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H Ibraheim M, Maher I, Khater I. ' In silico' repurposing new inhibitors of EGFR and VEGFR-2 kinases via biophysical mechanisms. J Biomol Struct Dyn 2024; 42:9571-9586. [PMID: 37753739 DOI: 10.1080/07391102.2023.2262038] [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: 06/09/2023] [Accepted: 08/20/2023] [Indexed: 09/28/2023]
Abstract
Epidermal growth factor receptor (EGFR) controls cell growth, death, and proliferation through a variety of signaling mechanisms. The expression of vascular endothelial growth factor receptor-2 (VEGFR-2) by endothelial cells from malignant tissues triggers a series of signaling pathways that lead to tumor angiogenesis and increase cancer cell survival, proliferation, migration, and vascular permeability. The aim is to find novel inhibitors for EGFR and VEGFR-2 kinases by molecular docking drug-likeness models, pharmacokinetic, interaction analysis, and molecular dynamic simulation. Over 482 ligands were tested against the kinases, there are about 20 compounds that had the best docking scores for the 2 kinases but only compound 2C inhibited them with the highest score values by binding to active sites pocket established through molecular docking study. Secondly, the drug-likeness score of 2C was very good compared to the other compounds. The pharmacokinetics, physicochemical properties, and toxicity of 2C were much better than sorafenib and erlotinib as references. Analysis of interaction showed a strong interaction between 2C and active sites of EGFR and VEGFR-2 kinases illustrated by calculation of halogen bonds, π-Cation Interactions, Hydrogen Bonds, and Hydrophobic Interactions. Finally, the molecular dynamic simulation was also used to assess the stability of the EGFR and VEGFR-2 kinases-2C complexes. The complexes' stability was validated by RMSD, Rg, RMSF, SASA, and several hydrogen bonds analysis. 2C was shown to interact stably with pocket residues after MD simulation. Compound 2C may be a promising way to slow the signaling cascade of proteins that are significant contributors to the spread of cancer.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mona H Ibraheim
- Physics Department, Faculty of Science, Zagazig University, Zagazig, Egypt
| | - Ibrahim Maher
- Physics Department, Faculty of Science, Zagazig University, Zagazig, Egypt
| | - Ibrahim Khater
- Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt
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2
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Ibraheim MH, Maher I, Khater I. In Silico Repurposing of a Novel Inhibitor (drug) of EGFR and VEGFR-2 Kinases of Cancer by Pharmacokinetics, Toxicity, Molecular Docking, and Molecular Dynamics Simulation. Appl Biochem Biotechnol 2024; 196:8332-8365. [PMID: 38782800 DOI: 10.1007/s12010-024-04958-8] [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] [Accepted: 04/16/2024] [Indexed: 05/25/2024]
Abstract
Vascular endothelial growth factor is an angiogenic that promotes the development and metastasis of tumors (VEGF). The epidermal growth factor receptor, or EGFR, controls the division, growth, and death of cells via several signaling pathways. It has been found that most of the tyrosine kinase EGFR/VEGFR-2 inhibited by drugs that the FDA has approved are so far. The main objective of the present study was to identify an efficacious and selective dual inhibitor of VEGFR-2/EGFR for the treatment of cancer. Out of the 400 ligands tested against the kinases, 12 compounds demonstrated the best docking scores through molecular docking for the two kinases. Of these, only compound SCHEMBL2435814 inhibited the kinases with the highest score values when compared to a reference, vandetanib, as a dual inhibitor of EGFR/VEGFR-2 kinases through interaction with the identified active sites pocket. Following drug-likeness score toxicity and pharmacokinetic testing, the two compounds, SCHEMBL2435814 and vandetanib, were analyzed to determine how the two kinases interacted with each other. The results of calculations of π-cation interactions, hydrogen bonds, and hydrophobic interactions demonstrated a strong interaction between the two kinases and SCHEMBL2435814. Eventually, molecular dynamic modeling was used to assess the stability of complexes. This demonstrated many characteristics, including RMSF, RMSD, SASA, RG, and H-bond analysis, which demonstrated that SCHEMBL2435814 with the two kinases was more stable than vandetanib over a 100ns simulation period. By suppressing EGFR/VEGFR-2, chemical SCHEMBL2435814 may be able to postpone the signaling pathway of proteins that are essential to the advancement of cancer.
