1
|
Ibrahim A, Ipinloju N, Aiyelabegan AO, Alfa-Ibrahim AA, Muhammad SA, Oyeneyin OE. Discovery of Potential Phytochemicals from Carica papaya Targeting BRCA-1 in Breast Cancer Treatment. Appl Biochem Biotechnol 2023; 195:7159-7175. [PMID: 36988843 DOI: 10.1007/s12010-023-04473-2] [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] [Accepted: 03/16/2023] [Indexed: 03/30/2023]
Abstract
The BRCA1 and BRCA2 are genes that encode a protein that ensures the integrity of DNA and prevents the unregulated cells from proliferating. Mutations in the sequence of these genes are associated with the birth of inherited breast cancers. The research for possible human breast cancer treatment remains a vital step in the drug development process. In this study, in silico investigations involving a computational method for the discovery of active phytochemicals from Carica papaya against the BRCA-1 gene were carried out. The in silico studies for these phytochemicals datasets as BRCA-1 breast cancer therapeutic agents showed promising results through pharmacokinetics and pharmacodynamics studies. The Carica papaya compounds were found to follow the rule of five and have good bioavailability. The ADMET and drug-likeness screening score of the identified ligands also recognized their potential as a promising drug candidate against BRCA-1 while the DFT also confirm better biological and chemical reactivity of Carica papaya compounds with excellent intra-molecular charge transfer between electron donor and electron acceptor site. The results of the molecular docking provided useful information on possible target-lead interactions, demonstrating that the newly developed leads showed a high affinity for BRCA-1 targets and might be investigated for further research.
Collapse
Affiliation(s)
- Abdulwasiu Ibrahim
- Drosophila Laboratory, Department of Biochemistry, University of Ibadan, Ibadan, Oyo State, Nigeria.
- Drosophila Research and Training Centre, Ibadan, Oyo State, Nigeria.
| | - Nureni Ipinloju
- Theoretical and Computational Chemistry Unit, Department of Chemical Sciences, Adekunle Ajasin University, Akungba Akoko, Ondo State, Nigeria
| | | | | | | | - Oluwatoba Emmanuel Oyeneyin
- Theoretical and Computational Chemistry Unit, Department of Chemical Sciences, Adekunle Ajasin University, Akungba Akoko, Ondo State, Nigeria
| |
Collapse
|
2
|
Ibrahim A, Ipinloju N, Atasie NH, Babalola RM, Muhammad SA, Oyeneyin OE. Discovery of Small Molecule PARKIN Activator from Antipsychotic/Anti-neuropsychiatric Drugs as Therapeutics for PD: an In Silico Repurposing Approach. Appl Biochem Biotechnol 2023; 195:5980-6002. [PMID: 36735144 DOI: 10.1007/s12010-023-04376-2] [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] [Accepted: 01/12/2023] [Indexed: 02/04/2023]
Abstract
Although there is presently no cure for Parkinson's disease (PD), the available therapies are only able to lessen symptoms and preserve the quality of life. Around 10 million people globally had PD as of 2020. The widely used standard drug has recently been revealed to have several negative effects. Additionally, there is a dearth of innovative compounds entering the market as a result of subpar ADMET characteristics. Drug repurposing provides a chance to reenergize the sluggish drug discovery process by identifying new applications for already-approved medications. As this strategy offers a practical way to speed up the process of developing alternative medications for PD. This study used a computer-aided technique to select therapeutic agent(s) from FDA-approved neuropsychiatric/psychotic drugs that can be adopted in the treatment of Parkinson's disease. In the current work, a computational approach via molecular docking, density functional theory (DFT), and pharmacokinetics were used to identify possible (anti)neuropsychiatric/psychotic medications for the treatment of PD. By using molecular docking, about eight (anti)neuropsychiatric/psychotic medications were tested against PARKIN, a key protein in PD. Based on the docking score, the best ligand in the trial was determined. The top hits were compared to the reference ligand levodopa (L-DOPA). A large proportion of the drugs displayed binding affinity that was relatively higher than L-DOPA. Also, DFT analysis confirms the ligand-receptor interactions and the molecular charge transfer. All the compounds were found to obey Lipinski's rule with acceptable pharmacokinetic properties. The current study has revealed the effectiveness of antineuropsychiatric/antipsychotic drugs against PARKIN in the treatment of PD and lumateperone was revealed to be the most promising candidate interacting with PARKIN.
