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Ibrahim MAA, Ali SSM, Abdeljawaad KAA, Abdelrahman AHM, Gabr GA, Shawky AM, Mekhemer GAH, Sidhom PA, Paré PW, Hegazy MEF. In-silico natural product database mining for novel neuropilin-1 inhibitors: molecular docking, molecular dynamics and binding energy computations. Journal of Taibah University for Science 2023. [DOI: 10.1080/16583655.2023.2182623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Affiliation(s)
- Mahmoud A. A. Ibrahim
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia, Egypt
- School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Sara S. M. Ali
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia, Egypt
| | - Khlood A. A. Abdeljawaad
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia, Egypt
| | - Alaa H. M. Abdelrahman
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia, Egypt
| | - Gamal A. Gabr
- Department of Pharmacology and Toxicology, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
- Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center, Giza, Egypt
| | - Ahmed M. Shawky
- Science and Technology Unit (STU), Umm Al-Qura University, Makkah, Saudi Arabia
| | - Gamal A. H. Mekhemer
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia, Egypt
| | - Peter A. Sidhom
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Tanta University, Tanta, Egypt
| | - Paul W. Paré
- Department of Chemistry & Biochemistry, Texas Tech University, Lubbock, TX, USA
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Ibrahim MAA, Abdelhamid MMH, Abdeljawaad KAA, Abdelrahman AHM, Mekhemer GAH, Sidhom PA, Sayed SRM, Paré PW, Hegazy MEF, Shoeib T. Pyronaridine as a Bromodomain-Containing Protein 4- N-Terminal Bromodomain (BRD4-BD1) Inhibitor: In Silico Database Mining, Molecular Docking, and Molecular Dynamics Simulation. Molecules 2023; 28:5713. [PMID: 37570684 PMCID: PMC10420099 DOI: 10.3390/molecules28155713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 07/21/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
BRD4 (bromodomain-containing protein 4) is an epigenetic reader that realizes histone proteins and promotes the transcription of genes linked to cancer progression and non-cancer diseases such as acute heart failure and severe inflammation. The highly conserved N-terminal bromodomain (BD1) recognizes acylated lysine residues to organize the expression of genes. As such, BD1 is essential for disrupting BRD4 interactions and is a promising target for cancer treatment. To identify new BD1 inhibitors, a SuperDRUG2 database that contains more than 4600 pharmaceutical compounds was screened using in silico techniques. The efficiency of the AutoDock Vina1.1.2 software to anticipate inhibitor-BRD4-BD1 binding poses was first evaluated based on the co-crystallized R6S ligand in complex with BRD4-BD1. From database screening, the most promising BRD4-BD1 inhibitors were subsequently submitted to molecular dynamics (MD) simulations integrated with an MM-GBSA approach. MM-GBSA computations indicated promising BD1 binding with a benzonaphthyridine derivative, pyronaridine (SD003509), with an energy prediction (ΔGbinding) of -42.7 kcal/mol in comparison with -41.5 kcal/mol for a positive control inhibitor (R6S). Pharmacokinetic properties predicted oral bioavailability for both ligands, while post-dynamic analyses of the BRD4-BD1 binding pocket demonstrated greater stability for pyronaridine. These results confirm that in silico studies can provide insight into novel protein-ligand regulators, specifically that pyronaridine is a potential cancer drug candidate.
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Affiliation(s)
- Mahmoud A. A. Ibrahim
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
- School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4000, South Africa
| | - Mahmoud M. H. Abdelhamid
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Khlood A. A. Abdeljawaad
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Alaa H. M. Abdelrahman
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Gamal A. H. Mekhemer
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Peter A. Sidhom
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Tanta University, Tanta 31527, Egypt
| | - Shaban R. M. Sayed
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Paul W. Paré
- Department of Chemistry & Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
| | - Mohamed-Elamir F. Hegazy
- Chemistry of Medicinal Plants Department, National Research Centre, 33 El-Bohouth St., Dokki, Giza 12622, Egypt
| | - Tamer Shoeib
- Department of Chemistry, The American University in Cairo, New Cairo 11835, Egypt
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Ibrahim MAA, Abdeljawaad KAA, Abdelrahman AHM, Abdelhamid MMH, Naeem MA, Mekhemer GAH, Sidhom PA, Sayed SRM, Paré PW, Hegazy MEF. SuperNatural inhibitors to reverse multidrug resistance emerged by ABCB1 transporter: Database mining, lipid-mediated molecular dynamics, and pharmacokinetics study. PLoS One 2023; 18:e0288919. [PMID: 37494356 PMCID: PMC10370898 DOI: 10.1371/journal.pone.0288919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 07/06/2023] [Indexed: 07/28/2023] Open
Abstract
An effective approach to reverse multidrug resistance (MDR) is P-glycoprotein (P-gp, ABCB1) transport inhibition. To identify such molecular regulators, the SuperNatural II database, which comprises > 326,000 compounds, was virtually screened for ABCB1 transporter inhibitors. The Lipinski rule was utilized to initially screen the SuperNatural II database, identifying 128,126 compounds. Those natural compounds were docked against the ABCB1 transporter, and those with docking scores less than zosuquidar (ZQU) inhibitor were subjected to molecular dynamics (MD) simulations. Based on MM-GBA binding energy (ΔGbinding) estimations, UMHSN00009999 and UMHSN00097206 demonstrated ΔGbinding values of -68.3 and -64.1 kcal/mol, respectively, compared to ZQU with a ΔGbinding value of -49.8 kcal/mol. For an investigation of stability, structural and energetic analyses for UMHSN00009999- and UMHSN00097206-ABCB1 complexes were performed and proved the high steadiness of these complexes throughout 100 ns MD simulations. Pharmacokinetic properties of the identified compounds were also predicted. To mimic the physiological conditions, MD simulations in POPC membrane surroundings were applied to the UMHSN00009999- and UMHSN00097206-ABCB1 complexes. These results demonstrated that UMHSN00009999 and UMHSN00097206 are promising ABCB1 inhibitors for reversing MDR in cancer and warrant additional in-vitro/in-vivo studies.
