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Elseginy SA. Identifying and characterising promising small molecule inhibitors of kinesin spindle protein using ligand-based virtual screening, molecular docking, molecular dynamics and MM‑GBSA calculations. J Comput Aided Mol Des 2024; 38:16. [PMID: 38556596 PMCID: PMC10982093 DOI: 10.1007/s10822-024-00553-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 02/22/2024] [Indexed: 04/02/2024]
Abstract
The kinesin spindle protein (Eg5) is a mitotic protein that plays an essential role in the formation of the bipolar spindles during the mitotic phase. Eg5 protein controls the segregation of the chromosomes in mitosis which renders it a vital target for cancer treatment. In this study our approach to identifying novel scaffold for Eg5 inhibitors is based on targeting the novel allosteric pocket (α4/α6/L11). Extensive computational techniques were applied using ligand-based virtual screening and molecular docking by two approaches, MOE and AutoDock, to screen a library of commercial compounds. We identified compound 8-(3-(1H-imidazol-1-ylpropylamino)-3-methyl-7-((naphthalen-3-yl)methyl)-1H-purine-2, 6 (3H,7H)-dione (compound 5) as a novel scaffold for Eg5 inhibitors. This compound inhibited cancer cell Eg5 ATPase at 2.37 ± 0.15 µM. The molecular dynamics simulations revealed that the identified compound formed stable interactions in the allosteric pocket (α4/α6/L11) of the receptor, indicating its potential as a novel Eg5 inhibitor.
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Affiliation(s)
- Samia A Elseginy
- Chemical Industries Research Division, Green Chemistry Department, National Research Centre, Cairo, 12622, Egypt.
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Abd El-Karim SS, Anwar MM, Ahmed NS, Syam YM, Elseginy SA, Aly HF, Younis EA, Khalil WKB, Ahmed KA, Mohammed FF, Rizk M. Discovery of novel benzofuran-based derivatives as acetylcholinesterase inhibitors for the treatment of Alzheimer's disease: Design, synthesis, biological evaluation, molecular docking and 3D-QSAR investigation. Eur J Med Chem 2023; 260:115766. [PMID: 37678141 DOI: 10.1016/j.ejmech.2023.115766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 08/23/2023] [Accepted: 08/24/2023] [Indexed: 09/09/2023]
Abstract
A series of novel benzofuran-based compounds 7a-s were designed, synthesized, and investigated in vitro as acetylcholinesterase inhibitors (AChEIs). Compounds 7c and 7e displayed promising inhibitory activity with IC50 values of 0.058 and 0.086 μM in comparison to donepezil with an IC50 value of 0.049 μM. The new molecules' antioxidant evaluation revealed that 7c, 7e, 7j, 7n, and 7q produced the strongest DPPH scavenging activity when compared to vitamin C. As it was the most promising AChEI, compound 7c was selected for further biological evaluation. Acute and chronic toxicity studies exhibited that 7c showed no signs of toxicity or adverse events, no significant differences in the blood profile, and an insignificant difference in hepatic enzymes, glucose, urea, creatinine, and albumin levels in the experimental rat group. Furthermore, 7c did not produce histopathological damage to normal liver, kidney, heart, and brain tissues, ameliorated tissue malonaldehyde (MDA) and glutathione (GSH) levels and reduced the expression levels of the APP and Tau genes in AD rats. Molecular docking results of compounds 7c and 7e showed good binding modes in the active site of the acetylcholinesterase enzyme, which are similar to the native ligand donepezil. 3D-QSAR analysis revealed the importance of the alkyl group in positions 2 and 3 of the phenyl moiety for the activity. Overall, these findings suggested that compound 7c could be deemed a promising candidate for the management of Alzheimer's disease.
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Affiliation(s)
- Somaia S Abd El-Karim
- Department of Therapeutic Chemistry, National Research Centre, P.O. Box 12262 El-Bohouth St, Cairo, Egypt.
| | - Manal M Anwar
- Department of Therapeutic Chemistry, National Research Centre, P.O. Box 12262 El-Bohouth St, Cairo, Egypt.