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Affiliation(s)
- Mona H Ibraheim
- Physics Department, Faculty of Science, Zagazig University, P.O.44519, Zagazig, Egypt
| | - Ibrahim Maher
- Physics Department, Faculty of Science, Zagazig University, P.O.44519, Zagazig, Egypt.
| | - Ibrahim Khater
- Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt
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3
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Shukla P, Srivastava P, Mishra A. On the potential activity of hyaluronic acid as an antimicrobial agent: experimental and computational validations. Bioprocess Biosyst Eng 2024:10.1007/s00449-024-03091-4. [PMID: 39343852 DOI: 10.1007/s00449-024-03091-4] [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: 11/08/2022] [Accepted: 09/12/2024] [Indexed: 10/01/2024]
Abstract
This century has seen the rise of antibiotic resistance as a significant public health problem. In addition, oxidative stress may also be a factor in selecting resistant strains of bacteria. The current study analyzed microbially produced hyaluronic acid's antibacterial activity and antioxidant activity. It had significant antibacterial action against strains of Staphylococcus aureus and Escherichia coli, with the IC50 value obtained being 487.65 µg mL-1 for antioxidant assay. Our molecular docking investigations of hyaluronic acid on tyrosyl-tRNA synthetase (Staphylococcus aureus: -6.13 kcal/mol, Escherichia coli: -5.79 kcal/mol) and topoisomerase II DNA gyrase (Staphylococcus aureus: -5.02 kcal/mol, Escherichia coli: -4.90 kcal/mol) confirmed the ligands' possible binding mode to the appropriate targets' sites. We also employed molecular dynamics simulation and showed that HA binds more strongly with 1JIL (-85.455 ± 12.623 kJ/mol) compared to 2YXN (-49.907 ± 64.191 kJ/mol), 5CDP (-47.285 ± 13.925 kJ/mol), and 6RKS (-45.306 ± 21.338 kJ/mol). We also report that the ligand forms several hydrogen bonds in molecular simulation, implying regular interaction with key residues of the enzymes. The results in this study indicate the potential use of HA in the vast field of applications having both asthetic and medicinal values.
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Affiliation(s)
- Priya Shukla
- School of Biochemical Engineering, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Pradeep Srivastava
- School of Biochemical Engineering, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Abha Mishra
- School of Biochemical Engineering, Indian Institute of Technology (Banaras Hindu University), Varanasi, India.
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4
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Sarma M, Borkotoky S, Dubey VK. Structure-based drug designing against Leishmania donovani using docking and molecular dynamics simulation studies: exploring glutathione synthetase as a drug target. J Biomol Struct Dyn 2024; 42:7628-7636. [PMID: 37491862 DOI: 10.1080/07391102.2023.2240429] [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: 06/12/2023] [Accepted: 07/18/2023] [Indexed: 07/27/2023]
Abstract
In the pursuit of developing novel anti-leishmanial agents, we conducted an extensive computational study to screen inhibitors from the FDA-approved ZINC database against Leishmania donovani glutathione synthetase. The three-dimensional structure of Leishmania donovani glutathione synthetase was constructed by homology modeling, using the crystallographic structure of Trypanosoma brucei glutathione synthetase as a template. Subsequently, molecular docking studies were carried out for a large number of compounds using AutoDock Vina. Among the screened compounds, we selected the top five with strong binding affinity to Leishmania donovani glutathione synthetase but having a very low affinity to its human homolog. Further investigations on protein-ligand complexes were done by conducting molecular dynamics (MD) simulation and MM/PBSA analysis. The results revealed that Olysio (Simeprevir) exhibited the lowest binding energy (-89.21 kcal/mol), followed by Telithromycin (-45.34 kcal/mol). These findings showed that these compounds have the potential to act as inhibitors of glutathione synthetase. Hence, our study provides valuable insights for the development of a novel therapeutic strategy against Leishmania donovani by targeting the glutathione synthetase enzyme.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Manash Sarma
- School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi, India
| | - Subhomoi Borkotoky
- School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi, India
| | - Vikash Kumar Dubey
- School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi, India
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Xu ZY, Du NN, La CS, Huang XX, Song SJ. Two pairs of bioactive cyclohexene alkaloid enantiomers from the roots of Piper nigrum. JOURNAL OF ASIAN NATURAL PRODUCTS RESEARCH 2024:1-10. [PMID: 38594843 DOI: 10.1080/10286020.2024.2335279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Accepted: 03/19/2024] [Indexed: 04/11/2024]
Abstract
Two pairs of cyclohexene amide alkaloid enantiomers were obtained from the root of Piper nigrum. Their plane structures were established by NMR and HRESIMS spectra. The absolute configurations of 1a/1b and 2a/2b were determined by the comparison between the experimental and calculated electronic circular dichroism (ECD) spectra. All identified compounds were tested for inhibitory effects on acetylcholinesterase (AChE) in vitro. Notably, compounds 1b and 2b showed strong inhibitory effects on AChE and the interaction between proteins and compounds was discussed by molecular docking studies.