Collapse
Affiliation(s)
- Abdulwasiu Ibrahim
- Drosophila Laboratory, Department of Biochemistry, University of Ibadan, Ibadan, Oyo State, Nigeria.
- Department of Biochemistry and Molecular Biology, Usmanu Danfodiyo University, Sokoto, Nigeria.
- Drosophila Research and Training Centre, Ibadan, Oyo State, Nigeria.
| | - Nureni Ipinloju
- Theoretical and Computational Chemistry Unit, Department of Chemical Sciences, Adekunle Ajasin University, Akungba Akoko, Ondo State, Nigeria.
| | | | | | | | - Oluwatoba Emmanuel Oyeneyin
- Theoretical and Computational Chemistry Unit, Department of Chemical Sciences, Adekunle Ajasin University, Akungba Akoko, Ondo State, Nigeria
| |
Collapse
|
3
|
Oyeneyin OE, Ibrahim A, Ipinloju N, Ademoyegun AJ, Ojo ND. Insight into the corrosion inhibiting potential and anticancer activity of 1-(4-methoxyphenyl)-5-methyl-N'-(2-oxoindolin-3-ylidene)-1H-1,2,3-triazole-4-carbohydrazide via computational approaches. J Biomol Struct Dyn 2023:1-18. [PMID: 37747068 DOI: 10.1080/07391102.2023.2260491] [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: 06/26/2023] [Accepted: 09/13/2023] [Indexed: 09/26/2023]
Abstract
Cancer is a major health concern globally. Orthodox and traditional medicine have actively been explored to manage this disease. Also, corrosion is a natural catastrophe that weakens and deteriorates metallic structures and their alloys causing major structural failures and severe economic implications. Designing and exploring multi-functional materials are beneficial since they are adaptive to different fields including engineering and pharmaceutics. In this study, we examined the anti-corrosion and anti-cancer potentials of 1-(4-methoxyphenyl)-5-methyl-N'-(2-oxoindolin-3-ylidene)-1H-1,2,3-triazole-4-carbohydrazide (MAC) using computational approaches. The molecular reactivity descriptors and charge distribution parameters of MAC were studied in gas and water at density functional theory (DFT) at B3LYP/6-311++G(d,p) theory level. The binding and mechanism of interaction between MAC and iron surface was studied using Monte Carlo (MC) and molecular dynamics (MD) simulation in hydrochloric acid medium. From the DFT, MC, and MD simulations, it was observed that MAC interacted spontaneously with iron surface essentially via van der Waal and electrostatic interactions. The near-parallel alignment of the corrosion inhibitor on iron plane facilitates its adsorption and isolation of the metal surface from the acidic solution. Further, the compound was docked in the binding pocket of anaplastic lymphoma kinase (ALK: 4FNZ) protein to assess its anti-cancer potential. The binding score, pharmacokinetics, and drug-likeness of MAC were compared with the reference drug (Crizotinib). The MAC displayed binding scores of -5.729 kcal/mol while Crizotinib has -3.904 kcal/mol. MD simulation of the complexes revealed that MAC is more stable and exhibits more favourable hydrogen bonding with the ALK receptor's active site than Crizotinib.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Oluwatoba Emmanuel Oyeneyin
- Theoretical and Computational Chemistry Unit, Adekunle Ajasin University, Akungba-Akoko, Nigeria
- School of Chemistry and Physics, University of Kwazulu-Natal, Durban, South Africa
| | - Abdulwasiu Ibrahim
- Department of Biochemistry and Molecular Biology, Usmanu Danfodiyo University, Sokoto Nigeria
| | - Nureni Ipinloju
- Theoretical and Computational Chemistry Unit, Adekunle Ajasin University, Akungba-Akoko, Nigeria
| | - Adeniyi John Ademoyegun
- Theoretical and Computational Chemistry Unit, Adekunle Ajasin University, Akungba-Akoko, Nigeria
| | | |
Collapse
|
4
|
Ipinloju N, Ibrahim A, da Costa RA, Adigun TB, Olubode SO, Abayomi KJ, Aiyelabegan AO, Esan TO, Muhammad SA, Oyeneyin OE. Quantum evaluation and therapeutic activity of (E)-N-(4-methoxyphenyl)-2-(4-(3-oxo-3-phenylprop-1-en-1-yl) phenoxy)acetamide and its modified derivatives against EGFR and VEGFR-2 in the treatment of triple-negative cancer via in silico approach. J Mol Model 2023; 29:159. [PMID: 37099048 DOI: 10.1007/s00894-023-05543-2] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 04/03/2023] [Indexed: 04/27/2023]