| | - Nesreen S Ahmed
- Department of Therapeutic Chemistry, National Research Centre, P.O. Box 12262 El-Bohouth St, Cairo, Egypt
| | - Yasmin M Syam
- Department of Therapeutic Chemistry, National Research Centre, P.O. Box 12262 El-Bohouth St, Cairo, Egypt
| | - Samia A Elseginy
- Green Chemistry Department, Chemical Industries Research Division, National Research Centre, P. O. Box 12622, El-Bohouth St, Dokki, Cairo, Egypt
| | - Hanan F Aly
- Department of Therapeutic Chemistry, National Research Centre, P.O. Box 12262 El-Bohouth St, Cairo, Egypt
| | - Eman A Younis
- Department of Therapeutic Chemistry, National Research Centre, P.O. Box 12262 El-Bohouth St, Cairo, Egypt
| | - Wagdy K B Khalil
- Department of Cell Biology, National Research Centre, P.O. Box 12262 El-Bohouth St, Dokki, Cairo, Egypt
| | - Kawkab A Ahmed
- Pathology Departments, Faculty of Veterinary Medicine, Cairo University, Giza, 12211, Egypt
| | - Faten F Mohammed
- Pathology Departments, Faculty of Veterinary Medicine, Cairo University, Giza, 12211, Egypt
| | - Maha Rizk
- Department of Therapeutic Chemistry, National Research Centre, P.O. Box 12262 El-Bohouth St, Cairo, Egypt
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Oksuzoglu E, Yilmaz S, Yenice Cakmak G, Ataei S, Yildiz I. Antitumor activity against human promyelocytic leukemia and in silico studies of some benzoxazines. J Biomol Struct Dyn 2023; 41:8175-8190. [PMID: 36300440 DOI: 10.1080/07391102.2022.2130989] [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: 07/26/2022] [Accepted: 09/24/2022] [Indexed: 10/31/2022]
Abstract
Cancer is one of the deadliest diseases in the world today, and the incidence of cancer is increasing. Leukemia is a type of blood cancer defined as the uncontrolled proliferation of abnormal leukocytes in the blood and bone marrow. The HL-60 (human promyelocytic leukemia) cell line, derived from a single patient with acute promyelocytic leukemia, provides a unique in vitro model system for studying the cellular and molecular events involved in the proliferation and differentiation of leukemic cells. In this study, antitumor activities on the HL-60 of some of the resynthesized benzoxazine derivatives (BXN-01 and BXN-02) were investigated. The results of in vitro studies obtained were compared a standard drug, etoposide. In vitro results showed that BXN-01 and BXN-02 were found to be extremely effective compared to etoposide (IC50 value: 10 µM) with IC50 values of 5 nM and 25 nM, respectively. Furthermore, molecular docking studies were carried out for preliminary prediction of possible interaction modes between compounds and the active site of the target macromolecules, hTopo IIα, HDAC2, and RXRA. Then, in silico ADME/Tox studies were performed to predict drug-likeness and pharmacokinetic properties of BXN-01 and BXN-02.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Emine Oksuzoglu
- Molecular Biology Division, Department of Biology, Faculty of Science and Letters, Aksaray University, Aksaray, Turkey
| | - Serap Yilmaz
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Trakya University, Edirne, Turkey
| | - Gozde Yenice Cakmak
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Trakya University, Edirne, Turkey
- Graduate School of Health Sciences, Ankara University, Ankara, Turkey
| | - Sanaz Ataei
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Ankara University, Ankara, Turkey
| | - Ilkay Yildiz
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Ankara University, Ankara, Turkey
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Aziz M, Ejaz SA, Alsfouk BA, Sultan A, Li C. Identification of potential inhibitors against E.coli via novel approaches based on deep learning and quantum mechanics-based atomistic investigations. Arch Biochem Biophys 2023; 747:109761. [PMID: 37734644 DOI: 10.1016/j.abb.2023.109761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 08/31/2023] [Accepted: 09/18/2023] [Indexed: 09/23/2023]
Abstract
Currently, drug resistance to commercially available antibiotics is imparting negative consequences to global health, and the development of novel antibiotics in a timely manner is a prime need of the hour. In the current study, an e-pharmacophore model was built using the 3D structure of DNA gyrase in complex with a standard inhibitor. The generated model was subjected to a pharmacophore based virtual screening against 45,257,086 molecules having 223,460,579 conformers available in MCULE database. Pharmacophore based screening retrieved eight molecules as top hit based on pharmacophoric features in comparison to standard inhibitors. Afterward, all eight compounds were subjected molecular docking based on deep learning algorithm. The molecular docking revealed that compound MCULE-6042843173 and MCULE-2362244223 had significant binding orientation inside active pocket of targeted protein with binding affinity of -9.52 and -9.24 kcal/mol respectively. In addition, density functional theory studies (DFT) were performed to evaluate quantum mechanics of top ranked compounds which were investigated through quantum mechanics (QM) computations which strongly assisted the findings of other in-silico investigations. Consequently, the MCULE-6042843173 and MCULE-2362244223 were subjected to MD simulation studies for evaluation of stability, hydrogen bond analysis, van der Waals interactions, and the contact profile of compounds with targeted amino acid residues. Findings of current study suggested MCULE-6042843173 and MCULE-2362244223 as potential and novel inhibitor of DNA Gyrase enzyme.
