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Abdelhakeem MM, Morcoss MM, Hanna DA, Lamie PF. Design, synthesis and in silico insights of novel 1,2,3-triazole benzenesulfonamide derivatives as potential carbonic anhydrase IX and XII inhibitors with promising anticancer activity. Bioorg Chem 2024; 144:107154. [PMID: 38309003 DOI: 10.1016/j.bioorg.2024.107154] [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: 11/16/2023] [Revised: 01/18/2024] [Accepted: 01/24/2024] [Indexed: 02/05/2024]
Abstract
Novel 1,2,3-triazole benzenesulfonamide derivatives were designed as inhibitors for the tumor- related hCA IX and XII isoforms. Most of the synthesized compounds showed good inhibitory activity against hCA IX and hCA XII isoforms. Compounds 4d, 5h and 6b, exhibited remarkable activity as hCA IX inhibitors, with Ki values in the range of 0.03 to 0.06 µM, more potent than AAZ. Additionally, compounds 5b and 6d, efficiently inhibited hCA XII isoform, with Ki value of 0.02 µM, respectively, similar to AAZ. Further investigation for those potent derivatives against MCF-7, Hep-3B and WI-38 cell lines was achieved. Compounds 4d and 6d exerted dual cytotoxic activity against MCF-7 and Hep-3B cell lines, with IC50 values of 3.35 & 2.12 µM against MCF-7 cell line and 1.72 & 1.56 µM against Hep-3B cell line, with high SI values ranged from 8.92 to 17.38 on both of the cell lines. Besides, they showed a high safety profile against normal human cell line, WI-38. Moreover, compound 5h had better cytotoxic effect on MCF-7 than the reference, DOX, with IC50 value of 4.02 µM. While, compounds 5b and 6b showed higher activity against Hep-3B if compared to the reference drug, 5-FU. From ADME study, compounds 4d, 5b, 6b and 6d obeyed Lipinski's rule of five, and they might be orally active derivatives, while, compound 5h exerted less oral bioavailability than the reference standard acetazolamide. Molecular docking and MDS studies predicted the binding mode and the stability of the target compounds inside hCA IX and hCA XII active sites, especially for compounds 5b and 6b.
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Affiliation(s)
- Marwa M Abdelhakeem
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Beni-Suef University, Beni-Suef 62514, Egypt
| | - Martha M Morcoss
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Nahda University, Beni-Suef 62513, Egypt
| | - Dina A Hanna
- Department of Pharmacology and Toxicology, Nahda University, Beni-Suef 62513, Egypt
| | - Phoebe F Lamie
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Beni-Suef University, Beni-Suef 62514, Egypt.
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Efficacy of Ceftazidime and Cefepime in the Management of COVID-19 Patients: Single Center Report from Egypt. Antibiotics (Basel) 2021; 10:antibiotics10111278. [PMID: 34827216 PMCID: PMC8614536 DOI: 10.3390/antibiotics10111278] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/15/2021] [Accepted: 10/17/2021] [Indexed: 12/23/2022] Open
Abstract
The purpose of this study was to explore the value of using cefepime and ceftazidime in treating patients with COVID-19. A total of 370 (162 males) patients, with RT-PCR-confirmed cases of COVID-19, were included in the study. Out of them, 260 patients were treated with cefepime or ceftazidime, with the addition of steroids to the treatment. Patients were divided into three groups: Group 1: patients treated with cefepime (124 patients); Group 2: patients treated with ceftazidime (136 patients); Group 3 (control group): patients treated according to the WHO guidelines and the Egyptian COVID-19 management protocol (110 patients)/ Each group was classified into three age groups: 18–30, 31–60, and >60 years. The dose of either cefepime or ceftazidime was 1000 mg twice daily for five days. Eight milligrams of dexamethasone were used as the steroidal drug. Careful follow-ups for the patients were carried out. In vitro and in silico Mpro enzyme assays were performed to investigate the antiviral potential of both antibiotics. The mean recovery time for Group 1 was 12 days, for Group 2 was 13 days, and for Group 3 (control) was 19 days. No deaths were recorded, and all patients were recovered without any complications. For Group 1, the recovery time was 10, 12, and 16 days for the age groups 18–30, 30–60, and >60 years, respectively. For Group 2, the recovery time was 11, 13, and 15 days for the age groups 18–30, 30–60, and >60 years, respectively. For Group 3 (control), the recovery time was 15, 16, and 17 days for the age groups 18–30, 30–60, and >60 years, respectively. Both ceftazidime and cefepime showed very good inhibitory activity towards SARS CoV-2′s Mpro, with IC50 values of 1.81 µM and 8.53 µM, respectively. In conclusion, ceftazidime and cefepime are efficient for the management of moderate and severe cases of COVID-19 due to their potential anti-SARS CoV-2 activity and low side effects, and, hence, the currently used complex multidrug treatment protocol can be replaced by the simpler one proposed in this study.
