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Ismail NZ, Khairuddean M, Alidmat MM, Abubakar S, Arsad H. Investigating the potential of mono-chalcone compounds in targeting breast cancer receptors through network pharmacology, molecular docking, molecular dynamics simulation, antiproliferative effects, and gene expressions. 3 Biotech 2024; 14:151. [PMID: 38737798 PMCID: PMC11087420 DOI: 10.1007/s13205-024-03991-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 04/17/2024] [Indexed: 05/14/2024] Open
Abstract
The study aims to investigate various aspects of synthesized mono-chalcone compounds 5 and 8 concerning breast cancer, including network pharmacology, molecular docking, molecular dynamics (MD) simulations, antiproliferative effects, and gene expressions. Initially, the compounds underwent a network pharmacology analysis targeting breast cancer-related targets, with MalaCards, SwissTargetPrediction, and PharmMapper identifying 70 breast cancer target receptors. Subsequently, protein-protein interaction (PPI) network analysis revealed two distinct target gene clusters. Survival analysis identified seven significant target genes following Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment and Gene Ontology (GO) evaluation. Molecular docking and MD simulations were conducted on these seven target genes (AKT2, BRAF, ESR1, FGFR1, IGF1, IGF1R, and KIT), revealing that compound 8 exhibited the highest binding affinities, as well as better stability and compactness when interacting with the targeted proteins. Next, the compounds underwent cell viability assay and gene expression analysis to validate the in silico findings. Both compounds demonstrated the ability to suppress breast cancer proliferation, with compound 8 showing increased selectivity in targeting breast cancer cells while causing minimal harm to normal breast cells. The suppression of breast cancer cell proliferation was attributed to decreased expression levels of AKT2, BRAF, FGFR1, IGF1, IGF1R, KIT, and ESR1. Hence, the results provide insights into the molecular interaction responsible for the anti-breast cancer capabilities of mono-chalcone compounds. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-024-03991-y.
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Affiliation(s)
- Noor Zafirah Ismail
- School of Chemical Sciences, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Melati Khairuddean
- School of Chemical Sciences, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | | | - Sadiq Abubakar
- School of Chemical Sciences, Universiti Sains Malaysia, 11800 Penang, Malaysia
- Department of Pure and Industrial Chemistry, Bayero University Kano, Kano, 3011 Nigeria
| | - Hasni Arsad
- Advanced Medical and Dental Institute, Universiti Sains Malaysia, Bertam, 13200 Kepala Batas, Penang Malaysia
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Tran DN, Hoang TTH, Nandanwar S, Ho VTTX, Pham VT, Vu HD, Nguyen XH, Nguyen HT, Nguyen TV, Nguyen TKV, Tran DL, Park M, Lee S, Pham TC. Dual anticancer and antibacterial activity of fluorescent naphthoimidazolium salts. RSC Adv 2023; 13:36430-36438. [PMID: 38099251 PMCID: PMC10719908 DOI: 10.1039/d3ra06555c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 12/05/2023] [Indexed: 12/17/2023] Open
Abstract
Cancer has emerged as a significant global health challenge, ranking as the second leading cause of death worldwide. Moreover, cancer patients frequently experience compromised immune systems, rendering them susceptible to bacterial infections. Combining anticancer and antibacterial properties in a single drug could lead to improved overall treatment outcomes and patient well-being. In this context, the present study focused on a series of hydrophilic naphthoimidazolium salts with donor groups (NI-R), aiming to create dual-functional agents with antibacterial and anticancer activities. Among these compounds, NI-TPA demonstrated notable antibacterial activity, particularly against drug-resistant bacteria, with MIC value of 7.8 μg mL-1. Furthermore, NI-TPA exhibited the most potent cytotoxicity against four different cancer cell lines, with an IC50 range of 0.67-2.01 μg mL-1. The observed high cytotoxicity of NI-TPA agreed with molecular docking and dynamic simulation studies targeting c-Met kinase protein. Additionally, NI-TPA stood out as the most promising candidate for two-photo excitation, fluorescence bioimaging, and localization in lysosomes. The study findings open new avenues for the design and development of imidazolium salts that could be employed in phototheranostic applications for cancer treatment and bacterial infections.