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Affiliation(s)
- Mahmoud A A Ibrahim
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia, Egypt
- School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Khlood A A Abdeljawaad
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia, Egypt
| | - Alaa H M Abdelrahman
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia, Egypt
| | - Mahmoud M H Abdelhamid
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia, Egypt
| | - Mohamed Ahmed Naeem
- Nutrition and Food Sciences, Ain Shams University Specialized Hospital, Ain Shams University, Cairo, Egypt
| | - Gamal A H Mekhemer
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia, Egypt
| | - Peter A Sidhom
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Tanta University, Tanta, Egypt
| | - Shaban R M Sayed
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Paul W Paré
- Department of Chemistry & Biochemistry, Texas Tech University, Lubbock, Texas, United States of America
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Ibrahim MAA, Abdeljawaad KAA, Abdelrahman AHM, Sidhom PA, Tawfeek AM, Mekhemer GAH, Abd El-Rahman MK, Dabbish E, Shoeib T. In-Silico Mining of the Toxins Database (T3DB) towards Hunting Prospective Candidates as ABCB1 Inhibitors: Integrated Molecular Docking and Lipid Bilayer-Enhanced Molecular Dynamics Study. Pharmaceuticals (Basel) 2023; 16:1019. [PMID: 37513931 PMCID: PMC10384459 DOI: 10.3390/ph16071019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/11/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
Multidrug resistance (MDR) is one of the most problematic issues in chemotherapeutic carcinoma therapy. The ABCB1 transporter, a drug efflux pump overexpressed in cancer cells, has been thoroughly investigated for its association with MDR. Thus, discovering ABCB1 inhibitors can reverse the MDR in cancer cells. In the current work, a molecular docking technique was utilized for hunting the most prospective ABCB1 inhibitors from the Toxin and Toxin-Target Database (T3DB). Based on the docking computations, the most promising T3DB compounds complexed with the ABCB1 transporter were subjected to molecular dynamics (MD) simulations over 100 ns. Utilizing the MM-GBSA approach, the corresponding binding affinities were computed. Compared to ZQU (calc. -49.8 kcal/mol), Emamectin B1a (T3D1043), Emamectin B1b (T3D1044), Vincristine (T3D4016), Vinblastine (T3D4017), and Vindesine (T3D2479) complexed with ABCB1 transporter demonstrated outstanding binding affinities with ΔGbinding values of -93.0, -92.6, -93.8, -92.2, and -90.8 kcal/mol, respectively. The structural and energetic investigations confirmed the constancy of the identified T3DB compounds complexed with the ABCB1 transporter during the 100 ns MD course. To mimic the physiological conditions, MD simulations were conducted for those identified inhibitors complexed with ABCB1 transporter in the presence of a POPC membrane. These findings revealed that Emamectin B1a, Emamectin B1b, Vincristine, Vinblastine, and Vindesine are promising ABCB1 inhibitors that can reverse the MDR. Therefore, subjecting those compounds to further in-vitro and in-vivo investigations is worthwhile.
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Affiliation(s)
- Mahmoud A A Ibrahim
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
- School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4000, South Africa
| | - Khlood A A Abdeljawaad
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Alaa H M Abdelrahman
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Peter A Sidhom
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Tanta University, Tanta 31527, Egypt
| | - Ahmed M Tawfeek
- Chemistry Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Gamal A H Mekhemer
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Mohamed K Abd El-Rahman
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
| | - Eslam Dabbish
- Department of Chemistry, The American University in Cairo, New Cairo 11835, Egypt
| | - Tamer Shoeib
- Department of Chemistry, The American University in Cairo, New Cairo 11835, Egypt
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Ibrahim MAA, Mahmoud AHM, Moussa NAM, Mekhemer GAH, Sayed SRM, Ahmed MN, Abd El-Rahman MK, Dabbish E, Shoeib T. Adsorption Features of Tetrahalomethanes (CX 4; X = F, Cl, and Br) on β12 Borophene and Pristine Graphene Nanosheets: A Comparative DFT Study. Molecules 2023; 28:5476. [PMID: 37513348 PMCID: PMC10386295 DOI: 10.3390/molecules28145476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/14/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
The potentiality of the β12 borophene (β12) and pristine graphene (GN) nanosheets to adsorb tetrahalomethanes (CX4; X = F, Cl, and Br) were investigated using density functional theory (DFT) methods. To provide a thorough understanding of the adsorption process, tetrel (XC-X3∙∙∙β12/GN)- and halogen (X3C-X∙∙∙β12/GN)-oriented configurations were characterized at various adsorption sites. According to the energetic manifestations, the adsorption process of the CX4∙∙∙β12/GN complexes within the tetrel-oriented configuration led to more desirable negative adsorption energy (Eads) values than that within the halogen-oriented analogs. Numerically, Eads values of the CBr4∙∙∙Br1@β12 and T@GN complexes within tetrel-/halogen-oriented configurations were -12.33/-8.91 and -10.03/-6.00 kcal/mol, respectively. Frontier molecular orbital (FMO) results exhibited changes in the EHOMO, ELUMO, and Egap values of the pure β12 and GN nanosheets following the adsorption of CX4 molecules. Bader charge transfer findings outlined the electron-donating property for the CX4 molecules after adsorbing on the β12 and GN nanosheets within the two modeled configurations, except the adsorbed CBr4 molecule on the GN sheet within the tetrel-oriented configuration. Following the adsorption process, new bands and peaks were observed in the band structure and density of state (DOS) plots, respectively, with a larger number in the case of the tetrel-oriented configuration than in the halogen-oriented one. According to the solvent effect affirmations, adsorption energies of the CX4∙∙∙β12/GN complexes increased in the presence of a water medium. The results of this study will serve as a focal point for experimentalists to better comprehend the adsorption behavior of β12 and GN nanosheets toward small toxic molecules.