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Affiliation(s)
- Zhi-Yong Xu
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Engineering Research Center of Natural Medicine Active Molecule Research & Development, Key Laboratory of Natural Bioactive Compounds Discovery & Modification, School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Liaoning 110016, China
| | - Ning-Ning Du
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Engineering Research Center of Natural Medicine Active Molecule Research & Development, Key Laboratory of Natural Bioactive Compounds Discovery & Modification, School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Liaoning 110016, China
| | - Chang-Sheng La
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Engineering Research Center of Natural Medicine Active Molecule Research & Development, Key Laboratory of Natural Bioactive Compounds Discovery & Modification, School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Liaoning 110016, China
| | - Xiao-Xiao Huang
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Engineering Research Center of Natural Medicine Active Molecule Research & Development, Key Laboratory of Natural Bioactive Compounds Discovery & Modification, School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Liaoning 110016, China
| | - Shao-Jiang Song
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Engineering Research Center of Natural Medicine Active Molecule Research & Development, Key Laboratory of Natural Bioactive Compounds Discovery & Modification, School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Liaoning 110016, China
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Lian MY, Dong SH, Ai YF, Duan ZK, Bai M, Huang XX, Song SJ. Eight structurally diverse components with anti-acetylcholinesterase activity from Daphne bholua. PHYTOCHEMISTRY 2024; 220:114015. [PMID: 38364884 DOI: 10.1016/j.phytochem.2024.114015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 02/06/2024] [Accepted: 02/08/2024] [Indexed: 02/18/2024]
Abstract
Eight structurally diverse components, including six undescribed ones, (±)-daphuarin A (1a/1b), daphuarin B (2), daphuarin D-E (4-6), together with a pair of new natural products (±)-daphuarin C (3a/3b) were isolated from the herb of Daphne bholua Buch.-Ham. ex D. Don. Their planar structures were elucidated by extensive spectroscopic analyses. The configurations were established with the assistance of quantum chemical calculations, together with the Custom DP4+ method. The inhibitory potentials of all isolates against acetylcholinesterase were evaluated.
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Affiliation(s)
- Mei-Ya Lian
- Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province, Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province, Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang, School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Shu-Hui Dong
- Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province, Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province, Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang, School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Yun-Fei Ai
- Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province, Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province, Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang, School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Zhi-Kang Duan
- Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province, Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province, Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang, School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Ming Bai
- Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province, Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province, Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang, School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Xiao-Xiao Huang
- Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province, Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province, Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang, School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, China; Basic Science Research Center Base (Pharmaceutical Science), Shandong province, Yantai University, Yantai, 264005, China.
| | - Shao-Jiang Song
- Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province, Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province, Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang, School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, China.
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7
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Li JY, Dong SH, Zhang X, Liu ZJ, Hao JL, Lin B, Bai M, Huang XX, Song SJ. Structurally diverse terpenoids from Elephantopus scaber L. and their acetylcholinesterase inhibitory activities. PHYTOCHEMISTRY 2023; 216:113892. [PMID: 37813132 DOI: 10.1016/j.phytochem.2023.113892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 10/07/2023] [Accepted: 10/07/2023] [Indexed: 10/11/2023]
Abstract
Three undescribed compounds elephantopuscabers A-C, along with one previously reported compound spirowallichiione, were isolated from Elephantopus scaber L. Their structures were determined via extensive NMR spectroscopic analysis, quantum chemical calculations, and single-crystal X-ray diffraction crystallography. A plausible biosynthetic pathway for spirowallichiione was proposed. All the isolated compounds were tested for their acetylcholinesterase inhibitory activities. Among them, elephantopuscaber B and C displayed promising inhibitory activities against AChE, and the binding sites were predicted by molecular docking.