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Affiliation(s)
- Dung Ngoc Tran
- Faculty of Chemistry, Hanoi National University of Education Hanoi Vietnam
| | | | - Sondavid Nandanwar
- Eco-friendly New Materials Research Center, Korea Research Institute of Chemical Technology 141 Gajeong-ro, Yuseong-gu Daejeon City Republic of Korea
| | | | - Van Thong Pham
- R&D Center, Vietnam Education and Technology Transfer JSC Cau Giay Hanoi Vietnam
| | - Huy Duc Vu
- Department of Radiology, School of Medicine, Daegu Catholic University Daegu 42472 Korea
| | - Xuan Ha Nguyen
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology 18 Hoang Quoc Viet, Cau Giay Hanoi Vietnam
| | - Huy Trung Nguyen
- Institute for Tropical Technology, Vietnam Academy of Science and Technology 18 Hoang Quoc Viet, Cau Giay Hanoi Vietnam
| | - Trang Van Nguyen
- Institute for Tropical Technology, Vietnam Academy of Science and Technology 18 Hoang Quoc Viet, Cau Giay Hanoi Vietnam
| | - Thuy Kieu Van Nguyen
- Industry 4.0 Convergence Bionics Engineering, Pukyong National University Busan 48513 Korea
| | - Dai Lam Tran
- Institute for Tropical Technology, Vietnam Academy of Science and Technology 18 Hoang Quoc Viet, Cau Giay Hanoi Vietnam
| | - Myeongkee Park
- Department of Chemistry, Pukyong National University Busan 48513 Korea
| | - Songyi Lee
- Industry 4.0 Convergence Bionics Engineering, Pukyong National University Busan 48513 Korea
- Department of Chemistry, Pukyong National University Busan 48513 Korea
| | - Thanh Chung Pham
- Institute for Tropical Technology, Vietnam Academy of Science and Technology 18 Hoang Quoc Viet, Cau Giay Hanoi Vietnam
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Rampogu S, Badvel P, Hoon Jo B, Kim Y, Kim SW, Lee KW. A review on Millepachine and its derivatives as potential multitarget anticancer agents. Biochem Biophys Res Commun 2023; 681:249-270. [PMID: 37793311 DOI: 10.1016/j.bbrc.2023.09.044] [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: 06/20/2023] [Revised: 09/04/2023] [Accepted: 09/18/2023] [Indexed: 10/06/2023]
Abstract
Chalcones have a long history of being used for many medical purposes. These are the most prestigious scaffolds in medicine. The potential of Millepachine and its derivatives to treat various malignancies has been demonstrated in this review. The anticancer effects of Millepachine and its derivatives on ovarian cancer, hepatocellular carcinoma, breast, liver, colon, cervical, prostate, stomach, and gliomas are highlighted in the current review. Several genes that are crucial in reducing the severity of the disease have been altered by these substances. They mainly work by preventing tubulin polymerizing. They also exhibit apoptosis and cell cycle arrest at the G2/M phase. Additionally, these compounds inhibit invasion and migration and have antiproliferative effects. Preclinical studies have shown that Millepachine and its derivatives offer exceptional potential for treating a number of cancers. These results need to be confirmed in clinical research in order to develop viable cancer therapies.
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Affiliation(s)
- Shailima Rampogu
- Department of Bio & Medical Big Data (BK4 Program), Division of Life Sciences, Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju, 52828, South Korea.
| | | | - Byung Hoon Jo
- Division of Applied Life Science, Gyeongsang National University, Jinju, 52828, Republic of Korea; ABC-RLRC, Gyeongsang National University, Jinju, 52828, Republic of Korea; Division of Life Science and Research Institute of Life Science, Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Yongseong Kim
- Department of Pharmaceutical Engineering, Kyungnam University, Changwon, 51767, Republic of Korea
| | - Seon-Won Kim
- Division of Applied Life Science (BK21 Four), ABC-RLRC, PMBBRC, Gyeongsang National University, Jinju, 52828, Republic of Korea.
| | - Keun Woo Lee
- Department of Bio & Medical Big Data (BK4 Program), Division of Life Sciences, Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju, 52828, South Korea.
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Tavasolikejani S, Farazin A. The effect of increasing temperature on simulated nanocomposites reinforced with SWBNNs and its effect on characteristics related to mechanics and the physical attributes using the MDs approach. Heliyon 2023; 9:e21022. [PMID: 37867868 PMCID: PMC10587535 DOI: 10.1016/j.heliyon.2023.e21022] [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: 08/07/2023] [Revised: 10/12/2023] [Accepted: 10/12/2023] [Indexed: 10/24/2023] Open
Abstract
This study examines the effect of increasing temperature (300, 350, 400, 450 and 500 K) on simulated nanocomposites reinforced with exploration of the impact of single-walled boron nitride nanotubes (SWBNNTs) on both the mechanical properties (including Young's modulus, Poisson's ratio, shear modulus, and bulk modulus) and the physical property of density, achieved through molecular dynamics (MDs) simulations. MDs utilized to simulate nanocomposite models consisting of five case studies of SWBNNs with different chiralities (5, 0), (10, 0), (15, 0), (20, 0), and (25, 0) as the reinforcement and using thermoplastic polyurethane (TPU) as the common matrix. The results reveal that with increasing temperature and chiralities of SWBNNTs, the density and Poisson's ratio increase dramatically, and Young's, shear, and bulk moduli decrease continuously. At a consistent temperature, there is a noteworthy trend in the mechanical properties of SWBNNTs with various chiralities. This includes the increase in Young's modulus, Poisson's ratio, shear modulus, and bulk modulus in the simulated nanocomposite, ranging from SWBNNTs (5, 0) to (25, 0). Similarly, the physical property of density exhibits an increasing trend from SWBNNTs (5, 0) to (20, 0) and then decreases at SWBNNTs (25, 0). To validate the accuracy of these findings, a Radial Distribution Function (RDF) diagram is generated using Materials Studio software.