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Affiliation(s)
- Mahmoud A A Ibrahim
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
- School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4000, South Africa
| | - Amna H M Mahmoud
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Nayra A M Moussa
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Gamal A H Mekhemer
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Shaban R M Sayed
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Muhammad Naeem Ahmed
- Department of Chemistry, The University of Azad Jammu and Kashmir, Muzaffarabad 13100, Pakistan
| | - Mohamed K Abd El-Rahman
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
| | - Eslam Dabbish
- Department of Chemistry, The American University in Cairo, New Cairo 11835, Egypt
| | - Tamer Shoeib
- Department of Chemistry, The American University in Cairo, New Cairo 11835, Egypt
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Ibrahim MAA, Hamad MHA, Mahmoud AHM, Mekhemer GAH, Sidhom PA, Sayed SRM, Moussa NAM, Rabee AIM, Dabbish E, Shoeib T. Adsorption of Favipiravir on pristine graphene nanosheets as a drug delivery system: a DFT study. RSC Adv 2023; 13:17465-17475. [PMID: 37304808 PMCID: PMC10253565 DOI: 10.1039/d3ra03227b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 05/29/2023] [Indexed: 06/13/2023] Open
Abstract
The efficiency of pristine graphene (GN) in the delivery process of the Favipiravir (FPV) anti-COVID-19 drug was herein revealed within the FPV⋯GN complexes in perpendicular and parallel configurations in terms of the density functional theory (DFT) method. Adsorption energy findings unveiled that the parallel configuration of FPV⋯GN complexes showed higher desirability than the perpendicular one, giving adsorption energy up to -15.95 kcal mol-1. This favorability could be interpreted as a consequence of the contribution of π-π stacking to the overall strength of the adsorption process in the parallel configuration. Frontier molecular orbitals (FMO) findings demonstrated the ability of the GN nanosheet to adsorb the FPV drug by the alteration in the EHOMO, ELUMO, and Egap values before and after the adsorption process. Based on Bader charge results, the FPV drug and GN sheet exhibited electron-donating and -accepting characters, respectively, which was confirmed by the negative sign of the computed charge transfer (Qt) values. The FPV(R)⋯T@GN complex showed the most desirable Qt value of -0.0377e, which was in synoptic with the adsorption energy pattern. Electronic properties of GN were also altered after the adsorption of the FPV drug in both configurations, with more observable changes in the parallel one. Interestingly, the Dirac point of the GN sheet coincided with the Fermi level after the adsorption process, indicating that the adsorption process unaffected the presence of the Dirac point. The occurrence of the adsorption process was also noticed by the existence of new bands and peaks in the band structure and DOS plots, respectively. Short recovery time rendered the GN nanosheet an efficient FPV drug delivery system. The obtained findings provide new insight into the biomedical applications of the GN sheet as a promising drug delivery system.
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Affiliation(s)
- Mahmoud A A Ibrahim
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University Minia 61519 Egypt
- School of Health Sciences, University of KwaZulu-Natal Westville Campus Durban 4000 South Africa
| | - Manar H A Hamad
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University Minia 61519 Egypt
| | - Amna H M Mahmoud
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University Minia 61519 Egypt
| | - Gamal A H Mekhemer
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University Minia 61519 Egypt
| | - Peter A Sidhom
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Tanta University Tanta 31527 Egypt
| | - Shaban R M Sayed
- Department of Botany and Microbiology, College of Science, King Saud University P.O. Box 2455 Riyadh 11451 Saudi Arabia
| | - Nayra A M Moussa
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University Minia 61519 Egypt
| | - Abdallah I M Rabee
- Leibniz-Institut für Katalyse Albert-Einstein-Str. 29 A 18059 Rostock Germany
| | - Eslam Dabbish
- Department of Chemistry, The American University in Cairo New Cairo 11835 Egypt
| | - Tamer Shoeib
- Department of Chemistry, The American University in Cairo New Cairo 11835 Egypt
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Ibrahim MAA, Hamad MHA, Mahmoud AHM, Mekhemer GAH, Sayed SRM, El-Rahman MKA, Sidhom PA, Dabbish E, Shoeib T. On the Use of Graphene Nanosheets for Drug Delivery: A Case Study of Cisplatin and Some of Its Analogs. Pharmaceutics 2023; 15:1640. [PMID: 37376088 DOI: 10.3390/pharmaceutics15061640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 05/23/2023] [Accepted: 05/30/2023] [Indexed: 06/29/2023] Open
Abstract
Graphene (GN) nanosheets have been widely exploited in biomedical applications as potential nanocarriers for various drugs due to their distinct physical and chemical properties. In this regard, the adsorption behavior of cisplatin (cisPtCl2) and some of its analogs on a GN nanosheet was investigated in perpendicular and parallel configurations by using density functional theory (DFT). According to the findings, the most significant negative adsorption energies (Eads) within the cisPtX2⋯GN complexes (where X = Cl, Br, and I) were observed for the parallel configuration, with values up to -25.67 kcal/mol at the H@GN site. Within the perpendicular configuration of the cisPtX2⋯GN complexes, three orientations were investigated for the adsorption process, namely, X/X, X/NH3, and NH3/NH3. The negative Eads values of the cisPtX2⋯GN complexes increased with the increasing atomic weight of the halogen atom. The Br@GN site showed the largest negative Eads values for the cisPtX2⋯GN complexes in the perpendicular configuration. The Bader charge transfer outcomes highlighted the electron-accepting properties of cisPtI2 within the cisPtI2⋯GN complexes in both configurations. The electron-donating character of the GN nanosheet increased as the electronegativity of the halogen atom increased. The band structure and density of state plots revealed the occurrence of the physical adsorption of the cisPtX2 on the GN nanosheet, which was indicated by the appearance of new bands and peaks. Based on the solvent effect outlines, the negative Eads values generally decreased after the adsorption process in a water medium. The recovery time results were in line with the Eads findings, where the cisPtI2 in the parallel configuration took the longest time to be desorbed from the GN nanosheet with values of 61.6 × 108 ms at 298.15 K. The findings of this study provide better insights into the utilization of GN nanosheets in drug delivery applications.
