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Melo TS, Andrade BS. Advancing rational pesticide development against Drosophila suzukii: bioinformatics tools and applications-a systematic review. J Mol Model 2024; 30:319. [PMID: 39222282 DOI: 10.1007/s00894-024-06113-w] [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: 02/26/2024] [Accepted: 08/15/2024] [Indexed: 09/04/2024]
Abstract
CONTEXT Drosophila suzukii (Matsumura, 1931) is a widespread agricultural pest responsible for significant damage to various soft-skinned fruit hosts. The revolutionary potential of bioinformatics in agriculture emerges from its ability to provide extensive information on pests, fungi, chemical resistance, implications of non-target species, and other critical aspects. This wealth of information allows researchers to engage in projects and applied research in diverse agricultural domains that face these challenges. In this context, bioinformatics tools play a fundamental role. The negative impact of pests on crops, resulting in substantial economic losses, has highlighted the importance of in silico methods. METHODS To achieve this, we conducted a systematic search in scientific databases using as keywords "Drosophila suzukii," "biopesticides," "simulations computational," and "in-silico." After applying the filters of relevance and publication date, we organized the articles and prioritized those that directly addressed that matched the keywords and the use of bioinformatics tools. Additionally, we included studies focusing on in silico assays of biopesticides, such as molecular docking. Our review aimed to present a collection of recent literature on biopesticides against Drosophila suzukii, emphasizing bioinformatics methods. Through this work, we strive to contribute to the literature of new perspectives on the development and efficiency of biopesticides, along with to advance research that may improve pest control strategies. RESULTS In the results of the systematic review, we found 2734 articles related to the selected keywords. Six of these articles directly address Drosophila suzukii and the use of bioinformatics tools in the search for alternatives in pest control. In the selected studies, we observed that two articles tend to focus on phylogenetic approaches, searching for gene sequences, amino acids, and constructing phylogenetic trees. The other three articles used molecular modeling and docking of receptors such as GABA and TRP with plant-derived and synthetic compounds to study intermolecular interactions. However, we identified gaps in these studies that could lead to further research in the biorational development of biopesticides using bioinformatics tools.
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Affiliation(s)
- Tarcisio Silva Melo
- Laboratory of Bioinformatics and Computational Chemistry, Department of Biological Sciences, State University of Southwest Bahia (UESB), Jequié, Bahia, Brazil.
- Graduate Program in Biotechnology, State University of Feira de Santana (UEFS), Feira de Santana, Bahia, Brazil.
| | - Bruno Silva Andrade
- Laboratory of Bioinformatics and Computational Chemistry, Department of Biological Sciences, State University of Southwest Bahia (UESB), Jequié, Bahia, Brazil
- Graduate Program in Biotechnology, State University of Feira de Santana (UEFS), Feira de Santana, Bahia, Brazil
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Phong NV, Kim HS, Park HJ, Yeom E, Yang SY. Assessing the Efficacy of Acanthoic Acid Isolated from Acanthopanax koreanum Nakai in Male Infertility: An In Vivo and In Silico Approach. Curr Issues Mol Biol 2024; 46:7411-7429. [PMID: 39057081 PMCID: PMC11276288 DOI: 10.3390/cimb46070440] [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: 06/14/2024] [Revised: 07/05/2024] [Accepted: 07/11/2024] [Indexed: 07/28/2024] Open
Abstract
Acanthoic acid, a diterpene isolated from the root bark of Acanthopanax koreanum Nakai, possesses diverse pharmacological activities, including anti-inflammatory, anti-diabetic, gastrointestinal protection, and cardiovascular protection. This study is the first to investigate the egg-hatching rates of Drosophila melanogaster affected by acanthoic acid. Notably, male flies supplemented with 10 μM acanthoic acid exhibited a strong increase in hatching rates compared with controls under adverse temperature conditions, suggesting a potential protective effect against environmental stressors. Molecular docking simulations revealed the binding affinities and specific interactions between acanthoic acid and proteins related to male infertility, including SHBG, ADAM17, and DNase I, with binding affinity values of -10.2, -6.8, and -5.8 kcal/mol, respectively. Following the docking studies, molecular dynamic simulations were conducted for a duration of 100 ns to examine the stability of these interactions. Additionally, a total binding energy analysis and decomposition analysis offered insights into the underlying energetic components and identified key contributing residues.