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Affiliation(s)
- Jia-Yi Li
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province; Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province; Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang; School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, Liaoning, 110016, China
| | - Shu-Hui Dong
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province; Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province; Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang; School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, Liaoning, 110016, China
| | - Xin Zhang
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province; Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province; Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang; School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, Liaoning, 110016, China
| | - Zi-Jian Liu
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province; Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province; Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang; School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, Liaoning, 110016, China
| | - Jin-Le Hao
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Bin Lin
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, 110016, China
| | - Ming Bai
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province; Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province; Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang; School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, Liaoning, 110016, China.
| | - Xiao-Xiao Huang
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province; Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province; Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang; School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, Liaoning, 110016, China; Basic Science Research Center Base (Pharmaceutical Science), Shandong province, Yantai University, Yantai, 264005, China.
| | - Shao-Jiang Song
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province; Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province; Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang; School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, Liaoning, 110016, China
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Ranjan P, Dubey VK. Novel chemical scaffold as potential drug against Leishmania donovani: Integrated computational and experimental approaches. J Cell Biochem 2023; 124:1404-1422. [PMID: 37566640 DOI: 10.1002/jcb.30455] [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: 06/06/2023] [Revised: 07/23/2023] [Accepted: 07/24/2023] [Indexed: 08/13/2023]
Abstract
In this study, we have screened a large number of Food and Drug Administration-approved compounds for novel anti-leishmanial molecules targeting the citrate synthase enzyme of the parasite. Based on their docking and molecular dynamic simulation statistics, five compounds were selected. These compounds followed Lipinski's rule of five. Additionally, in vitro, antileishmanial and cytotoxicity studies were performed. The three compounds, Abemaciclib, Bazedoxifene, and Vorapaxar, had shown effective anti-leishmanial activities with IC50 values of 0.92 ± 0.02, 0.65 ± 0.09, and 6.1 ± 0.91 against Leishmania donovani promastigote and with EC50 values of 1.52 ± 0.37, 2.11 ± 0.38, 10.4 ± 1.27 against intramacrophagic amastigote without significantly harming macrophage cells. Among them, from in silico and antileishmanial activities studies, Abemaciclib had been selected based on their less binding energy, good antileishmanial activities, and also a significant difference in their binding energy with human citrate synthase for cell death mechanistic studies using flow cytometry and a DNA fragmentation assay. The action of this compound resulted in an increased reactive oxygen species production, depolarization of mitochondrial membrane potential, DNA damage, and an increase in the sub-G1 cell population. These properties are the hallmarks of apoptosis which were further confirmed by apoptotic assay. Based on the above result, this anticancer compound Abemaciclib could be employed as a potential treatment option for leishmaniasis after further confirmation.
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Affiliation(s)
- Preeti Ranjan
- School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi, Uttar Pradesh, India
| | - Vikash Kumar Dubey
- School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi, Uttar Pradesh, India
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Dong SH, Lian MY, Han JL, Ai YF, Zhou XF, Bai M, Huang XX, Song SJ. Rapid screening of diarylpentanoids from Daphne bholua. PHYTOCHEMISTRY 2023; 209:113614. [PMID: 36804187 DOI: 10.1016/j.phytochem.2023.113614] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 02/15/2023] [Accepted: 02/16/2023] [Indexed: 06/18/2023]
Abstract
Fractionation motivated by biological activity screening and NMR characteristic signals analysis led to the isolation of seventeen diarylpentanoids from the whole plant of Daphne bholua Buch.-Ham. ex D. Don, among which nine compounds were undescribed. Their structures and stereochemistry were determined by comprehensive spectroscopic data, J-based configurational analysis, and quantum chemical calculations. The inhibitory potentials of all isolates against acetylcholinesterase were evaluated in vitro and in silico.
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Affiliation(s)
- Shu-Hui Dong
- Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province; Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang; School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, Liaoning Province, People's Republic of China
| | - Mei-Ya Lian
- Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province; Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang; School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, Liaoning Province, People's Republic of China
| | - Jin-Ling Han
- Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province; Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang; School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, Liaoning Province, People's Republic of China
| | - Yun-Fei Ai
- Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province; Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang; School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, Liaoning Province, People's Republic of China
| | - Xiao-Fang Zhou
- Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province; Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang; School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, Liaoning Province, People's Republic of China
| | - Ming Bai
- Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province; Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang; School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, Liaoning Province, People's Republic of China
| | - Xiao-Xiao Huang
- Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province; Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang; School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, Liaoning Province, People's Republic of China
| | - Shao-Jiang Song
- Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province; Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang; School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, Liaoning Province, People's Republic of China.