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Affiliation(s)
- Mahmoud A A Ibrahim
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
- School of Health Sciences, University of KwaZulu-Natal, Westville, Durban 4000, South Africa
| | - Manar H A Hamad
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Amna H M Mahmoud
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Gamal A H Mekhemer
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Shaban R M Sayed
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Mohamed K Abd El-Rahman
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
| | - Peter A Sidhom
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Tanta University, Tanta 31527, Egypt
| | - Eslam Dabbish
- Department of Chemistry, The American University in Cairo, New Cairo 11835, Egypt
| | - Tamer Shoeib
- Department of Chemistry, The American University in Cairo, New Cairo 11835, Egypt
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Mekhemer GAH, Mohamed HAA, Bumajdad A, Zaki MI. Lattice-charge imbalance and redox catalysis over perovskite-type ferrite- and manganite-based mixed oxides as studied by XRD, FTIR, UV-Vis DRS, and XPS. Sci Rep 2023; 13:7453. [PMID: 37156861 PMCID: PMC10167207 DOI: 10.1038/s41598-023-34065-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 04/24/2023] [Indexed: 05/10/2023] Open
Abstract
In the present investigation, two sets of pure and substituted ferrite- and manganite-based mixed oxides were prepared within the stoichiometric formula[Formula: see text], where A = Bi or La, A' = Sr, B = Fe or Mn, B' = Co, x = 0 or 0.2, by calcination at 700 °C (for 1 h) of corresponding metal citrate xerogels. Materials thus obtained were examined for bulk and surface characteristics using X-ray diffractometry, ex situ Fourier transform infrared spectroscopy, UV-Vis diffuse reflectance spectroscopy, X-ray photoelectron spectroscopy, and N2 sorptiometry. Their redox catalytic activity was evaluated towards a 2-propanol dehydrogenation reaction in the gas phase by employing in situ Fourier transform infrared spectroscopy. The results obtained could help reveal that (1) the presence of Bi (versus La) and Mn (versus Fe) facilitated the formation of polymeric crystalline phases assuming lattice-charge imbalance (due to excess positive charge), (2) the surface exposure of the excess positive charge was manifested in the generation of Mn sites having various oxidation states ≥ 3+, (3) the consequent development of visible light absorptions at 498-555 nm suggested occurrence of electron double-exchange facilitated by the formation of Mnn+-O2--Mn(n+1)+ Zener-type linkages, and (4) the exposure of such linkages at the surface warrants the establishment of the electron-mobile environment necessitated by the redox catalytic activity. Moreover, the relationship between the alcohol dehydrogenation activity and the magnitude of the lattice-charge imbalance (i.e., the net excess positive charge) of the catalysts was highlighted.
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Affiliation(s)
- Gamal A H Mekhemer
- Chemistry Department, Faculty of Science, Minia University, El-Minia, 61519, Egypt
| | - Hagar A A Mohamed
- Chemistry Department, Faculty of Science, Minia University, El-Minia, 61519, Egypt
| | - Ali Bumajdad
- Chemistry Department, Faculty of Science, Kuwait University, P.O. Box 5969, 13060, Safat, Kuwait
| | - Mohamed I Zaki
- Chemistry Department, Faculty of Science, Minia University, El-Minia, 61519, Egypt.