Abstract
The most dangerous subtype of breast cancer, triple-negative breast cancer (TNBC), accounts for 25% of all breast cancer-related deaths and 15% of all breast cancer cases. TNBC is distinguished by the lack of immunohistochemical expression of HER2, progesterone receptors, or oestrogen receptors. Although it has been reported that upregulation of EGFR and VEGFR-2 is associated with TNBC progression, no proven effective targeted therapy exists at this time. We used structural bioinformatics methods, including density functional theory, molecular docking, molecular dynamic simulation, pharmacokinetic and drug-likeness models, to identify promising EGFR/VEGFR-2 inhibitors from N-(4-methoxyphenyl)-2-[4-(3-oxo-3-phenylprop-1-en-1-yl) phenoxy] acetamide and six of its modified derivatives in light of the lack of effective targets inhibitor Version 14 of Spartan software was used to analyse density functional theory. The Schrodinger software suite 2018's Maestro interface was used for the molecular docking analysis, and the admetSAR and swissADME servers were used for drug-likeness and absorption, distribution, metabolism, excretion, and toxicity. All of the compounds showed strong electronic characteristics. Additionally, all of the tested compounds met the ADMET and drug-likeness requirements without a single instance of Lipinski's rule of five violations. Additionally, the molecules' levels of affinity for the target proteins varied. The highest binding affinities were demonstrated by the MOLb-VEGFR-2 complex (- 9.925 kcal/mol) and the MOLg-EGFR complex (- 5.032 kcal/mol). The interaction of the molecules in the domain of the EGFR and VEGFR-2 receptors was also better understood through molecular dynamic simulation of the complex.
Collapse
Affiliation(s)
- Nureni Ipinloju
- Theoretical and Computational Chemistry Unit, Department of Chemical Sciences, Adekunle Ajasin University, Akungba Akoko, Ondo State, Nigeria.
| | - Abdulwasiu Ibrahim
- Department of Biochemistry and Molecular Biology, Usmanu Danfodiyo University, Sokoto, Nigeria.
| | - Renato Araujo da Costa
- Institute of Education, Science and Technology of Para (IFPA), Campus Abaetetuba, Abaetetuba, Para, Brazil
| | | | - Samuel Olawale Olubode
- Department of Biochemistry, Adekunle Ajasin University, Akungba Akoko, Ondo State, Nigeria
| | - Kehinde Joan Abayomi
- Faculty of Medical Laboratory Science, Usmanu DanFodiyo University, Sokoto, Nigeria
| | | | - Timothy Oluwaseun Esan
- Department of Chemical Sciences, Bamidele Olumilua University of Education Science and Technology, Ikere-Ekiti, Ekiti State, Nigeria
| | | | - Oluwatoba Emmanuel Oyeneyin
- Theoretical and Computational Chemistry Unit, Department of Chemical Sciences, Adekunle Ajasin University, Akungba Akoko, Ondo State, Nigeria.
| |
Collapse
|
5
|
Oyeneyin OE, Obadawo BS, Owolabi TO, Metibemu DS, Ipinloju N, Fagbohungbe KH, Modamori HO, Olatoye VO. Investigation of the Anticancer Potential of 2-alkoxycarbonylallyl Esters
Against Metastatic Murine Breast Cancer Line 4T1 Targeting the EGFR:
A Combined Molecular Docking, QSAR, and Machine Learning Approach. LETT DRUG DES DISCOV 2022. [DOI: 10.2174/1570180819666220512111613] [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] [Indexed: 11/22/2022]
Abstract
Background:
The search for novel and potent anticancer drugs is imperative. This present
study aims to unravel the mechanisms of action of 2-alkoxyecarbonyl esters using robust model(s) that
can accurately predict the bioactivity of novel compounds. Twenty-four potential anticancer 2-
alkoxycarbonylallyl ester compounds obtained from the literature were employed in building a 3D-QSAR
model.