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10
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Mateev E, Kondeva-Burdina M, Georgieva M, Zlatkov A. Repurposing of FDA-approved drugs as dual-acting MAO-B and AChE inhibitors against Alzheimer's disease: An in silico and in vitro study. J Mol Graph Model 2023; 122:108471. [PMID: 37087882 DOI: 10.1016/j.jmgm.2023.108471] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/30/2023] [Accepted: 04/03/2023] [Indexed: 04/25/2023]
Abstract
An in silico consensus molecular docking approach and in vitro evaluations were adopted in the present study to explore a dataset of FDA-approved drugs as novel multitarget MAO-B/AChE agents in the treatment of Alzheimer's disease (AD). GOLD 5.3 and Glide were employed in the virtual assessments and consensus superimpositions of the obtained poses were applied to increase the reliability of the docking protocols. Furthermore, the top ranked molecules were subjected to binding free energy calculations using MM/GBSA, Induced fit docking (IFD) simulations, and a literature review. Consequently, the top four multitarget drugs were examined for their in vitro MAO-B and AChE inhibition effects. The consensus molecular docking identified Dolutegravir, Rebamipide, Loracarbef and Diflunisal as potential multitarget drugs. The biological data demonstrated that most of the docking scores were in good correlation with the in vitro experiments, however the theoretical simulations in the active site of MAO-B identified two false-positives - Rebamipide and Diflunisal. Dolutegravir and Loracarbef were accessed as active MAO-B inhibitors, while Dolutegravir, Rebamapide and Diflunisal as potential AChE inhibitors. The antiretroviral agent Dolutegravir exhibited the most potent multitarget activity - 41% inhibition of MAO-B (1 μM) and 68% inhibition of AChE (10 μM). Visualizations of the intermolecular interactions of Dolutegravir in the active sites of MAO-B and AChE revealed the formation of several stable hydrogen bonds. Overall, Dolutegravir was identified as a potential anti-AD drug, however further in vivo evaluations should be considered.
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Affiliation(s)
- Emilio Mateev
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Medical University, Sofia, Bulgaria.
| | - Magdalena Kondeva-Burdina
- Department of Pharmacology, Pharmacotherapy and Toxicology, Faculty of Pharmacy, Medical University, Sofia, Bulgaria
| | - Maya Georgieva
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Medical University, Sofia, Bulgaria
| | - Alexander Zlatkov
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Medical University, Sofia, Bulgaria
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Integrated computational and experimental approach for novel anti-leishmanial molecules by targeting Dephospho-coenzyme A kinase. Int J Biol Macromol 2023; 232:123441. [PMID: 36708902 DOI: 10.1016/j.ijbiomac.2023.123441] [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: 10/14/2022] [Revised: 01/07/2023] [Accepted: 01/23/2023] [Indexed: 01/27/2023]
Abstract
Coenzyme A acts as a necessary cofactor for many enzymes and is a part of many biochemical processes. One of the critical enzymes involved in Coenzyme A synthesis is Dephospho-coenzyme A-kinase (DPCK). In this study, we have used integrated computational and experimental approaches for promising inhibitors of DPCK using the natural products available in the ZINC database for anti-leishmanial drug development. The top hit compounds chosen after molecular docking were Veratramine, Azulene, Hupehenine, and Hederagenin. The free binding energy of Veratramine, Azulene, Hupehenine, and Hederagenin was estimated. Besides the favourable binding point, the ligands also showed good hydrogen bonding and other interactions with key residues of the enzyme's active site. The natural compounds were also experimentally investigated for their effect on the L. donovani promastigotes and murine macrophage (J774A.1). A good antileishmanial activity by the compounds on the promastigotes was observed as estimated by the MTT assay. The in-vitro experiments revealed that Hupehenine (IC50 = 7.34 ± 0.37 μM) and Veratramine (IC50 = 12.46 ± 2.28 μM) exhibited better inhibition than Hederagenin (IC50 = 23.36 ± 0.54 μM) and Azulene (IC50 = 24.42 ± 3.28 μM). This work has identified novel anti-leishmanial molecules possibly acting through the inhibition of DPCK.