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Ibrahim MAA, Abdeljawaad KAA, Jaragh-Alhadad LA, Oraby HF, Atia MAM, Alzahrani OR, Mekhemer GAH, Moustafa MF, Shawky AM, Sidhom PA, Abdelrahman AHM. Potential drug candidates as P-glycoprotein inhibitors to reverse multidrug resistance in cancer: an in silico drug discovery study. J Biomol Struct Dyn 2023; 41:13977-13992. [PMID: 36883864 DOI: 10.1080/07391102.2023.2176360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 01/29/2023] [Indexed: 03/09/2023]
Abstract
The failure of chemotherapy in the treatment of carcinoma is mainly due to the development of multidrug resistance (MDR), which is largely caused by the overexpression of P-glycoprotein (P-gp/ABCB1/MDR1). Until recently, the 3D structure of the P-gp transporter has not been experimentally resolved, which restricted the discovery of prospective P-gp inhibitors utilizing in silico techniques. In this study, the binding energies of 512 drug candidates in clinical or investigational stages were assessed as potential P-gp inhibitors employing in silico methods. On the basis of the available experimental data, the performance of the AutoDock4.2.6 software to predict the drug-P-gp binding mode was initially validated. Molecular docking and molecular dynamics (MD) simulations combined with molecular mechanics-generalized Born surface area (MM-GBSA) binding energy computations were subsequently conducted to screen the investigated drug candidates. Based on the current results, five promising drug candidates, namely valspodar, dactinomycin, elbasvir, temsirolimus, and sirolimus, showed promising binding energies against P-gp transporter with ΔGbinding values of -126.7, -112.1, -111.9, -102.9, and -101.4 kcal/mol, respectively. The post-MD analyses revealed the energetical and structural stabilities of the identified drug candidates in complex with the P-gp transporter. Furthermore, in order to mimic the physiological conditions, the potent drugs complexed with the P-gp were subjected to 100 ns MD simulations in an explicit membrane-water environment. The pharmacokinetic properties of the identified drugs were predicted and demonstrated good ADMET characteristics. Overall, these results indicated that valspodar, dactinomycin, elbasvir, temsirolimus, and sirolimus hold promise as prospective P-gp inhibitors and warrant further invitro/invivo investigations.
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Affiliation(s)
- Mahmoud A A Ibrahim
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia, Egypt
- School of Health Sciences, University of KwaZulu-Natal, Westville, Durban, South Africa
| | - Khlood A A Abdeljawaad
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia, Egypt
| | | | - Hesham Farouk Oraby
- Deanship of Scientific Research, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Mohamed A M Atia
- Molecular Genetics and Genome Mapping Laboratory, Genome Mapping Department, Agricultural Genetic Engineering Research Institute (AGERI), ARC, Giza, Egypt
| | - Othman R Alzahrani
- Department of Biology, Faculty of Sciences, University of Tabuk, Tabuk, Saudi Arabia
| | - Gamal A H Mekhemer
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia, Egypt
| | - Mahmoud F Moustafa
- Department of Biology, College of Science, King Khalid University, Abha, Saudi Arabia
- Department of Botany and Microbiology, Faculty of Science, South Valley University, Qena, Egypt
| | - Ahmed M Shawky
- Science and Technology Unit (STU), Umm Al-Qura University, Makkah, Saudi Arabia
| | - Peter A Sidhom
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Tanta University, Tanta, Egypt
| | - Alaa H M Abdelrahman
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia, Egypt
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10
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Ibrahim MAA, Mahmoud AHM, Mekhemer GAH, Shawky AM, Soliman MES, Moussa NAM. Adsorption Behavior of Toxic Carbon Dichalcogenides (CX 2; X = O, S, or Se) on β12 Borophene and Pristine Graphene Sheets: A DFT Study. Nanomaterials (Basel) 2022; 12:nano12193411. [PMID: 36234539 PMCID: PMC9565509 DOI: 10.3390/nano12193411] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 09/21/2022] [Accepted: 09/23/2022] [Indexed: 05/27/2023]
Abstract
The adsorption of toxic carbon dichalcogenides (CX2; X = O, S, or Se) on β12 borophene (β12) and pristine graphene (GN) sheets was comparatively investigated. Vertical and parallel configurations of CX2⋯β12/GN complexes were studied herein via density functional theory (DFT) calculations. Energetic quantities confirmed that the adsorption process in the case of the parallel configuration was more desirable than that in the vertical analog and showed values up to −10.96 kcal/mol. The strength of the CX2⋯β12/GN complexes decreased in the order CSe2 > CS2 > CO2, indicating that β12 and GN sheets showed significant selectivity for the CSe2 molecule with superb potentiality for β12 sheets. Bader charge transfer analysis revealed that the CO2⋯β12/GN complexes in the parallel configuration had the maximum negative charge transfer values, up to −0.0304 e, outlining the electron-donating character of CO2. The CS2 and CSe2 molecules frequently exhibited dual behavior as electron donors in the vertical configuration and acceptors in the parallel one. Band structure results addressed some differences observed for the electronic structures of the pure β12 and GN sheets after the adsorption process, especially in the parallel configuration compared with the vertical one. According to the results of the density of states, new peaks were observed after adsorbing CX2 molecules on the studied 2D sheets. These results form a fundamental basis for future studies pertaining to applications of β12 and GN sheets for detecting toxic carbon dichalcogenides.
