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Karthick K, Abishek K, Angel Jemima E. In Silico Study, Protein Kinase Inhibition and Molecular Docking Study of Benzimidazole Derivatives. Bioinform Biol Insights 2024; 18:11779322241247635. [PMID: 38854784 PMCID: PMC11159556 DOI: 10.1177/11779322241247635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 03/28/2024] [Indexed: 06/11/2024] Open
Abstract
Kinase enzymes play an important role in cellular proliferation, and inhibition of their activity is a major goal of cancer therapy. Protein kinase inhibitors as benzimidazole derivatives can be applied for prevention or treatment of cancers through inhibition of cell proliferation. To evaluate their protein kinase inhibitory effects, as well as the in silico study for active benzimidazole derivatives. Benzimidazole derivatives has presented significant therapeutic potential against several disorders and known to have numerous biological activities (such as antibacterial, antiviral and anti-inflammatory). Benzimidazole derivatives have shown significant potential in the reduction of viral load as well as in enhancing immunity. To forecast absorption, distribution, metabolism, excretion and toxicity, simply known as ADMET and the Lipinski rule of five parameters of the examined substances, the admetSAR and Swiss ADME were used. The ADMET predictions revealed that the compounds had good and safe pharmacokinetic features, making them acceptable for further development as therapeutic candidates in clinical trials. This study primarily focused on blocking 2 key targets of kinase proteins (CDK4/CycD1 and Aurora B). 2-Phenylbenzimidazole has shown the greatest inhibitory potential (with a binding energy of -8.2 kcal/mol) against protein kinase inhibitors. This study results would pave the potential lead medication for anticancer therapeutic strategies.
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Affiliation(s)
- Kamaraj Karthick
- Department of Chemistry, Rajalakshmi Institute of Technology, Chennai, Tamil Nadu, India
| | - Kamaraj Abishek
- Department of Zoology, Sadakathullah Appa College, Tirunelveli, Tamil Nadu, India
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Al-Otaibi JS, Mary YS, Mary YS, Mondal A, Acharjee N, Rajendran Nair DS. Investigation of the interaction of thymine drugs with Be 12O 12 and Ca 12O 12 nanocages: A quantum chemical study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 308:123728. [PMID: 38056182 DOI: 10.1016/j.saa.2023.123728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 11/28/2023] [Accepted: 12/01/2023] [Indexed: 12/08/2023]
Abstract
Based on the DFT in a Wb97xd/6-311+G* level of theory, the interaction of thymine derivatives with Be12O12 and Ca12O12 nanocages was investigated. It was found that adsorption energies of thymine molecules on the Be12/Ca12-O12 surface was around -43.16, -60.06 and -29.62, -50.71, -45.95, -30.27 kcal/mol, for thymine (TH1), 1-amino thymine (TH2) and thymine glycol (TH3), respectively and this result supported the drug's adsorption. Additionally, according to the FMOs and MEP studies, a charge transfer from TH's to nanocages. Additionally, both molecular orbitals demonstrate that the LUMO and HOMO are primarily found on the BeO's surface.
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Affiliation(s)
- Jamelah S Al-Otaibi
- Department of Chemistry, College of Science, Princess Nourah Bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia.
| | - Y Sheena Mary
- Department of Physics, FMNC, University of Kerala, Kollam, Kerala, India
| | | | - Asmita Mondal
- Department of Chemistry, Durgapur Government College, J. N. Avenue, Paschim Bardhaman, West Bengal, India
| | - Nivedita Acharjee
- Department of Chemistry, Durgapur Government College, J. N. Avenue, Paschim Bardhaman, West Bengal, India
| | - Deepthi S Rajendran Nair
- Department of Ophthalmology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
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Spectroscopic, reactivity analysis and docking studies of 3-(adamantan-1-yl)-4-(4-fluorophenyl)-1-[(4-phenylpiperazin-1-yl)methyl]-4,5-dihdyro-1H-1,2,4-triazole—5-thione: DFT and MD simulations. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2022.134418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Ullah Z, Jee Kim H, Sheena Mary Y, Belboukhari N, Sekkoum K, Kraimi A, Zhan X, Wook Kwon H. Unlocking the Potential of Ovalene: A Dual-Purpose Sensor and Drug Enhancer. J Mol Liq 2023. [DOI: 10.1016/j.molliq.2023.121540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
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Al-Otaibi JS, Mary YS, Mary YS, Acharjee N, Churchill DG. Spectroscopic studies of 5-fluoro-1H-pyrimidine-2,4-dione adsorption on nanorings, solvent effects and SERS analysis. COMPUT THEOR CHEM 2022. [DOI: 10.1016/j.comptc.2022.113873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Ullah Z, Sattar F, Jee Kim H, Jang S, Sheena Mary Y, Zhan X, Wook Kwon H. Computational study of toxic gas removal. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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Al-Otaibi JS, Mary YS, Mary YS, Acharjee N, Churchill DG. Theoretical study of glycoluril by highly symmetrical magnesium oxide Mg 12O 12 nanostructure: adsorption, detection, SERS enhancement, and electrical conductivity study. J Mol Model 2022; 28:332. [PMID: 36163521 DOI: 10.1007/s00894-022-05332-3] [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: 07/01/2022] [Accepted: 09/21/2022] [Indexed: 12/07/2022]
Abstract
Using metal substrates that are nanoscale in size, surface-enhanced Raman scattering (SERS) is a technique for enhancing the Raman signal of biomolecules. Numerous industries including sensing materials, adsorption and medical devices, use nanomaterials like nanocages and nanoclusters. To discover a possible novel sensor platform involving a small metal cluster and a curved rigid substrate, we used density functional theoretical (DFT) simulations to explore the adsorption of glycoluril (GLC), a prospective drug intermediate, on a pure magnesium oxide cage (Mg12O12). This well defined cage was used as (i) an exact probable structure that could be used as well as (ii) a general model for MgO nanostructures. We also investigated the mono Al-doped Mg12O12 nanocage version Mg11AlO12. All computations were performed at the M06-2X level of theory. The GLC binds to the Mg12O12 nanocage by way of strong donor-acceptor interactions. The adsorption is releasing - 45.80 kcal mol-1 of energy. Due to Al doping, the energy gap of GLC-Mg11AlO12 (1.91 eV) is reduced from that of GLC-Mg12O12 (4.28 eV) and hence there is an increase in electrical conductivity of GLC-Mg11AlO12. The electronic change in the nanocage's conductivity can be transformed into an electrical signal which can be used to detect the presence of the drug analyte. In addition, when a GLC molecule is present, the work function of the nanocage is also reduced. The MgO nanocage, we conclude, is a work function type as well as a possible electronic sensor for GLC drug detection. GLC desorption from the Mg11AlO12 surface recovers more quickly in comparison with Mg12O12 recovery time. The AIM and NCIs assessed in this study were performed to help analyze the electronic structures of the complexes. Our findings pave the possibility for Mg11AlO12 nanostructures to be used in drug recognition.
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Affiliation(s)
- Jamelah S Al-Otaibi
- Department of Chemistry, College of Science, Princess Nourah Bint Abdulrahman University, P.O. Box 84428, Riyadh, 11671, Saudi Arabia.
| | | | | | - Nivedita Acharjee
- Department of Chemistry, Durgapur Government College, District-Paschim Bardhaman, Durgapur, West Bengal, India
| | - David G Churchill
- Department of Chemistry, Molecular Logic Gate Laboratory, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea. .,Therapeutic Bioengineering Section, KAIST Institute for Health Science and Technology (KIHST), Daejeon, Republic of Korea.
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