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Ngo ST, Mai BK, Derreumaux P, Vu VV. Adequate prediction for inhibitor affinity of Aβ 40 protofibril using the linear interaction energy method. RSC Adv 2019; 9:12455-12461. [PMID: 35515829 PMCID: PMC9063661 DOI: 10.1039/c9ra01177c] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 04/11/2019] [Indexed: 11/21/2022] Open
Abstract
The search for efficient inhibitors targeting Aβ oligomers and fibrils is an important issue in Alzheimer's disease treatment. As a consequence, an accurate and computationally cheap approach to estimate the binding affinity for many ligands interacting with Aβ peptides is very important. Here, the calculated binding free energies of 30 ligands interacting with 12Aβ11-40 peptides using the linear interaction energy (LIE) approach are found to be in good correlation with experimental data (R = 0.79). The binding affinities of these complexes are also calculated by using free energy perturbation (FEP) and molecular mechanic/Poisson-Boltzmann surface area (MM/PBSA) methods. The time-consuming FEP method provides results with similar correlation (R = 0.72), whereas MM/PBSA calculations show very low correlation with experimental data (R = 0.27). In all complexes, van der Waals interactions contribute much more than electrostatic interactions. The LIE model, which is much less time-consuming than both the FEP and MM/PBSA methods, opens the door to accurate and rapid affinity prediction of ligands with Aβ peptides and the design of new ligands.
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Affiliation(s)
- Son Tung Ngo
- Laboratory of Theoretical and Computational Biophysics, Ton Duc Thang University Ho Chi Minh City Vietnam
- Faculty of Applied Sciences, Ton Duc Thang University Ho Chi Minh City Vietnam
| | - Binh Khanh Mai
- Institute for Computational Science and Technology (ICST), Quang Trung Software City Ho Chi Minh City Vietnam
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, IBPC, Université Paris Diderot 13 rue Pierre et Marie Curie 75005 Paris France
- Laboratory of Theoretical Chemistry, Ton Duc Thang University Ho Chi Minh City Vietnam
- Faculty of Pharmacy, Ton Duc Thang University Ho Chi Minh City Vietnam
| | - Van V Vu
- NTT Hi-Tech Institute, Nguyen Tat Thanh University Ho Chi Minh City Vietnam
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Evenseth LM, Warszycki D, Bojarski AJ, Gabrielsen M, Sylte I. In Silico Methods for the Discovery of Orthosteric GABA B Receptor Compounds. Molecules 2019; 24:E935. [PMID: 30866507 PMCID: PMC6429233 DOI: 10.3390/molecules24050935] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 02/20/2019] [Accepted: 03/01/2019] [Indexed: 12/27/2022] Open
Abstract
The GABAB receptor (GABAB-R) is a heterodimeric class C G protein-coupled receptor comprised of the GABAB1a/b and GABAB2 subunits. The endogenous orthosteric agonist γ-amino-butyric acid (GABA) binds within the extracellular Venus flytrap (VFT) domain of the GABAB1a/b subunit. The receptor is associated with numerous neurological and neuropsychiatric disorders including learning and memory deficits, depression and anxiety, addiction and epilepsy, and is an interesting target for new drug development. Ligand- and structure-based virtual screening (VS) are used to identify hits in preclinical drug discovery. In the present study, we have evaluated classical ligand-based in silico methods, fingerprinting and pharmacophore mapping and structure-based in silico methods, structure-based pharmacophores, docking and scoring, and linear interaction approximation (LIA) for their aptitude to identify orthosteric GABAB-R compounds. Our results show that the limited number of active compounds and their high structural similarity complicate the use of ligand-based methods. However, by combining ligand-based methods with different structure-based methods active compounds were identified in front of DUDE-E decoys and the number of false positives was reduced, indicating that novel orthosteric GABAB-R compounds may be identified by a combination of ligand-based and structure-based in silico methods.
