alkoxypyridin-3-ol QMPs with 10 alkoxy groups and five amine leaving groups to improve AChE resurrection. These compounds are predicted in silico to cross the blood-brain barrier and treat AChE in the central nervous system. This library resurrected 7.9% activity of OP-aged recombinant human AChE after 24 h at 250 μM, a 4-fold increase from our 2018 report. The best QMP (1b), with a 6-methoxypyridin-3-ol core and a diethylamine leaving group, recovered 20.8% (1 mM), 34% (4 mM), and 42.5% (predicted maximum) of methylphosphonate-aged AChE activity over 24 h. Seven QMPs recovered activity from AChE aged with Soman and a VX degradation product (EA-2192). We hypothesize that QMPs form the quinone methide (QM) to realkylate the phosphylated serine residue as the first step of resurrection. We calculated thermodynamic energetics for QM formation, but there was no trend with the experimental biochemical data. Molecular docking studies revealed that QMP binding to OP-aged AChE is not the determining factor for the observed biochemical trends; thus, QM formation may be enzyme-mediated.
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Affiliation(s)
- William K Clay
- Department of Chemistry and Biochemistry, College of Arts and Sciences, The Ohio State University, Columbus, Ohio 43210, United States
| | - Anne K Buck
- Department of Chemistry and Biochemistry, College of Arts and Sciences, The Ohio State University, Columbus, Ohio 43210, United States
| | - Yiran He
- Department of Chemistry and Biochemistry, College of Arts and Sciences, The Ohio State University, Columbus, Ohio 43210, United States
| | - Dalyanne N Hernández Sánchez
- Department of Chemistry and Biochemistry, College of Arts and Sciences, The Ohio State University, Columbus, Ohio 43210, United States
| | - Nathan A Ward
- Department of Chemistry and Biochemistry, College of Arts and Sciences, The Ohio State University, Columbus, Ohio 43210, United States
| | - Jeremy M Lear
- Department of Chemistry and Biochemistry, College of Arts and Sciences, The Ohio State University, Columbus, Ohio 43210, United States
| | - Kenny Q Nguyen
- Department of Chemistry and Biochemistry, College of Arts and Sciences, The Ohio State University, Columbus, Ohio 43210, United States
| | - Benjamin H Clark
- Department of Chemistry and Biochemistry, College of Arts and Sciences, The Ohio State University, Columbus, Ohio 43210, United States
| | - Ryan J Sapia
- Department of Chemistry and Biochemistry, College of Arts and Sciences, The Ohio State University, Columbus, Ohio 43210, United States
| | - Remy F Lalisse
- Department of Chemistry and Biochemistry, College of Arts and Sciences, The Ohio State University, Columbus, Ohio 43210, United States
| | - Aishwarya Sriraman
- Oak Ridge Institute for Science and Education, 1299 Bethel Valley Road, Oak Ridge, Tennessee 37830, United States
- U.S. Army Medical Research Institute of Chemical Defense, 8350 Ricketts Point Road, Aberdeen Proving Ground, Maryland 21010, United States
| | - C Linn Cadieux
- U.S. Army Medical Research Institute of Chemical Defense, 8350 Ricketts Point Road, Aberdeen Proving Ground, Maryland 21010, United States
| | - Craig A McElroy
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Christopher S Callam
- Department of Chemistry and Biochemistry, College of Arts and Sciences, The Ohio State University, Columbus, Ohio 43210, United States
| | - Christopher M Hadad
- Department of Chemistry and Biochemistry, College of Arts and Sciences, The Ohio State University, Columbus, Ohio 43210, United States
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48
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Xu Y, Yang J, Han X, Gan C, Wei X. Active substance and mechanisms of Actinidia chinensis Planch for the treatment of breast cancer was explored based on network pharmacology and in silico study. Medicine (Baltimore) 2024; 103:e37829. [PMID: 38608062 PMCID: PMC11018190 DOI: 10.1097/md.0000000000037829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 03/15/2024] [Indexed: 04/14/2024] Open
Abstract
In this paper, our objective was to investigate the potential mechanisms of Actinidia chinensis Planch (ACP) for breast cancer treatment with the application of network pharmacology, molecular docking, and molecular dynamics. "Mihoutaogen" was used as a key word to query the Traditional Chinese Medicine Systems Pharmacology database for putative ingredients of ACP and its related targets. DrugBank, GeneCards, Online Mendelian Inheritance in Man, and therapeutic target databases were used to search for genes associated with "breast cancer." Using Cytoscape 3.9.0 we then constructed the protein-protein interaction and drug-ingredient-target-disease networks. An enrichment analysis of Kyoto encyclopedia of genes and genomes pathway and gene ontology were performed to exploration of the signaling pathways associated with ACP for breast cancer treatment. Discovery Studio software was applied to molecular docking. Finally, the ligand-receptor complex was subjected to a 50-ns molecular dynamics simulation using the Desmond_2020.4 tools. Six main active ingredients and 176 targets of ACP and 2243 targets of breast cancer were screened. There were 118 intersections of targets for both active ingredients and diseases. Tumor protein P53 (TP53), AKT serine/threonine kinase 1 (AKT1), estrogen receptor 1 (ESR1), Erb-B2 receptor tyrosine kinase 2 (ERBB2), epidermal growth factor receptor (EGFR), Jun Proto-Oncogene (JUN), and Heat Shock Protein 90 Alpha Family Class A Member 1 (HSP90AA1) selected as the most important genes were used for verification by molecular docking and molecular dynamics simulation. The primary active compounds of ACP against breast cancer were predicted preliminarily, and its mechanism was studied, thereby providing a theoretical basis for future clinical studies.