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Affiliation(s)
| | - Ashkan Farazin
- Department of Solid Mechanics, Faculty of Mechanical Engineering, University of Kashan, P.O. Box 87317-53153, Kashan, Iran
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Rampogu S, Shaik MR, Khan M, Khan M, Oh TH, Shaik B. CBPDdb: a curated database of compounds derived from Coumarin-Benzothiazole-Pyrazole. Database (Oxford) 2023; 2023:baad062. [PMID: 37702993 PMCID: PMC10498939 DOI: 10.1093/database/baad062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 08/01/2023] [Accepted: 08/26/2023] [Indexed: 09/14/2023]
Abstract
The present article describes the building of a small-molecule web server, CBPDdb, employing R-shiny. For the generation of the web server, three compounds were chosen, namely coumarin, benzothiazole and pyrazole, and their derivatives were curated from the literature. The two-dimensional (2D) structures were drawn using ChemDraw, and the .sdf file was created employing Discovery Studio Visualizer v2017. These compounds were read on the R-shiny app using ChemmineR, and the dataframe consisting of a total of 1146 compounds was generated and manipulated employing the dplyr package. The web server is provided with JSME 2D sketcher. The descriptors of the compounds are obtained using propOB with a filter. The users can download the filtered data in the .csv and .sdf formats, and the entire dataset of a compound can be downloaded in .sdf format. This web server facilitates the researchers to screen plausible inhibitors for different diseases. Additionally, the method used in building the web server can be adapted for developing other small-molecule databases (web servers) in RStudio. Database URL: https://srampogu.shinyapps.io/CBPDdb_Revised/.
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Affiliation(s)
| | - Mohammed Rafi Shaik
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Merajuddin Khan
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Mujeeb Khan
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Tae Hwan Oh
- School of Chemical Engineering, Yeungnam University, Gyeongsan 38541, Republic of Korea
| | - Baji Shaik
- School of Chemical Engineering, Yeungnam University, Gyeongsan 38541, Republic of Korea
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Rampogu S, Jung TS, Ha MW, Lee KW. Repurposing and computational design of PARP inhibitors as SARS-CoV-2 inhibitors. Sci Rep 2023; 13:10583. [PMID: 37386052 PMCID: PMC10310815 DOI: 10.1038/s41598-023-36342-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 06/01/2023] [Indexed: 07/01/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) is a recent pandemic that caused serious global emergency. To identify new and effective therapeutics, we employed a drug repurposing approach. The poly (ADP ribose) polymerase inhibitors were used for this purpose and were repurposed against the main protease (Mpro) target of severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2). The results from these studies were used to design compounds using the 'Grow Scaffold' modules available on Discovery Studio v2018. The three designed compounds, olaparib 1826 and olaparib 1885, and rucaparib 184 demonstrated better CDOCKER docking scores for Mpro than their parent compounds. Moreover, the compounds adhered to Lipinski's rule of five and demonstrated a synthetic accessibility score of 3.55, 3.63, and 4.30 for olaparib 1826, olaparib 1885, and rucaparib 184, respectively. The short-range Coulombic and Lennard-Jones potentials also support the potential binding of the modified compounds to Mpro. Therefore, we propose these three compounds as novel SARS-CoV-2 inhibitors.
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Affiliation(s)
- Shailima Rampogu
- Department of Bio and Medical Big Data (BK4 Program), Division of Life Sciences, Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), Jinju, Republic of Korea.
| | - Tae Sung Jung
- Laboratory of Aquatic Animal Diseases, College of Veterinary Medicine, Research Institute of Natural Science, Gyeongsang National University, Jinju, 52828, Republic of Korea.
| | - Min Woo Ha
- Interdisciplinary Graduate Program in Advanced Convergence Technology and Science, Jeju National University, 102 Jejudaehak-ro, Jeju, 63243, Republic of Korea.
| | - Keun Woo Lee
- Department of Bio and Medical Big Data (BK4 Program), Division of Life Sciences, Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), Jinju, Republic of Korea.
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