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Samykannu G, Mariyappan N, Natarajan J. Molecular interaction and MD-simulations: investigation of Sizofiran as a promising anti-cancer agent targeting eIF4E in colorectal cancer. In Silico Pharmacol 2024; 12:33. [PMID: 38655099 PMCID: PMC11033251 DOI: 10.1007/s40203-024-00206-3] [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: 02/24/2024] [Accepted: 03/28/2024] [Indexed: 04/26/2024] Open
Abstract
CRC has a major global health impact due to high mortality rates. CRC shows high expression of eukaryotic translation initiation factor (eIF4E) protein, the rapid development of lung, bladder, colon, prostate, breast, head, and neck cancer is attributed to the dysregulation of eIF4E making an important target for treatment. Targeting eIF4E-mediated translation is a promising anti-cancer strategy. Many organic compounds that inhibit eIF4E are being studied clinically. The compound Sizofiran has emerged as a promising eIF4E inhibitor candidate, but its exact mechanism of action is unclear. In an effort to close this discrepancy by clarifying the mechanism of the interactions between phytochemical substances and eIF4E, molecular docking and dynamics studies were conducted. Molecular docking studies found Sizofiran (- 12.513 kcal/mol) has the most affinity eIF4E binding energy out of 93 phytochemicals, 5 current drugs, and 4 known inhibitors. This positions it as a top eIF4E inhibitor candidate. An alignment of eIF4E protein sequences from multiple pathogens revealed that the glutamate103 interacting residues are evolutionarily conserved across the different eIF4E proteins. Further insights from 100 ns of MD simulations supported Sizofiran having superior stability and eIF4E inhibition compared to reference compounds. Designed Sizofiran-related compounds showed better activity than the current drugs such as Camptosar, Sorafenib, Regorafenib, Doxorubicin, and Kenpaullone, indicating strong potential to suppress CRC progression by targeting eIF4E. This research aims to significantly aid development of improved eIF4E-targeting drugs for cancer treatment. Graphical abstract Showing the Graphical abstract of the complete study. Supplementary Information The online version contains supplementary material available at 10.1007/s40203-024-00206-3.
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Affiliation(s)
- Gopinath Samykannu
- Data Mining and Text Mining Laboratory, Department of Bioinformatics, Bharathiar University, Coimbatore, TamilNadu India
| | - Nandhini Mariyappan
- Molecular Modelling and Designing Laboratory, Department of Physics, Bharathiar University, Coimbatore, TamilNadu India
| | - Jeyakumar Natarajan
- Data Mining and Text Mining Laboratory, Department of Bioinformatics, Bharathiar University, Coimbatore, TamilNadu India
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Odunitan TT, Saibu OA, Apanisile BT, Omoboyowa DA, Balogun TA, Awe AV, Ajayi TM, Olagunju GV, Mahmoud FM, Akinboade M, Adeniji CB, Abdulazeez WO. Integrating biocomputational techniques for Breast cancer drug discovery via the HER-2, BCRA, VEGF and ER protein targets. Comput Biol Med 2024; 168:107737. [PMID: 38000249 DOI: 10.1016/j.compbiomed.2023.107737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/03/2023] [Accepted: 11/16/2023] [Indexed: 11/26/2023]
Abstract
Computational modelling remains an indispensable technique in drug discovery. With myriad of high computing resources, and improved modelling algorithms, there has been a high-speed in the drug development cycle with promising success rate compared to the traditional route. For example, lapatinib; a well-known anticancer drug with clinical applications was discovered with computational drug design techniques. Similarly, molecular modelling has been applied to various disease areas ranging from cancer to neurodegenerative diseases. The techniques ranges from high-throughput virtual screening, molecular mechanics with generalized Born and surface area solvation (MM/GBSA) to molecular dynamics simulation. This review focuses on the application of computational modelling tools in the identification of drug candidates for Breast cancer. First, we begin with a succinct overview of molecular modelling in the drug discovery process. Next, we take note of special efforts on the developments and applications of combining these techniques with particular emphasis on possible breast cancer therapeutic targets such as estrogen receptor (ER), human epidermal growth factor receptor 2 (HER2), vascular endothelial growth factor (VEGF), breast cancer gene 1 (BRCA1), and breast cancer gene 2 (BRCA2). Finally, we discussed the search for covalent inhibitors against these receptors using computational techniques, advances, pitfalls, possible solutions, and future perspectives.