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Affiliation(s)
- Mahmoud A. A. Ibrahim
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
- School of Health Sciences, University of KwaZulu-Natal, Westville, Durban 4000, South Africa
| | - Amna H. M. Mahmoud
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Gamal A. H. Mekhemer
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Ahmed M. Shawky
- Science and Technology Unit (STU), Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Mahmoud E. S. Soliman
- Molecular Bio-Computation and Drug Design Research Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville, Durban 4000, South Africa
| | - Nayra A. M. Moussa
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
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11
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Ibrahim MAA, Moussa NAM, Saad SMA, Ahmed MN, Shawky AM, Soliman MES, Mekhemer GAH, Rady ASSM. σ-Hole and LP-Hole Interactions of Pnicogen···Pnicogen Homodimers under the External Electric Field Effect: A Quantum Mechanical Study. ACS Omega 2022; 7:11264-11275. [PMID: 35415328 PMCID: PMC8992284 DOI: 10.1021/acsomega.2c00176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/11/2022] [Indexed: 06/14/2023]
Abstract
σ-Hole and lone-pair (lp)-hole interactions within σ-hole···σ-hole, σ-hole···lp-hole, and lp-hole···lp-hole configurations were comparatively investigated on the pnicogen···pnicogen homodimers (PCl3)2, for the first time, under field-free conditions and the influence of the external electric field (EEF). The electrostatic potential calculations emphasized the impressive versatility of the examined PCl3 monomers to participate in σ-hole and lp-hole pnicogen interactions. Crucially, the sizes of σ-hole and lp-hole were enlarged under the influence of the positively directed EEF and decreased in the case of reverse direction. Interestingly, the energetic quantities unveiled more favorability of the σ-hole···lp-hole configuration of the pnicogen···pnicogen homodimers, with significant negative interaction energies, than σ-hole···σ-hole and lp-hole···lp-hole configurations. Quantum theory of atoms in molecules and noncovalent interaction index analyses were adopted to elucidate the nature and origin of the considered interactions, ensuring their closed shell nature and the occurrence of attractive forces within the studied homodimers. Symmetry-adapted perturbation theory-based energy decomposition analysis alluded to the dispersion force as the main physical component beyond the occurrence of the examined interactions. The obtained findings would be considered as a fundamental underpinning for forthcoming studies pertinent to chemistry, materials science, and crystal engineering.
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Affiliation(s)
- Mahmoud A. A. Ibrahim
- Computational
Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Nayra A. M. Moussa
- Computational
Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Sherif M. A. Saad
- Computational
Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Muhammad Naeem Ahmed
- Department
of Chemistry, The University of Azad Jammu
and Kashmir, Muzaffarabad 13100, Pakistan
| | - Ahmed M. Shawky
- Science
and Technology Unit (STU), Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Mahmoud E. S. Soliman
- Molecular
Modelling and Drug Design Research Group, School of Health Sciences, University of KwaZulu-Natal, Westville, Durban 4000, South Africa
| | - Gamal A. H. Mekhemer
- Computational
Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Al-shimaa S. M. Rady
- Computational
Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
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12
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Ibrahim MAA, Abdelrahman AHM, Badr EAA, Almansour NM, Alzahrani OR, Ahmed MN, Soliman MES, Naeem MA, Shawky AM, Sidhom PA, Mekhemer GAH, Atia MAM. Naturally occurring plant-based anticancerous candidates as prospective ABCG2 inhibitors: an in silico drug discovery study. Mol Divers 2022; 26:3255-3277. [DOI: 10.1007/s11030-022-10389-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 01/05/2022] [Indexed: 02/06/2023]
Abstract
Abstract
ATP-binding cassette transporter G2 (ABCG2) is an efflux transporter related to the clinical multidrug resistance (MDR) phenomenon. Identifying ABCG2 inhibitors could help discover extraordinary curative strategies for carcinoma remediation. Hitherto, there is no medication drug inhibiting ABCG2 transporter, notwithstanding that a considerable number of drugs have been submitted to clinical-trial and investigational phases. In the search for unprecedented chemical compounds that could inhibit the ABCG2 transporter, an in silico screening was conducted on the Naturally Occurring Plant-based Anticancer Compound-Activity-Target (NPACT) database containing 1574 compounds. Inhibitor-ABCG2 binding affinities were estimated based on molecular docking and molecular minimization (MM) calculations and compared to a co-crystallized inhibitor (BWQ) acting as a reference inhibitor. Molecular dynamics (MD) simulations pursued by molecular mechanics-generalized Born surface area (MM-GBSA) binding energy estimations were further executed for compounds with MM-GBSA//MM binding energies lower than BWQ (calc. − 60.5 kcal/mol). NPACT00968 and NPACT01545 demonstrated auspicious inhibitory activities according to binding affinities (ΔGbinding) over the 100 ns MD simulations that were nearly one and a half folds compared to BWQ (− 100.4, − 94.7, and − 62.9 kcal/mol, respectively). Throughout the 100 ns MD simulations, structural and energetical analyses unveiled outstanding stability of the ABCG2 transporter when bound with NPACT00968 and NPACT01545. In silico calculations hold a promise for those two inhibitors as drug candidates of ABCG2 transporter and emphasize that further in vitro and in vivo experiments are guaranteed.
Graphical abstract
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13
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Ibrahim MAA, Badr EAA, Abdelrahman AHM, Almansour NM, Mekhemer GAH, Shawky AM, Moustafa MF, Atia MAM. In Silico Targeting Human Multidrug Transporter ABCG2 in Breast Cancer: Database Screening, Molecular Docking, and Molecular Dynamics Study. Mol Inform 2021; 41:e2060039. [PMID: 34491628 DOI: 10.1002/minf.202060039] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 08/25/2021] [Indexed: 12/24/2022]
Abstract
ABCG2 is a substantial member of the ABC transporter superfamily that plays a significant role in multidrug resistance in cancer. Until recently, the 3D structure of ABCG2 has not been resolved, which resulted in the limitation of developing potential ABCG2 inhibitors using structure-based drug discovery. Herein, eMolecules, ChEMBL, and ChEBI databases, containing >25 million compounds, were virtually screened against the ABCG2 transporter in homodimer form. Performance of AutoDock4.2.6 software to predict inhibitor-ABCG2 binding mode and affinity were validated on the basis of available experimental data. The explored databases were filtered based on docking scores. The most potent hits with binding affinities higher than that of experimental bound ligand (MZ29) were then selected and subjected to molecular mechanics minimization, followed by binding energy calculation using molecular mechanics-generalized Born surface area (MM-GBSA) approach. Furthermore, molecular dynamics simulations for 50 ns, followed by MM-GBSA binding energy calculations, were performed for the promising compounds, unveiling eight potential inhibitors with binding affinities <-55.8 kcal/mol. Structural and energetic analyses demonstrated the stability of the eight identified inhibitors over the 50 ns MD simulation. This research sheds light on the potentiality of the identified ABCG2 inhibitors as a therapeutic approach to overcome multidrug resistance cancer therapy.