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Affiliation(s)
- Mubashir Aziz
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan
| | - Syeda Abida Ejaz
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan.
| | - Bshra A Alsfouk
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah Bint Abdulrahman University, P.O Box 84428, Riyadh, 11671, Saudi Arabia
| | - Ahlam Sultan
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah Bint Abdulrahman University, P.O Box 84428, Riyadh, 11671, Saudi Arabia
| | - Chen Li
- Department of Biology, Chemistry, Pharmacy, Free University of Berlin, Berlin, 14195, Germany.
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An In-Silico Evaluation of Anthraquinones as Potential Inhibitors of DNA Gyrase B of Mycobacterium tuberculosis. Microorganisms 2022; 10:microorganisms10122434. [PMID: 36557686 PMCID: PMC9783175 DOI: 10.3390/microorganisms10122434] [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: 10/24/2022] [Revised: 11/14/2022] [Accepted: 11/17/2022] [Indexed: 12/13/2022] Open
Abstract
The World Health Organization reported that tuberculosis remains on the list of the top ten threats to public health worldwide. Among the main causes is the limited effectiveness of treatments due to the emergence of resistant strains of Mycobacterium tuberculosis. One of the main drug targets studied to combat M. tuberculosis is DNA gyrase, the only enzyme responsible for regulating DNA topology in this specie and considered essential in all bacteria. In this context, the present work tested the ability of 2824 anthraquinones retrieved from the PubChem database to act as competitive inhibitors through interaction with the ATP-binding pocket of DNA gyrase B of M. tuberculosis. Virtual screening results based on molecular docking identified 7122772 (N-(2-hydroxyethyl)-9,10-dioxoanthracene-2-sulfonamide) as the best-scored ligand. From this anthraquinone, a new derivative was designed harbouring an aminotriazole moiety, which exhibited higher binding energy calculated by molecular docking scoring and free energy calculation from molecular dynamics simulations. In addition, in these last analyses, this ligand showed to be stable in complex with the enzyme and further predictions indicated a low probability of cytotoxic and off-target effects, as well as an acceptable pharmacokinetic profile. Taken together, the presented results show a new synthetically accessible anthraquinone with promising potential to inhibit the GyrB of M. tuberculosis.
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Zhang T, Jiao X, Peng X, Wang H, Zou Y, Xiao Y, Liu R, Li Z. Non-invasive drug delivery systems mediated by nanocarriers and molecular dynamics simulation for posterior eye disease therapeutics: Virtual screening, construction and comparison. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Ahsan MJ, Yusuf M, Salahuddin, Bakht MA, Taleuzzaman M, Vashishtha B, Thiriveedhi A. Green Synthesis, Biological Evaluation, and Molecular Docking of 4'-(Substituted Phenyl)Spiro[Indoline-3,3'-[1,2,4]Triazolidine]-2,5'-Diones. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2101491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Affiliation(s)
- Mohamed Jawed Ahsan
- Department of Pharmaceutical Chemistry, Maharishi Arvind College of Pharmacy, Jaipur, India
| | - Mohammad Yusuf
- Department of Clinical Pharmacy, College of Pharmacy, Taif University, Taif, Saudi Arabia
| | - Salahuddin
- Department of Pharmaceutical Chemistry, Noida Institute of Engineering and Technology (Pharmacy Institute), Greater Noida, India
| | - Md. Afroz Bakht
- Department of Chemistry, College of Science and Humanity Studies, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Mohamad Taleuzzaman
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Maulana Azad University, Jodhpur, India
| | - Bharat Vashishtha
- Department of Pharmacology, Sardar Patel College of Pharmacy, Anand, India
| | - Arunkumar Thiriveedhi
- Vignan's Foundation for Science, Technology and Research Deemed to Be University Guntur, Andhra Pradesh, India
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