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Affiliation(s)
- Tope T Odunitan
- Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria; Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
| | - Oluwatosin A Saibu
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, NM, USA.
| | - Boluwatife T Apanisile
- Department of Nutrition and Dietetics, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Damilola A Omoboyowa
- Department of Biochemistry, Adekunle Ajasin University, Akungba-Akoko, Oyo State, Nigeria
| | - Toheeb A Balogun
- Department of Biological Sciences, University of California, San Diego, CA, USA
| | - Adeyoola V Awe
- Department of Medical Laboratory Science, Lead City, University, Ibadan, Oyo State, Nigeria
| | - Temitope M Ajayi
- Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Grace V Olagunju
- Department of Molecular Biology, New Mexico State University, Las Cruces, NM, USA
| | - Fatimah M Mahmoud
- Department of Molecular Biology, New Mexico State University, Las Cruces, NM, USA
| | - Modinat Akinboade
- Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Catherine B Adeniji
- Department of Environmental Management and Toxicology, Lead City University, Ibadan, Oyo State, Nigeria
| | - Waliu O Abdulazeez
- Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
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Integrated approach for studying bioactive compounds from Cladosporium spp. against estrogen receptor alpha as breast cancer drug target. Sci Rep 2022; 12:22446. [PMID: 36575224 PMCID: PMC9794773 DOI: 10.1038/s41598-022-22038-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 10/07/2022] [Indexed: 12/28/2022] Open
Abstract
Cladosporium spp. have been reported for their great diversity of secondary metabolites which represent as a prominent base material for verifying the biological activities. Several bioactive compounds which have antimicrobial, cytotoxic, quorum sensing inhibitory and phytotoxic activities have been isolated from Cladosporium species. Most of them are still needed to be explored for their anticancer properties. Therefore, the present study is focused on screening and identifying the bioactive compounds of Cladosporium spp. for their anticancer activity via the integrated approaches of Molecular Docking (MD), Molecular Dynamics Simulation (MDS) and Density Functional Theory (DFT) studies. A total of 123 bioactive compounds of Cladosporium spp. were explored for their binding affinity with the selected breast cancer drug target receptor such as estrogen receptor alpha (PDB:6CBZ). The Molecular Docking studies revealed that amongst the bioactive compounds screened, Altertoxin X and Cladosporol H showed a good binding affinity of - 10.5 kcal/mol and - 10.3 kcal/mol, respectively, with the estrogen receptor alpha when compared to the reference compound (17[Formula: see text]-Estradiol: - 10.2 kcal/mol). The MDS study indicated the stable binding patterns and conformation of the estrogen receptor alpha-Altertoxin X complex in a stimulating environment. In addition, in silico absorption, distribution, metabolism, excretion and toxicity (ADMET) study suggested that Altertoxin X has a good oral bioavailability with a high LD[Formula: see text] value of 2.375 mol/kg and did not cause any hepatotoxicity and skin sensitization. In summary, the integrated approaches revealed that Altertoxin X possesses a promising anticancer activity and could serve as a new therapeutic drug for breast cancer treatment.
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Integration of in vitro and in-silico analysis of Caulerpa racemosa against antioxidant, antidiabetic, and anticancer activities. Sci Rep 2022; 12:20848. [PMID: 36460661 PMCID: PMC9718753 DOI: 10.1038/s41598-022-24021-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 11/08/2022] [Indexed: 12/03/2022] Open
Abstract
Marine algae are found to be excellent in their nutritional and potential therapeutic properties. This study explores the antidiabetic and anticancer potential of fractionated polyphenolic extract of Caulerpa racemosa, green macroalgae. Crude polyphenolic extract (CPE) of C. racemosa and its fractions (n-hexane, ethyl acetate, chloroform, and distilled water) were tested for its total phenol and flavonoid contents and antioxidant potential. The ethyl acetate fraction was subjected to gas chromatography/mass spectrometry (GC/MS). The in vitro antidiabetic activity was assessed by alpha-amylase, glucosidase inhibition and anti-glycation assays. Also, in-silico studies were conducted to test the binding affinities between caulerpin with alpha-glucosidase enzyme and estrogen receptor (ER) active sites. Each fraction was tested for its in vitroin vitroanticancer activity by CellTiter-Glo and MTT cell proliferation assays. The total phenolic and flavonoid contents and the antioxidant potential of the crude extract were observed to be dose dependent. The GC/MS analysis of the ethyl acetate fraction yielded 47 peaks, whereas n-hexadecanoic acid and hexadecanoic acid methyl ester showed the highest compatibility percentages of 99% and 96%, respectively. The CPE exhibited a higher potential in both alpha-amylase inhibitory and anti-glycation activities. The ethyl acetate fraction was more effective against alpha-glucosidase inhibition. Molecular docking revealed a high binding affinity between the alpha-glucosidase enzyme and caulerpin and showed high binding affinity toward caulerpin, with H-bond interactions. The in vitro anticancer analyses revealed that chloroform fraction and CPE exhibited moderate activity on the KAIMRC1 cell line. Also, the CPE exhibited high specificity compared to the standard drug in anticancer studies. Our findings evidence the pharmacological potential of the CPE of C. racemosa, and bioactive compounds of the species may be utilized as lead molecules to develop anti-diabetic and anti-cancer drugs.