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Affiliation(s)
- Yujing Xu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, P. R. China
| | - Jinrong Yang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, P. R. China
| | - Xiaoyu Han
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, P. R. China
| | - Chunchun Gan
- School of Medicine, Quzhou College of Technology, Quzhou 324000, P. R. China
| | - Xiaopeng Wei
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, P. R. China
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Güleç Ö, Türkeş C, Arslan M, Demir Y, Dincer B, Ece A, İrfan Küfrevioğlu Ö, Beydemir Ş. Novel spiroindoline derivatives targeting aldose reductase against diabetic complications: Bioactivity, cytotoxicity, and molecular modeling studies. Bioorg Chem 2024; 145:107221. [PMID: 38387398 DOI: 10.1016/j.bioorg.2024.107221] [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: 10/30/2023] [Revised: 02/01/2024] [Accepted: 02/16/2024] [Indexed: 02/24/2024]
Abstract
Despite significant developments in therapeutic strategies, Diabetes Mellitus remains an increasing concern, leading to various complications, e.g., cataracts, neuropathy, retinopathy, nephropathy, and several cardiovascular diseases. The polyol pathway, which involves Aldose reductase (AR) as a critical enzyme, has been focused on by many researchers as a target for intervention. On the other hand, spiroindoline-based compounds possess remarkable biological properties. This guided us to synthesize novel spiroindoline oxadiazolyl-based acetate derivatives and investigate their biological activities. The synthesized molecules' structures were confirmed herein, using IR, NMR (1H and 13C), and Mass spectroscopy. All compounds were potent inhibitors with KI constants spanning from 0.186 ± 0.020 μM to 0.662 ± 0.042 μM versus AR and appeared as better inhibitors than the clinically used drug, Epalrestat (EPR, KI: 0.841 ± 0.051 μM). Besides its remarkable inhibitory profile compared to EPR, compound 6k (KI: 0.186 ± 0.020 μM) was also determined to have an unusual pharmacokinetic profile. The results showed that 6k had less cytotoxic effect on normal mouse fibroblast (L929) cells (IC50 of 569.58 ± 0.80 μM) and reduced the viability of human breast adenocarcinoma (MCF-7) cells (IC50 of 110.87 ± 0.42 μM) more than the reference drug Doxorubicin (IC50s of 98.26 ± 0.45 μM and 158.49 ± 2.73 μM, respectively), thus exhibiting more potent anticancer activity. Moreover, molecular dynamic simulations for 200 ns were conducted to predict the docked complex's stability and reveal significant amino acid residues that 6k interacts with throughout the simulation.
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Affiliation(s)
- Özcan Güleç
- Department of Chemistry, Faculty of Arts and Sciences, Sakarya University, 54187 Sakarya, Turkey
| | - Cüneyt Türkeş
- Department of Biochemistry, Faculty of Pharmacy, Erzincan Binali Yıldırım University, 24002 Erzincan, Turkey.
| | - Mustafa Arslan
- Department of Chemistry, Faculty of Arts and Sciences, Sakarya University, 54187 Sakarya, Turkey.