Objectives:
The objective of this study is to determine the predictive ability of the GFA-based QSAR
models and extreme machine learning models and compare them. The lead compounds and newly designed
compounds were docked at the active site of a human epidermal growth factor receptor (EGFR)
kinase domain to determine their binding modes and affinity.
Methods:
QikProp program and Spartan packages were employed for screening compounds for druglikeness
and toxicity. QSAR models were equally used to predict the bioactivities of these molecules
using the Material Studio package. Molecular docking of the molecules at the active site of an EGFR
receptor, 1M17, was done using Auto dock tools.
Results:
The model of choice, with r2pred (0.857), satisfied the recommended standard for a stable and
reliable model. The low value of r2, Q2 for several trials and cRp2 (0.779 ≥ 0.5) and the high value of
correlation coefficient r2 for the training set (0.918) and test set (0.849) provide credence to the predictability
of the model. The superior inhibition of EGFR displayed by the lead compounds (20 and 21) with
binding energies of 6.70 and 7.00 kcalmol-1, respectively, is likely due to the presence of double bonds
and α-ester groups. ADMET screening showed that these compounds are highly druggable. The designed
compounds (A and B) displayed better inhibition of EGFR.
Conclusion:
The QSAR model used here performed better than the Random Forest Regression model for
predicting the bioactivity of these anticancer compounds, while the designed compounds (A and B) performed
better with higher binding affinity than the lead compounds. Implementing the developed model
would be helpful in the search for novel anticancer agents.
Collapse
Affiliation(s)
- Oluwatoba Emmanuel Oyeneyin
- Department of Chemical Sciences, Theoretical and Computational Chemistry Unit, Adekunle Ajasin University, Akungba-Akoko, Ondo State, Nigeria
| | | | - Taoreed Olakunle Owolabi
- Department of Physics and Electronics, Adekunle Ajasin University, Akungba-
Akoko, Ondo State, Nigeria
| | | | - Nureni Ipinloju
- Department of Chemical
Sciences, Theoretical and Computational Chemistry Unit, Adekunle Ajasin University, Akungba-Akoko, Ondo State,
Nigeria
| | - Kehinde Henry Fagbohungbe
- Department of Chemical
Sciences, Theoretical and Computational Chemistry Unit, Adekunle Ajasin University, Akungba-Akoko, Ondo State,
Nigeria
| | - Helen Omonipo Modamori
- Department of Chemistry, Federal University of Agriculture, Makurdi, Benue State, Nigeria
| | - Victor Olanrewaju Olatoye
- Department of Chemical
Sciences, Theoretical and Computational Chemistry Unit, Adekunle Ajasin University, Akungba-Akoko, Ondo State,
Nigeria
| |
Collapse
|
6
|
Akinyele OF, Adekunle AS, Olayanju DS, Oyeneyin OE, Durodola SS, Ojo ND, Akinmuyisitan AA, Ajayeoba TA, Olasunkanmi LO. Synthesis and Corrosion Inhibition Studies of (E)-3-(2-(4‑chloro-2-nitrophenyl)diazenyl)-1-nitrosonaphthalen-2-ol on Mild Steel dissolution in 0.5 M HCl Solution- Experimental, DFT and Monte Carlo Simulations. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133738] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
|
7
|
Obadawo BS, Oyeneyin OE, Olanrewaju AA, Metibemu DS, Emaleku SA, Owolabi TO, Ipinloju N. Predicting the Anticancer Activity of 2-alkoxycarbonylallyl Esters against MDA-MB-231 Breast Cancer - QSAR, Machine Learning and Molecular Docking. Curr Drug Discov Technol 2022; 19:e110822207398. [PMID: 35959613 DOI: 10.2174/1570163819666220811094019] [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: 03/17/2022] [Revised: 05/17/2022] [Accepted: 05/24/2022] [Indexed: 01/27/2023]
Abstract
BACKGROUND The continuous increase in mortality of breast cancer and other forms of cancer due to the failure of current drugs, resistance, and associated side effects calls for the development of novel and potent drug candidates. METHODS In this study, we used the QSAR and extreme learning machine models in predicting the bioactivities of some 2-alkoxycarbonylallyl esters as potential drug candidates against MDA-MB-231 breast cancer. The lead candidates were docked at the active site of a carbonic anhydrase target. RESULTS The QSAR model of choice satisfied the recommended values and was statistically significant. The R2pred (0.6572) was credence to the predictability of the model. The extreme learning machine ELM-Sig model showed excellent performance superiority over other models against MDAMB- 231 breast cancer. Compound 22 with a docking score of 4.67 kcal mol-1 displayed better inhibition of the carbonic anhydrase protein, interacting through its carbonyl bonds. CONCLUSION The extreme learning machine's ELM-Sig model showed excellent performance superiority over other models and should be exploited in the search for novel anticancer drugs.