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Fu L, Zhao L, Liang M, Ran K, Fu J, Qiu H, Li F, Shu M. Identification of potential CAMKK2 inhibitors based on virtual screening and molecular dynamics simulation. MOLECULAR SIMULATION 2022. [DOI: 10.1080/08927022.2022.2123945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- Le Fu
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, People’s Republic of China
- Qianjiang Central Hospital of Chongqing, Chongqing, People’s Republic of China
| | - Linan Zhao
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, People’s Republic of China
| | - Meichen Liang
- Qianjiang Central Hospital of Chongqing, Chongqing, People’s Republic of China
| | - Kun Ran
- Qianjiang Central Hospital of Chongqing, Chongqing, People’s Republic of China
| | - Jing Fu
- Qianjiang Central Hospital of Chongqing, Chongqing, People’s Republic of China
| | - Haoyu Qiu
- Qianjiang Central Hospital of Chongqing, Chongqing, People’s Republic of China
| | - Fei Li
- Qianjiang Central Hospital of Chongqing, Chongqing, People’s Republic of China
| | - Mao Shu
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, People’s Republic of China
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Khan BA, Ashfaq M, Muhammad S, Munawar KS, Tahir MN, Al-Sehemi AG, Alarfaji SS. Exploring Highly Functionalized Tetrahydropyridine as a Dual Inhibitor of Monoamine Oxidase A and B: Synthesis, Structural Analysis, Single Crystal XRD, Supramolecular Assembly Exploration by Hirshfeld Surface Analysis, and Computational Studies. ACS OMEGA 2022; 7:29452-29464. [PMID: 36033707 PMCID: PMC9404513 DOI: 10.1021/acsomega.2c03909] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 08/02/2022] [Indexed: 06/15/2023]
Abstract
Ethyl 4-(4-fluorophenylamino)-2,6-bis(4-(trifluoromethyl)phenyl)-1-(4-fluoro-phenyl)-1,2,5,6-tetrahydropyridine-3-carboxylate (FTEAA) has been synthesized efficiently in an iodine-catalyzed five-component reaction of 4-fluoroaniline, 4-trifluoromethyl benzaldehyde, and ethyl acetoacetate in methanol at 55 °C for 12 h. Various spectro-analytical techniques such as 1H and 13C NMR and Fourier-transform infrared spectroscopy have validated the structure of FTEAA. Further confirmation of the structure of FTEAA has been established on the basis of single-crystal X-ray diffraction analysis. The supramolecular assembly of FTEAA in terms of strong and comparatively weak noncovalent interactions is fully investigated by Hirshfeld surface analysis, the interaction energy between pairs of molecules, and energy frameworks. The void analysis is conducted to explore the strength and stability of the crystal structure. Furthermore, molecular docking analysis was computationally performed to see the potential intermolecular interactions between the selected proteins and FTEAA. The binding interaction energies are found to be -8.8 and -9.6 kcal/mol for the proteins MAO-B (PDB ID: 2V5Z) and MAO-A (PDB ID: 2Z5X), respectively. These reasonably good binding energies (more negative values) indicate the efficient associations between the FTEAA and target proteins. The proteins and FTEAA were also analyzed for intermolecular interactions. FTEAA and proteins interact in a variety of ways, like conventional hydrogen bonds, carbon-hydrogen bonds, alkyl, π-alkyl, and halide interactions.
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Affiliation(s)
- Bilal Ahmad Khan
- Department
of Chemistry, University of Azad Jammu and
Kashmir, Muzaffarabad 13100, Azad Jammu and Kashmir, Pakistan
| | - Muhammad Ashfaq
- Department
of Physics, University of Sargodha, Sargodha, Punjab 40100, Pakistan
| | - Shabbir Muhammad
- Department
of Chemistry, College of Science, King Khalid
University, P.O. Box 9004, Abha 61413, Saudi Arabia
| | - Khurram Shahzad Munawar
- Institute
of Chemistry, University of Sargodha, Sargodha 40100, Pakistan
- Department
of Chemistry, University of Mianwali, Mianwali 42200, Pakistan
| | | | - Abdullah G. Al-Sehemi
- Department
of Chemistry, College of Science, King Khalid
University, P.O. Box 9004, Abha 61413, Saudi Arabia
| | - Saleh S. Alarfaji
- Department
of Chemistry, College of Science, King Khalid
University, P.O. Box 9004, Abha 61413, Saudi Arabia
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