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Affiliation(s)
- Linn M Evenseth
- Molecular Pharmacology and Toxicology, Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, NO-9037 Tromsø, Norway.
| | - Dawid Warszycki
- Department of Medicinal Chemistry, Institute of Pharmacology, Polish Academy of Science, Smetna 12, 31-343 Kraków, Poland.
| | - Andrzej J Bojarski
- Department of Medicinal Chemistry, Institute of Pharmacology, Polish Academy of Science, Smetna 12, 31-343 Kraków, Poland.
| | - Mari Gabrielsen
- Molecular Pharmacology and Toxicology, Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, NO-9037 Tromsø, Norway.
| | - Ingebrigt Sylte
- Molecular Pharmacology and Toxicology, Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, NO-9037 Tromsø, Norway.
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Alchemical determination of drug-receptor binding free energy: Where we stand and where we could move to. J Mol Graph Model 2017; 71:233-241. [DOI: 10.1016/j.jmgm.2016.11.018] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 11/24/2016] [Accepted: 11/29/2016] [Indexed: 01/05/2023]
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Ferenczy GG. Computation of Drug-Binding Thermodynamics. THERMODYNAMICS AND KINETICS OF DRUG BINDING 2015. [DOI: 10.1002/9783527673025.ch3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Zhao W, Bai JK, Li HM, Chen T, Tang YJ. Tubulin structure-based drug design for the development of novel 4β-sulfur-substituted podophyllum tubulin inhibitors with anti-tumor activity. Sci Rep 2015; 5:10172. [PMID: 25959922 PMCID: PMC4426677 DOI: 10.1038/srep10172] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 04/01/2015] [Indexed: 11/29/2022] Open
Abstract
The well-characterized anti-tubulin agent, podophyllotoxin (PTOX), with the 4′-position methoxyl group, targets the colchicines domain located between α- and β-tubulin. Two guanosine triphosphate (GTP) analogs of the tubulin-binding region were synthesized from PTOX, where a hydroxyl group was substituted with a carbon-sulfur bond. These compounds, 4-MP-PTOX and 4-TG-PTOX, reduce the dosage and greatly improve the therapeutic effect for microtubule damage in cancer cells. Here we characterize the anti-tubulin properties of these compounds. We found the stronger inhibition of tubulin polymerization (the concentration of 50% growth inhibition, GI50 < 2 μM) for compounds 4-TG-PTOX and 4-MP-PTOX, which were better than that of PTOX or colchicine. The cytotoxicity of two designed compounds on tumor cells was also significantly enhanced by comparing to those of PTOX and colchicines. The ΔH value of 4-MP-PTOX and 4-TG-PTOX binding to tubulin by isothermal titration calorimetry (ITC) was found to be −7.4 and −5.3 kcal·mol−1, respectively. The wide range of enthalpy values across the series may reflect entropy/enthalpy compensation effects. Fragments 6-mercaptopurine (MP) and 6-thioguanine (TG) likely enhance the affinity of 4-MP-PTOX and 4-TG-PTOX binding to tubulin by increasing the number of binding sites. The correctness of rational drug design was strictly demonstrated by a bioactivity test.
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Affiliation(s)
- Wei Zhao
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Hubei University of Technology, Wuhan 430068 China
| | - Jia-Ke Bai
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Hubei University of Technology, Wuhan 430068 China
| | - Hong-Mei Li
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Hubei University of Technology, Wuhan 430068 China
| | - Tao Chen
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072 China
| | - Ya-Jie Tang
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Hubei University of Technology, Wuhan 430068 China
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SAR analysis and biological studies of synthesized podophyllum derivates obtained by N linkage modification at C-4 position. Bioorg Med Chem 2014; 22:6183-92. [DOI: 10.1016/j.bmc.2014.08.025] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 08/21/2014] [Accepted: 08/22/2014] [Indexed: 11/21/2022]
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Jia X, Zeng J, Zhang JZH, Mei Y. Accessing the applicability of polarized protein-specific charge in linear interaction energy analysis. J Comput Chem 2014; 35:737-47. [PMID: 24500844 DOI: 10.1002/jcc.23547] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2013] [Revised: 11/15/2013] [Accepted: 01/05/2014] [Indexed: 12/12/2022]
Abstract
The reliability of the linear interaction energy (LIE) depends on the atomic charge model used to delineate the Coulomb interaction between the ligand and its environment. In this work, the polarized protein-specific charge (PPC) implementing a recently proposed fitting scheme has been examined in the LIE calculations of the binding affinities for avidin and β-secretase binding complexes. This charge fitting scheme, termed delta restrained electrostatic potential, bypasses the prevalent numerical difficulty of rank deficiency in electrostatic-potential-based charge fitting methods via a dual-step fitting strategy. A remarkable consistency between the predicted binding affinities and the experimental measurement has been observed. This work serves as a direct evidence of PPC's applicability in rational drug design.