Collapse
Affiliation(s)
| | - Oluwatoba Emmanuel Oyeneyin
- Department of Chemical Sciences, Theoretical and Computational Chemistry Unit, Adekunle Ajasin University, Akungba-Akoko, Ondo State, Nigeria
| | | | | | - Sunday Adeola Emaleku
- Department of Biochemistry, Adekunle Ajasin University, Akungba-Akoko, Ondo State, Nigeria
| | - Taoreed Olakunle Owolabi
- Department of Physics and Electronics, Adekunle Ajasin University, Akungba-Akoko, Ondo State, Nigeria
| | - Nureni Ipinloju
- Department of Chemical Sciences, Theoretical and Computational Chemistry Unit, Adekunle Ajasin University, Akungba-Akoko, Ondo State, Nigeria
| |
Collapse
|
8
|
Oyeneyin OE, Ojo ND, Ipinloju N, Agbaffa EB, Emmanuel AV. Investigation of the corrosion inhibition potentials of some 2-(4-(substituted)arylidene)-1H-indene-1,3-dione derivatives: density functional theory and molecular dynamics simulation. Beni-Suef Univ J Basic Appl Sci 2022. [DOI: 10.1186/s43088-022-00313-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Corrosion is a threat to material strength and durability. Electron-rich organic inhibitor may offer good corrosion mitigation potentials. In this work, anti-corrosion potentials of nine derivatives of 1H-indene-1,3-dione have been investigated using density functional theory (DFT) approach and molecular dynamics (MD) simulation. Chemical reactivity descriptors like energies of lowest unoccupied molecular orbital (ELUMO), highest occupied molecular orbital (EHOMO), electron affinity (A), ionization potential (I), energy gap (ΔEgap), global hardness (η), global softness (σ), electronegativity (χ), electrophilicity (ω), number of transferred electrons (ΔN) and back-donation (ΔEback-donation) were computed at DFT/B3LYP/6-31G(d) theoretical level. The local reactive sites and the charge partitioning on the compounds were studied using Fukui indices and molecular electrostatic potential (MEP) surface analysis. The adsorption behavior and the binding energy of the inhibitors on Fe (110) surface in hydrochloric acid solution were investigated using MD simulation.
Results
The high chemical reactivity, kinetic instability and good corrosion inhibition potentials demonstrated by the inhibitors are rationalized based on their high EHOMO, A, σ, ΔN, ΔEback-donation, and low ΔEgap, ELUMO, I and η. A wide difference of approximately 2.4–3.2 eV between the electronegativities of iron and the 1H-inden-1,3-diones suggests good charge transfer tendency from the latter to the low-lying vacant d-orbitals of iron. The heteroatoms (O and N) and the aromatic moieties are the nucleophilic sites on the inhibitors for effective adsorption on the metal surface as shown by condensed Fukui dual functions and MEP analysis. The MD simulation shows good interaction and strong binding energy between the inhibitor and Fe (110) surface.