| | - Yeliz Demir
- Department of Pharmacy Services, Nihat Delibalta Göle Vocational High School, Ardahan University, 75700 Ardahan, Turkey
| | - Busra Dincer
- Department of Pharmacology, Faculty of Pharmacy, Ondokuz Mayıs University, 55020 Samsun, Turkey
| | - Abdulilah Ece
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Biruni University, 34010 İstanbul, Turkey
| | | | - Şükrü Beydemir
- Department of Biochemistry, Faculty of Pharmacy, Anadolu University, 26470 Eskişehir, Turkey; Bilecik Şeyh Edebali University, 11230 Bilecik, Turkey
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50
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Frota HF, Lorentino CMA, Barbosa PF, Ramos LS, Barcellos IC, Giovanini L, Souza LOP, Oliveira SSC, Abosede OO, Ogunlaja AS, Pereira MM, Branquinha MH, Santos ALS. Antifungal potential of the new copper(II)-theophylline/1,10-phenanthroline complex against drug-resistant Candida species. Biometals 2024; 37:321-336. [PMID: 37917351 DOI: 10.1007/s10534-023-00549-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 10/03/2023] [Indexed: 11/04/2023]
Abstract
Candida spp. are the commonest fungal pathogens worldwide. Antifungal resistance is a problem that has prompted the discovery of novel anti-Candida drugs. Herein, 25 compounds, some of them containing copper(II), cobalt(II) and manganese(II) ions, were initially evaluated for inhibiting the growth of reference strains of Candida albicans and Candida tropicalis. Eight (32%) of the compounds inhibited the proliferation of these yeasts, displaying minimum inhibitory concentrations (MICs) ranging from 31.25 to 250 μg/mL and minimum fungicidal concentration (MFCs) from 62.5 to 250 μg/mL. Drug-likeness/pharmacokinetic calculated by SwissADME indicated that the 8 selected compounds were suitable for use as topical drugs. The complex CTP, Cu(theo)2phen(H2O).5H2O (theo = theophylline; phen = 1,10-phenanthroline), was chosen for further testing against 10 medically relevant Candida species that were resistant to fluconazole/amphotericin B. CTP demonstrated a broad spectrum of action, inhibiting the growth of all 20 clinical fungal isolates, with MICs from 7.81 to 62.5 μg/mL and MFCs from 15.62 to 62.5 μg/mL. Conversely, CTP did not cause lysis in erythrocytes. The toxicity of CTP was evaluated in vivo using Galleria mellonella and Tenebrio molitor. CTP had no or low levels of toxicity at doses ranging from 31.25 to 250 μg/mL for 5 days. After 24 h of treatment, G. mellonella larvae exhibited high survival rates even when exposed to high doses of CTP (600 μg/mL), with the 50% cytotoxic concentration calculated as 776.2 μg/mL, generating selectivity indexes varying from 12.4 to 99.4 depending on each Candida species. These findings suggest that CTP could serve as a potential drug to treat infections caused by Candida species resistant to clinically available antifungals.
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Affiliation(s)
- Heloisa F Frota
- Laboratório de Estudos Avançados de Microrganismos Emergentes e Resistentes (LEAMER), Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, 21941-901, Brazil
- Programa de Pós-Graduação Em Bioquímica (PPGBq), Instituto de Química, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, 21941-909, Brazil
| | - Carolline M A Lorentino
- Laboratório de Estudos Avançados de Microrganismos Emergentes e Resistentes (LEAMER), Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, 21941-901, Brazil
| | - Pedro F Barbosa
- Laboratório de Estudos Avançados de Microrganismos Emergentes e Resistentes (LEAMER), Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, 21941-901, Brazil
| | - Lívia S Ramos
- Laboratório de Estudos Avançados de Microrganismos Emergentes e Resistentes (LEAMER), Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, 21941-901, Brazil
| | - Iuri C Barcellos
- Laboratório de Estudos Avançados de Microrganismos Emergentes e Resistentes (LEAMER), Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, 21941-901, Brazil
- Instituto Federal de Educação, Ciência e Tecnologia do Rio de Janeiro (IFRJ), Rio de Janeiro, RJ, 20270-220, Brazil
| | - Lucas Giovanini
- Laboratório de Estudos Avançados de Microrganismos Emergentes e Resistentes (LEAMER), Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, 21941-901, Brazil
| | - Lucieri O P Souza
- Laboratório de Estudos Avançados de Microrganismos Emergentes e Resistentes (LEAMER), Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, 21941-901, Brazil
| | - Simone S C Oliveira
- Laboratório de Estudos Avançados de Microrganismos Emergentes e Resistentes (LEAMER), Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, 21941-901, Brazil
| | - Olufunso O Abosede
- Department of Chemistry, Federal University Otuoke, P.M.B 126, Yenagoa, Bayelsa State, Nigeria
- Department of Chemistry, Nelson Mandela University, PO Box 77000, Port Elizabeth, 6031, South Africa
| | - Adeniyi S Ogunlaja
- Department of Chemistry, Nelson Mandela University, PO Box 77000, Port Elizabeth, 6031, South Africa
| | - Matheus M Pereira
- Chemical Engineering Processes and Forest Products Research Centre (CIEPQPF), Department of Chemical Engineering, University of Coimbra, 3030-790, Coimbra, Portugal
| | - Marta H Branquinha
- Laboratório de Estudos Avançados de Microrganismos Emergentes e Resistentes (LEAMER), Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, 21941-901, Brazil
- Rede Micologia RJ - Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ), Rio de Janeiro, 21941-901, Brazil
| | - André L S Santos
- Laboratório de Estudos Avançados de Microrganismos Emergentes e Resistentes (LEAMER), Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes (IMPG), Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, 21941-901, Brazil.
- Programa de Pós-Graduação Em Bioquímica (PPGBq), Instituto de Química, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, 21941-909, Brazil.
- Rede Micologia RJ - Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ), Rio de Janeiro, 21941-901, Brazil.
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