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Rajput A, Sharma P, Kumar N, Kaur S, Arora S. Neuroprotective activity of novel phenanthrene derivative from Grewia tiliaefolia by in vitro and in silico studies. Sci Rep 2023; 13:2444. [PMID: 36765125 PMCID: PMC9918530 DOI: 10.1038/s41598-023-29446-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 02/06/2023] [Indexed: 02/12/2023] Open
Abstract
Medicinal plants possess range of phytochemicals accountable for their diverse biological activities. Presently, such compounds have been isolated from medicinal plants, characterized and evaluated for their pharmacological potential. In the present study, the efforts have been made to isolate the compound(s) from Grewia tiliaefolia Vahl., plant known for its ameliorative effect on brain related diseases such as anxiety, depression, cognitive disorders and Parkinson's disease. Plant extract was subjected to isolation of compound(s) using column chromatography and isolated compound was characterized by NMR FTIR and LCMS. The isolated compound was novel with the IUPAC name of the compound is propyl 3-hydroxy-10,13-dimethyl-6,7,8,9,10,11,12,13,14,15,16,17-dodecahydro-3H-cyclopenta[a]phenanthrene-17-carboxylate, designated as A-1 and has not been reported before. A-1 was further evaluated for its antioxidant potential using in vitro antioxidant assays (2,2-diphenyl-1-picryl-hydrazyl-hydrate, DPPH assay and reducing power assay, RPA). Also, Acetylcholinesterase (AChE) inhibitory potential of A-1 and extract was analysed. Results showed that A-1 exhibited significantly higher antioxidant activity in both DPPH and RPA assay as compared to plant extract. In case of AChE inhibitory activity again, A-1 has shown significantly higher activity as compared to plant extract. In silico study was conducted to predict its action on proteins playing crucial role in neurological and neurodegenerative disorders such as gamma amino butyric acid (GABA) receptor and glutamate α amino-3-hydroxyl-5-methyl-4-isoxazolepropionic acid (Glu AMPA) receptor in epilepsy and AChE enzyme in Alzheimer's diseases. The compound has shown interaction in following order: AChE > GABA receptor > Glu AMPA receptor. Further, molecular dynamic simulations and ADME studies of A-1 and AChE enzyme revealed that A-1 yielded good results in all parameters and hence can relieve Alzheimer's like symptoms.
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Affiliation(s)
- Ankita Rajput
- Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar, Punjab, India
| | - Palvi Sharma
- Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar, Punjab, India
| | - Nitish Kumar
- Department of Pharmaceutical Sciences, Guru Nanak Dev University, Amritsar, Punjab, India
| | - Sarabjit Kaur
- Department of Pharmaceutical Sciences, Guru Nanak Dev University, Amritsar, Punjab, India.
| | - Saroj Arora
- Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar, Punjab, India.
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13
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Wang YX, Xu ZY, Qin SY, Du NN, Yao GD, Lin B, Huang XX, Song SJ. Novel Bisamide Alkaloids Enantiomers from Pepper Roots ( Piper nigrum L.) with Acetylcholinesterase Inhibitory and Anti-Neuroinflammatory Effects. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:15487-15498. [PMID: 36450093 DOI: 10.1021/acs.jafc.2c06733] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The roots of Piper nigrum L., a seasoning for cooking various types of broths, are renowned for their high nutritional content and potential medicinal benefits. In this study, nine pairs of novel cyclohexene-type bisamide alkaloids (1a/1b-9a/9b) were isolated from the pepper roots using molecular network analysis strategies. Their structures were determined by extensive spectroscopic data, electronic circular dichroism (ECD) calculations, and X-ray diffraction analyses. Using an intermolecular Diels-Alder reaction, a strategy for the synthesis of bisamide alkaloids from different monomeric amide alkaloids was developed. Furthermore, these compounds were chirally separated for the first time, and compounds 3a and 5a/5b showed significant anti-neuroinflammation effects in the models of lipopolysaccharide(LPS)-induced BV2 microglial cells. Meanwhile, compounds 6b and 7a displayed concentration-dependent inhibitory activities against acetylcholinesterase with IC50 values of 6.05 ± 1.10 and 3.81 ± 0.10 μM, respectively. These findings confirmed that these bisamide alkaloids could be applied in functional food formulations and pharmaceutical products as well as facilitate the further development and usage of pepper roots.