Conclusions
Effective surface coverage and displacement of H3O+, Cl− and water molecules from Fe (110) surface by the inhibitors indicate good corrosion inhibition properties of the inden-1,3-diones. 2-((4,7-dimethylnaphthalen-1-yl)methylene)-1H-indene-1,3(2H)-dione display low energy gap, strongest binding interaction and most stabilized iron-inhibitor configuration, hence, the best anti-corrosion potential.
Graphical abstract
Collapse
|
9
|
Ramalingam A, Kuppusamy M, Sambandam S, Medimagh M, Oyeneyin OE, Shanmugasundaram A, Issaoui N, Ojo ND. Synthesis, spectroscopic, topological, hirshfeld surface analysis, and anti-covid-19 molecular docking investigation of isopropyl 1-benzoyl-4-(benzoyloxy)-2,6-diphenyl-1,2,5,6-tetrahydropyridine-3-carboxylate. Heliyon 2022; 8:e10831. [PMID: 36211997 PMCID: PMC9526874 DOI: 10.1016/j.heliyon.2022.e10831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/08/2022] [Accepted: 09/26/2022] [Indexed: 01/18/2023] Open
Abstract
Isopropyl 1-benzoyl-4-(benzoyloxy)-2,6-diphenyl-1,2,5,6-tetrahydropyridine-3-carboxylate (IDPC) was synthesized and characterized via spectroscopic (FT-IR and NMR) techniques. Hirshfeld surface and topological analyses were conducted to study structural and molecular properties. The energy gap (Eg), frontier orbital energies (EHOMO, ELUMO) and reactivity parameters (like chemical hardness and global hardness) were calculated using density functional theory with B3LYP/6–311++G (d,p) level of theory. Molecular docking of IDPC at the active sites of SARS-COVID receptors was investigated. IDPC molecule crystallized in the centrosymmetric triclinic (P1¯) space group. The topological and Hirshfeld surface analysis revealed that covalent, non-covalent and intermolecular H-bonding interactions, and electron delocalization exist in the molecular framework. Higher binding score (-6.966 kcal/mol) of IDPC at the active site of SARS-COVID main protease compared to other proteases suggests that IDPC has the potential of blocking polyprotein maturation. H-bonding and π-cationic and interactions of the phenyl ring and carbonyl oxygen of the ligand indicate the effective inhibiting potential of the compound against the virus.
Collapse
|
10
|
Kumar A, Sambandam S, Ramalingam A, Krishnamoorthy R, Arumugam D, Oyeneyin OE. Synthesis, molecular docking of 3-(2-chloroethyl)-2,6-diphenylpiperidin-4-one: Hirshfeld surface, spectroscopic and DFT based analyses. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132993] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
|
11
|
Metibemu DS, Oyeneyin OE, Metibemu AO, Adeniran OY, Omotuyi IO. vHTS, 3-D Pharmacophore, QSAR and Molecular docking Studies for the Identification of Phyto-derived ATP-Competitive Inhibitors of the BCR-ABL Kinase Domain. Curr Drug Discov Technol 2021; 19:e021221198480. [PMID: 34856909 DOI: 10.2174/1570163819666211202092632] [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: 08/06/2021] [Revised: 09/14/2021] [Accepted: 09/23/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Chronic myelogenous leukaemia (CML) constitutes about 15% of adult leukaemia and is characterized by the overproduction of immature myeloid cells. METHODS In this study, a virtual high throughput screening (vHTS) technique was employed to screen a library of phytochemicals of reported anti-cancer plants. A docking score of -10 kcalmol-1 was used as the cut-off for the selection of phyto-compounds for pharmacophore-based virtual screening. Statistically robust and thoroughly validated QSAR model (R = 0.914, R2 = 0.836, Adjusted R2 = 0.764, LOO-CV= 0.6680) was derived for the inhibition of BCR-ABL kinase domain. RESULTS The virtual screening, pharmacophore screening, QSAR model and molecular docking techniques applied herein revealed ellagic acid, a polyphenolic compound, as a potential competitive inhibitor of the BCR-ABL kinase domain. Ellagic acid binds to the inactive ABL state and forms similar interactions with key residues within the BCR-ABL Kinase domain as obtained in ponatinib (possesses inhibitory effects on the ABL thr-315I mutant). It forms hydrogen bond interaction with thr-315 residue (the gatekeeper residue). It is not likely to be prone to the various mutations associated with nilotinib because of its small size. CONCLUSION The procedure of VHTs, Pharmacophore, QSAR, and molecular docking applied in this study could help in detecting more anti-CML compounds.