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Affiliation(s)
- Mahmoud A A Ibrahim
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia, 61519, Egypt
| | - Esraa A A Badr
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia, 61519, Egypt
| | - Alaa H M Abdelrahman
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia, 61519, Egypt
| | - Nahlah Makki Almansour
- Department of Biology, College of Science, University of Hafr Al Batin, Hafr Al Batin, 1803, Saudi Arabia
| | - Gamal A H Mekhemer
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia, 61519, Egypt
| | - Ahmed M Shawky
- Science and Technology Unit (STU), Umm Al-Qura University, Makkah, 21955, Saudi Arabia
| | - Mahmoud F Moustafa
- Department of Biology, College of Science, King Khalid University, Abha, 9004, Saudi Arabia.,Department of Botany & Microbiology, Faculty of Science, South Valley University, Qena, Egypt
| | - Mohamed A M Atia
- Molecular Genetics and Genome Mapping Laboratory, Genome Mapping Department, Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, 12619, Egypt
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14
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Ibrahim MAA, Badr EAA, Abdelrahman AHM, Almansour NM, Shawky AM, Mekhemer GAH, Alrumaihi F, Moustafa MF, Atia MAM. Prospective Drug Candidates as Human Multidrug Transporter ABCG2 Inhibitors: an In Silico Drug Discovery Study. Cell Biochem Biophys 2021; 79:189-200. [PMID: 33954893 DOI: 10.1007/s12013-021-00985-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/08/2021] [Indexed: 12/22/2022]
Abstract
Breast cancer resistance protein (ABCG2) is a human ATP-binding cassette (ABC) that plays a paramount role in multidrug resistance (MDR) in cancer therapy. The discovery of ABCG2 inhibitors could assist in designing unprecedented therapeutic strategies for cancer treatment. There is as yet no approved drug targeting ABCG2, although a large number of drug candidates have been clinically investigated. In this work, binding affinities of 181 drug candidates in clinical-trial or investigational stages as ABCG2 inhibitors were inspected using in silico techniques. Based on available experimental data, the performance of AutoDock4.2.6 software was first validated to predict the inhibitor-ABCG2 binding mode and affinity. Combined molecular docking calculations and molecular dynamics (MD) simulations, followed by molecular mechanics-generalized Born surface area (MM-GBSA) binding energy calculations, were then performed to filter out the studied drug candidates. From the estimated docking scores and MM-GBSA binding energies, six auspicious drug candidates-namely, pibrentasvir, venetoclax, ledipasvir, avatrombopag, cobicistat, and revefenacin-exhibited auspicious binding energies with value < -70.0 kcal/mol. Interestingly, pibrentasvir, venetoclax, and ledipasvir were observed to show even higher binding affinities with the ABCG2 transporter with binding energies of < -80.0 kcal/mol over long MD simulations of 100 ns. The stabilities of these three promising candidates in complex with ABCG2 transporter were demonstrated by their energetics and structural analyses throughout the 100 ns MD simulations. The current study throws new light on pibrentasvir, venetoclax, and ledipasvir as curative options for multidrug resistant cancers by inhibiting ABCG2 transporter.
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Affiliation(s)
- Mahmoud A A Ibrahim
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia, Egypt.
| | - Esraa A A Badr
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia, Egypt
| | - Alaa H M Abdelrahman
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia, Egypt
| | - Nahlah Makki Almansour
- Department of Biology, College of Science, University of Hafr Al Batin, Hafr Al Batin, Saudi Arabia
| | - Ahmed M Shawky
- Science and Technology Unit (STU), Umm Al-Qura University, Makkah, Saudi Arabia
| | - Gamal A H Mekhemer
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia, Egypt
| | - Faris Alrumaihi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Mahmoud F Moustafa
- Department of Biology, College of Science, King Khalid University, Abha, Saudi Arabia.,Department of Botany & Microbiology, Faculty of Science, South Valley University, Qena, Egypt
| | - Mohamed A M Atia
- Molecular Genetics and Genome Mapping Laboratory, Genome Mapping Department, Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt.