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Affiliation(s)
- Yu-Xi Wang
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province; Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province; Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang; School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110164, China
| | - Zhi-Yong Xu
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province; Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province; Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang; School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China
| | - Shu-Yan Qin
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province; Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province; Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang; School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China
| | - Ning-Ning Du
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province; Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province; Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang; School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China
| | - Guo-Dong Yao
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province; Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province; Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang; School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China
| | - Bin Lin
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Xiao-Xiao Huang
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province; Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province; Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang; School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China
| | - Shao-Jiang Song
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province; Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province; Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang; School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China
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Chemical constituents from Daphne giraldii and their cytotoxicities and inhibitory activities against acetylcholinesterase. Fitoterapia 2022; 163:105327. [DOI: 10.1016/j.fitote.2022.105327] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 09/30/2022] [Accepted: 09/30/2022] [Indexed: 02/08/2023]
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15
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Handa T, Kundu D, Dubey VK. Perspectives on evolutionary and functional importance of intrinsically disordered proteins. Int J Biol Macromol 2022; 224:243-255. [DOI: 10.1016/j.ijbiomac.2022.10.120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 10/08/2022] [Accepted: 10/10/2022] [Indexed: 11/05/2022]
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16
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Du NN, Bai M, Zhang X, Zhou L, Huang XX, Song SJ. Coumarins from Sarcandra glabra (Thunb.) Nakai and Acetylcholinesterase Inhibiting Activity. Chem Biodivers 2022; 19:e202200558. [PMID: 36036517 DOI: 10.1002/cbdv.202200558] [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: 06/10/2022] [Accepted: 08/29/2022] [Indexed: 11/08/2022]
Abstract
Nine coumarins including a pair of new enantiomers ( 1a / 1b ) and seven known compounds ( 2-8 ) were isolated from Sarcandra glabra (Thunb.) Nakai. Among them, compounds 1a and 1b were naturally occurring coumarin-phenylpropanoid conjugate enantiomers. Their structures were identified by NMR and ECD calculations. Compounds 1-8 were tested for acetylcholinesterase (AchE) inhibiting activity. The results of the enzymology experiment showed that compound 3 demonstrated obvious AchE inhibitory activity which showed an IC 50 value of 1.982 ± 0.003 μ M, and the binding sites were predicted by molecular docking.
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Affiliation(s)
- Ning-Ning Du
- Shenyang Pharmaceutical University, School of Traditional Chinese Materia Medica, wenhua road, No 103, Shenyang, CHINA
| | - Ming Bai
- Shenyang Pharmaceutical University, School of Traditional Chinese Materia Medica, wenhua road, No 103, Shenyang, CHINA
| | - Xin Zhang
- Shenyang Pharmaceutical University, School of Traditional Chinese Materia Medica, wenhua road, No 103, Shenyang, CHINA
| | - Le Zhou
- Shenyang Pharmaceutical University, School of Traditional Chinese Materia Medica, wenhua road, No 103, Shenyang, CHINA
| | - Xiao-Xiao Huang
- Shenyang Pharmaceutical University, School of Traditional Chinese Materia Medica, wenhua road, No 103, Shenyang, CHINA
| | - Shao-Jiang Song
- Shenyang Pharmaceutical University, School of Traditional Chinese Materia Medica, wenhua road, No 103, 110016, Shenyang, CHINA
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Ahmed ZB, Hefied F, Mahammed TH, Seidel V, Yousfi M. Identification of potential
anti‐Alzheimer
agents from
Pistacia atlantica
Desf. galls using
UPLC
fingerprinting, chemometrics, and molecular docking analyses. J FOOD PROCESS PRES 2022. [DOI: 10.1111/jfpp.16916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ziyad Ben Ahmed
- Laboratoire des Sciences Fondamentale Université Amar Telidji Laghouat Algérie
- Department of Analytical Chemistry, Applied Chemometrics and Molecular Modelling, Vrije Universiteit Brussel (VUB), Brussels Belgium
| | - Fatiha Hefied
- Laboratoire des Sciences Fondamentale Université Amar Telidji Laghouat Algérie
| | | | - Veronique Seidel
- Natural Products Research Laboratory, Strathclyde Institute of Pharmacy and Biomedical Sciences University of Strathclyde Glasgow UK
| | - Mohamed Yousfi
- Laboratoire des Sciences Fondamentale Université Amar Telidji Laghouat Algérie
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