Collapse
Affiliation(s)
| | - Oluwatoba Emmanuel Oyeneyin
- Theoretical and Computational Chemistry Unit, Department of Chemical Sciences, Adekunle Ajasin University, Akungba-Akoko, Ondo State. Nigeria
| | | | | | - Idowu Olaposi Omotuyi
- Department of Biochemistry, Adekunle Ajasin University, Akungba-Akoko, Ondo State. Nigeria
| |
Collapse
|
12
|
Oyeneyin OE, Obadawo BS, Orimoloye SM, Akintemi EO, Ipinloju N, Asere AM, Owolabi TO. Prediction of Inhibition Activity of BET Bromodomain Inhibitors using Grid Search-Based Extreme Learning Machine and Molecular Docking. LETT DRUG DES DISCOV 2021. [DOI: 10.2174/1570180818666210521215433] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
Inhibition activity of the epigenetic readers, such as bromodomain and extra-
C terminal domain protein family, is of high significance in many therapeutic applications due to
their ability to regulate gene expression as well as the chromatin structure by binding to acetylysine
residues.
Objectives:
In order to effectively and quickly determine the inhibition activity of these compounds
for the desired therapeutic application, this work presents a grid search-based extreme learning machine
computational intelligence method through which the inhibition activity of forty different
compounds of substituted 4-phenylisoquinolinones was determined.
Methods:
The prediction and generalization capacity of the developed model were assessed using
four different error metrics, which include root mean square error, mean absolute error, mean absolute
percentage deviation, and correlation coefficient between the measured values and predicted
activities. The lead compound (37), together with a kinase inhibitor, LY294002, and a bromodomain
and extra-C terminal inhibitor, CPI-0610, was docked with a bromodomain-containing protein 4
bromodomain 1, 6P05.
Results:
The developed model performed better than the existing model with percentage improvement
of 44.48%, 35.08%, 20.44%, and 1.23% on the basis of mean absolute percentage deviation,
mean absolute error, root mean square error, and correlation coefficient, respectively. The lead compound
has a better binding score than LY294002 and CPI-0610.
Conclusion:
Implementation of the developed model would help in searching for anti-inflammatory
as well as anticancer agents for effective therapeutic application.
Collapse
Affiliation(s)
| | - Babatunde Samuel Obadawo
- Theoretical and Computational Chemistry Unit, Department of Chemical Sciences, Adekunle Ajasin University, Akungba-Akoko, Ondo State,Nigeria
| | - Segun Michael Orimoloye
- Department of Computer Science, Adekunle Ajasin University, Akungba-Akoko, Ondo State,Nigeria
| | - Eric Oluwafisayo Akintemi
- Chemistry Unit, Department of Physical Sciences, College of Natural and Applied Sciences, Wesley University, Ondo,Nigeria
| | - Nureni Ipinloju
- Department of Chemical Sciences, Adekunle Ajasin University, Akungba-Akoko, Ondo State,Nigeria
| | - Adeola M. Asere
- Department of Physics and Electronics, Adekunle Ajasin University, Akungba-Akoko, Ondo State,Nigeria
| | - Taoreed O. Owolabi
- Department of Physics and Electronics, Adekunle Ajasin University, Akungba-Akoko, Ondo State,Nigeria
| |
Collapse
|
13
|
Oyeneyin OE, Obadawo BS, Olanrewaju AA, Owolabi TO, Gbadamosi FA, Ipinloju N, Modamori HO. Predicting the bioactivity of 2-alkoxycarbonylallyl esters as potential antiproliferative agents against pancreatic cancer (MiaPaCa-2) cell lines: GFA-based QSAR and ELM-based models with molecular docking. J Genet Eng Biotechnol 2021; 19:38. [PMID: 33689046 PMCID: PMC7947105 DOI: 10.1186/s43141-021-00133-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 02/04/2021] [Indexed: 02/08/2023]
Abstract