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Ibrahim MAA, Saad SMA, Al-Fahemi JH, Mekhemer GAH, Ahmed SA, Shawky AM, Moussa NAM. External electric field effects on the σ-hole and lone-pair hole interactions of group V elements: a comparative investigation. RSC Adv 2021; 11:4022-4034. [PMID: 35424345 PMCID: PMC8694126 DOI: 10.1039/d0ra09765a] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 12/31/2020] [Indexed: 11/21/2022] Open
Abstract
σ-hole and lone-pair (lp) hole interactions of trivalent pnicogen-bearing (ZF3) compounds were comparatively scrutinized, for the first time, under field-free and external electric field (EEF) conditions. Conspicuously, the sizes of the σ-hole and lp-hole were increased by applying an EEF along the positive direction, while the sizes of both holes decreased through the reverse EEF direction. The MP2 energetic calculations of ZF3⋯FH/NCH complexes revealed that σ-holes exhibited more impressive interaction energies compared to the lp-holes. Remarkably, the strengths of σ-hole and lp-hole interactions evolved with the increment of the positive value of the considered EEF; i.e., the interaction energy increased as the utilized EEF value increased. Unexpectedly, under field-free conditions, nitrogen-bearing complexes showed superior strength for their lp-hole interactions than phosphorus-bearing complexes. However, the reverse picture was exhibited for the interaction energies of nitrogen- and phosphorus-bearing complexes interacting within lp-holes by applying the high values of a positively directed EEF. These results significantly demonstrate the crucial influence of EEF on the strength of σ-hole and lp-hole interactions, which in turn leads to an omnipresent enhancement for variable fields, including biological simulations and material science.
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Affiliation(s)
- Mahmoud A A Ibrahim
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University Minia 61519 Egypt
| | - Sherif M A Saad
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University Minia 61519 Egypt
| | - Jabir H Al-Fahemi
- Chemistry Department, Faculty of Applied Sciences, Umm Al-Qura University Makkah 21955 Saudi Arabia
| | - Gamal A H Mekhemer
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University Minia 61519 Egypt
| | - Saleh A Ahmed
- Chemistry Department, Faculty of Applied Sciences, Umm Al-Qura University Makkah 21955 Saudi Arabia
- Chemistry Department, Faculty of Science, Assiut University Assiut 71516 Egypt
| | - Ahmed M Shawky
- Science and Technology Unit (STU), Umm Al-Qura University Makkah 21955 Saudi Arabia
- Central Laboratory for Micro-analysis, Minia University Minia 61519 Egypt
| | - Nayra A M Moussa
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University Minia 61519 Egypt
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16
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Zaki MI, Knözinger H, Tesche B, Mekhemer GAH, Bongard HJ. Chemical and morphological consequences of acidification of pure, phosphated, and phosphonated CaO: influence of CO2 adsorption. Langmuir 2008; 24:6745-6753. [PMID: 18512873 DOI: 10.1021/la8000366] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
In situ Fourier transform infrared (FTIR) spectroscopy was employed to characterize the adsorption behavior (as a function of pressure or time) and surface species of CO2 molecules on pure, phosphated, and phosphonated CaO. Carbonate and bicarbonate species were found to form on the pure oxide, whereas on the phosphated and phosphonated oxide samples the carbonate species were found to substitute favorably some of the OH(-) and PO4(3-) groups thereon exposed, respectively. Before and after carbonation, the test samples were further examined by in situ FTIR spectroscopy of adsorbed pyridine species, scanning electron microscopy, and energy dispersive X-ray spectroscopy. Then they were in situ acidified by exposure to a wet atmosphere of HCl vapor at 673 K for 10 min and re-examined similarly to reveal the influence of CO2 adsorption on the chemical and morphological consequences of acidification. The results obtained show the carbonate substitution of PO4(3-) groups to enhance agglomeration of the otherwise fine, longitudinal material particles into much bulkier ones and to render the otherwise more stable phosphonate groups less stable to acid treatment than the phosphate groups. Moreover, the bulky particle agglomerates of the carbonated test samples were detectably eroded following the acid treatment.
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Affiliation(s)
- Mohamed I Zaki
- Chemistry Department, Faculty of Science, Minia University, El-Minia 61519, Egypt.
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Zaki MI, Knözinger H, Tesche B, Mekhemer GAH. Influence of phosphonation and phosphation on surface acid–base and morphological properties of CaO as investigated by in situ FTIR spectroscopy and electron microscopy. J Colloid Interface Sci 2006; 303:9-17. [PMID: 16934283 DOI: 10.1016/j.jcis.2006.07.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2006] [Revised: 07/04/2006] [Accepted: 07/06/2006] [Indexed: 11/17/2022]
Abstract
Pure, phosphated, and phosphonated CaO samples were prepared and characterized by X-ray powder diffractometry, FTIR spectroscopy, scanning electron microscopy, and energy-dispersive X-ray microprobing. Surface acid-base properties were probed by in situ FTIR spectroscopy of adsorbed CO (at 85 K), CDCl3 (at RT), CO2 (at RT), and methyl butynol decomposition reactions (at 473 K). Results obtained have shown phosphate and, to a larger extent, phosphonate additives to enhance the strength of Lewis acid sites exposed on CaO surfaces, at the expense of the Lewis base site strength. The phosphonation has been found, moreover, to make CaO particles grow in a preferential direction and be less susceptible to rehydration. These findings may establish surface chemical attributes for the application of the methylene bisphosphonate (MBP) class of drugs to hamper acid-induced resorption of bone materials (osteoporosis).
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Affiliation(s)
- Mohamed I Zaki
- Chemistry Department, Faculty of Science, Minia University, El-Minia 61519, Egypt.
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18
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Mekhemer GAH. Surface structure and acid–base properties of lanthanum oxide dispersed on silica and alumina catalysts. Phys Chem Chem Phys 2002. [DOI: 10.1039/b204056p] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Riemer T, Spielbauer D, Hunger M, Mekhemer GAH, Knözinger H. Superacid properties of sulfated zirconia as measured by Raman and1H MAS NMR spectroscopy. ACTA ACUST UNITED AC 1994. [DOI: 10.1039/c39940001181] [Citation(s) in RCA: 97] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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