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Affiliation(s)
- Xiangyu Jia
- State Key Laboratory of Precision Spectroscopy, Department of Physics, Institute of Theoretical and Computational Science, East China Normal University, Shanghai, 200062, China
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Mishra SK, Sund J, Åqvist J, Koča J. Computational prediction of monosaccharide binding free energies to lectins with linear interaction energy models. J Comput Chem 2012; 33:2340-50. [DOI: 10.1002/jcc.23081] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Revised: 06/25/2012] [Accepted: 07/09/2012] [Indexed: 01/28/2023]
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Kortagere S, Lill M, Kerrigan J. Role of computational methods in pharmaceutical sciences. Methods Mol Biol 2012; 929:21-48. [PMID: 23007425 DOI: 10.1007/978-1-62703-050-2_3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Abstract
Over the past two decades computational methods have eased up the financial and experimental burden of early drug discovery process. The in silico methods have provided support in terms of databases, data mining of large genomes, network analysis, systems biology on the bioinformatics front and structure-activity relationship, similarity analysis, docking, and pharmacophore methods for lead design and optimization. This review highlights some of the applications of bioinformatics and chemoinformatics methods that have enriched the field of drug discovery. In addition, the review also provided insights into the use of free energy perturbation methods for efficiently computing binding energy. These in silico methods are complementary and can be easily integrated into the traditional in vitro and in vivo methods to test pharmacological hypothesis.
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Affiliation(s)
- Sandhya Kortagere
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA.
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In silico inspired design and synthesis of a novel tubulin-binding anti-cancer drug: folate conjugated noscapine (Targetin). J Comput Aided Mol Des 2011; 26:233-47. [DOI: 10.1007/s10822-011-9508-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2011] [Accepted: 12/01/2011] [Indexed: 10/14/2022]
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Theoretical studies of 1,4-dihydropyridine-3,5-dicarboxamides as possible inhibitors of Mycobacterium tuberculosis enoyl reductase. MONATSHEFTE FUR CHEMIE 2011. [DOI: 10.1007/s00706-011-0542-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Naik PK, Chatterji BP, Vangapandu SN, Aneja R, Chandra R, Kanteveri S, Joshi HC. Rational design, synthesis and biological evaluations of amino-noscapine: a high affinity tubulin-binding noscapinoid. J Comput Aided Mol Des 2011; 25:443-54. [PMID: 21544622 DOI: 10.1007/s10822-011-9430-4] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2011] [Accepted: 04/16/2011] [Indexed: 10/18/2022]
Abstract
Noscapine and its derivatives are important microtubule-interfering agents shown to have potent anti-tumor activity. The binding free energies (ΔG (bind)) of noscapinoids computed using linear interaction energy (LIE) method with a surface generalized Born (SGB) continuum solvation model were in agreement with the experimental ΔG (bind) with average root mean square error of 0.082 kcal/mol. This LIE-SGB model guided us in designing a novel derivative of noscapine, amino-noscapine [(S)-3-((R)-9-amino-4-methoxy-6-methyl-5,6,7,8-tetrahydro [1, 3] dioxolo[4,5-g]isoquinolin-5-yl)-6,7-dimethoxy isobenzo-furan-1(3H)-one] that has higher tubulin binding activity (predicted ΔG (bind) = -6.438 kcal/mol and experimental ΔG (bind) = -6.628 kcal/mol) than noscapine, but does not significantly change the total extent of the tubulin subunit/polymer ratio. The modes of interaction of amino-noscapine with the binding pocket of tubulin involved three hydrogen bonds and are distinct compared to noscapine which involved only one hydrogen bond. Also the patterns of non-bonded interactions are albeit different between both the lignads. The 'blind docking' approach (docking of ligand with different binding sites of a protein and their evaluations) as well as the reasonable accuracy of calculating ΔG (bind) using LIE-SGB model constitutes the first evidence that this class of compounds binds to tubulin at a site overlapping with colchicine-binding site or close to it. Our results revealed that amino-noscapine has better anti-tumor activity than noscapine.
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Affiliation(s)
- Pradeep K Naik
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA.
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