BACKGROUND The number of cancer-related deaths is on the increase, combating this deadly disease has proved difficult owing to resistance and some serious side effects associated with drugs used to combat it. Therefore, scientists continue to probe into the mechanism of action of cancer cells and designing novel drugs that could combat this disease more safely and effectively. Here, we developed a genetic function approximation model to predict the bioactivity of some 2-alkoxyecarbonyl esters and probed into the mode of interaction of these molecules with an epidermal growth factor receptor (3POZ) using the three-dimensional quantitative structure activity relationship (QSAR), extreme learning machine (ELM), and molecular docking techniques. RESULTS The developed QSAR model with predicted (R2pred) of 0.756 showed that the model was fit to be validated parameter for a built model and also proved that the developed model could be used in practical situation, R2 for training set (0.9929) and test set (0.8397) confirmed that the model could successfully predict the activity of new compounds due to its correlation with the experimental activity, the models generated with ELM models showed improved prediction of the activity of the molecules. The lead compounds (22 and 23) had binding energies of -6.327 and -7.232 kcalmol-1 for 22 and 23 respectively and displayed better inhibition at the binding sites of 3POZ when compared with that of the standard drug, chlorambucil (-6.0 kcalmol-1). This could be attributed to the presence of double bonds and the α-ester groups. CONCLUSION The QSAR and ELM models had good prognostic ability and could be used to predict the bioactivity of novel anti-proliferative drugs.
Collapse
Affiliation(s)
- Oluwatoba Emmanuel Oyeneyin
- Theoretical and Computational Chemistry Unit, Adekunle Ajasin University, Akungba-Akoko, Ondo State, Nigeria
- Department of Chemical Sciences, Adekunle Ajasin University, Akungba-Akoko, Ondo State, Nigeria
| | - Babatunde Samuel Obadawo
- Theoretical and Computational Chemistry Unit, Adekunle Ajasin University, Akungba-Akoko, Ondo State, Nigeria.
- Department of Chemical Sciences, Adekunle Ajasin University, Akungba-Akoko, Ondo State, Nigeria.
| | | | - Taoreed Olakunle Owolabi
- Department of Physics and Electronics, Adekunle Ajasin University, Akungba-Akoko, Ondo State, Nigeria
| | | | - Nureni Ipinloju
- Theoretical and Computational Chemistry Unit, Adekunle Ajasin University, Akungba-Akoko, Ondo State, Nigeria
- Department of Chemical Sciences, Adekunle Ajasin University, Akungba-Akoko, Ondo State, Nigeria
| | | |
Collapse
|
14
|
Oyeneyin OE, Adejoro IA, Ogunyemi BT, Esan OT. Structural and solvent dependence on the molecular and nonlinear optical properties of 10-octyl thiophene-based phenothiazine and substituted derivatives – a theoretical approach. Journal of Taibah University for Science 2018. [DOI: 10.1080/16583655.2018.1485274] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Oluwatoba Emmanuel Oyeneyin
- Department of Chemical Sciences, Adekunle Ajasin University, Akungba-Akoko, Ondo State, Nigeria
- Department of Chemistry, University of Ibadan, Nigeria
| | - Isaiah Ajibade Adejoro
- Department of Chemistry, University of Ibadan, Nigeria
- Department of Chemistry, University of Medical Science, Ondo, Nigeria
| | - Babatunde Temitope Ogunyemi
- Department of Chemistry, University of Ibadan, Nigeria
- Department of Chemistry, Federal University, Otuoke, Nigeria
| | | |
Collapse
|
15
|
Ajibade Adejoro I, Emmanuel Oyeneyin O, Temitope Ogunyemi B. Computational Investigation on Substituent and Solvent Effects on the Electronic, Geometric and Spectroscopic Properties of Azobenzene and Some Substituted Derivatives. ACTA ACUST UNITED AC 2015. [DOI: 10.11648/j.ijctc.20150306.12] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|