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Affiliation(s)
- Nguyen Viet Phong
- Department of Biology Education, Teachers College and Institute for Phylogenomics and Evolution, Kyungpook National University, Daegu 41566, Republic of Korea;
| | - Hyo-Sung Kim
- School of Life Science and Biotechnology, College of Natural Sciences, Kyungpook National University, Daegu 41566, Republic of Korea;
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea
- KNU-G LAMP Project Group, KNU-Institute of Basic Sciences, School of Life Sciences, College of Natural Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Hyun-Jung Park
- Department of Plant Life and Resource Science, Sangji University, Wonju-si 26339, Republic of Korea;
| | - Eunbyul Yeom
- School of Life Science and Biotechnology, College of Natural Sciences, Kyungpook National University, Daegu 41566, Republic of Korea;
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea
- KNU-G LAMP Project Group, KNU-Institute of Basic Sciences, School of Life Sciences, College of Natural Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Seo Young Yang
- Department of Biology Education, Teachers College and Institute for Phylogenomics and Evolution, Kyungpook National University, Daegu 41566, Republic of Korea;
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Khan K, Albalawi K, Abbas MN, Burki S, Musad Saleh EA, Al Mouslem A, Alsaiari AA, A Zaki ME, Khan AU, Alotaibi G, Jalal K. Pharmacokinetics and drug-likeness of anti-cancer traditional Chinese medicine: molecular docking and molecular dynamics simulation study. J Biomol Struct Dyn 2024; 42:3295-3306. [PMID: 37279114 DOI: 10.1080/07391102.2023.2216758] [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: 09/23/2022] [Accepted: 05/03/2023] [Indexed: 06/08/2023]
Abstract
MCM7 (Minichromosome Maintenance Complex Component 7) is a component of the DNA replication licensing factor, which controls DNA replication. The MCM7 protein is linked to tumor cell proliferation and has a function in the development of several human cancers. Several types of cancer may be treated by inhibiting the protein, as it is strongly produced throughout this process. Significantly, Traditional Chinese Medicine (TCM), which has a long history of clinical adjuvant use against cancer, is rapidly gaining traction as a valuable medical resource for the development of novel cancer therapies, including immunotherapy. Therefore, the goal of the research was to find small molecular therapeutic candidates against the MCM7 protein that may be used to treat human cancers. A computational-based virtual screening of 36,000 natural TCM libraries is carried out for this goal using a molecular docking and dynamic simulation technique. Thereby, ∼8 novel potent compounds i.e., ZINC85542762, ZINC95911541, ZINC85542617, ZINC85542646, ZINC85592446, ZINC85568676, ZINC85531303, and ZINC95914464 were successfully shortlisted, each having the capacity to penetrate the cell as potent inhibitors for MCM7 to curb this disorder. These selected compounds were found to have high binding affinities compared to the reference (AGS compound) i.e. < -11.0 kcal/mol. ADMET and pharmacological properties showed that none of these 8 compounds poses any toxic property (carcinogenicity) and have anti-metastatic, and anticancer activity. Additionally, MD simulations were run to assess the compounds' stability and dynamic behavior with the MCM7 complex for about 100 ns. Finally, ZINC95914464, ZINC95911541, ZINC85568676, ZINC85592446, ZINC85531303, and ZINC85542646 are identified as highly stable within the complex throughout the 100 ns simulations. Moreover, the results of binding free energy suggested that the selected virtual hits significantly bind to the MCM7 which implied these compounds may act as a potential MCM7 inhibitor. However, in vitro testing protocols are required to further support these results. Further, assessment through various lab-based trial methods can assist with deciding the action of the compound that will give options in contrast to human cancer immunotherapy.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kanwal Khan
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
| | - Karma Albalawi
- Department of Chemistry, Faculty of Science, University of Tabuk, Tabuk, Saudi Arabia
| | | | - Samiullah Burki
- Institute of Pharmaceutical Sciences, Jinnah Sindh medical University, Karachi, Pakistan
| | - Ebraheem Abdu Musad Saleh
- Chemistry Department, College of Arts & Science, Prince Sattam Bin Abdulaziz University, Wadi Al-Dawasir, Saudi Arabia
| | - Abdulaziz Al Mouslem
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Saudi Arabia
| | - Ahad Amer Alsaiari
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Magdi E A Zaki
- Department of Chemistry, Faculty of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi Arabia
| | - Afaq Ullah Khan
- School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang, PR China
| | - Ghallab Alotaibi
- Department of Pharmaceutical Sciences, College of Pharmacy, Shaqra University, Shaqra, KSA
| | - Khurshid Jalal
- HEJ Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan
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Xie J, Zhang X, Meng D, Li Y, Deng P. Identification of potentially high drug-like VEGFR2/c-Met dual-target type II kinase inhibitors with symmetric skeletons based on structural screening. J Biomol Struct Dyn 2024; 42:1249-1267. [PMID: 37042992 DOI: 10.1080/07391102.2023.2199082] [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: 12/23/2022] [Accepted: 03/29/2023] [Indexed: 04/13/2023]
Abstract
Vascular endothelial growth factor receptor 2 (VEGFR2) and c-Mesenchymal epithelial transition factor (c-Met) are tyrosine kinase receptors associated with the occurrence of malignant tumors. Studies have shown that inhibition of VEGFR2 promotes a feedback increase in c-Met, a mechanism linked to the emergence of resistance to VEGFR2 inhibitors. Therefore, treatment targeting both VEGFR2 and c-Met will have better application prospects. In this study, hierarchical virtual screening was performed on ZINC15, Molport and Mcule-ULTIMATE databases to identify potential VEGFR2/c-Met dual inhibitors. Firstly, the best pharmacophore model for each target was used to cross-screen the three databases, and the compounds that could match the two pharmacophore models were then retained based on the Fit Value of the respective crystal ligands. Compounds ZINC, MOL, and MLB named after their database sources were retained by binding pattern analysis and docking assessment. ADMET predictions indicated that ZINC had significantly higher oral bioavailability compared to the approved drug cabozantinib. This is likely due to ZINC's unique symmetrical backbone with less structure complexity, which may reduce the occurrence of adverse effects. Molecular dynamics simulations and binding free energy analysis showed that all three hit compounds were able to stably bind at the active site, but only ZINC could form high occupancy of hydrogen bonds with both VEGFR2 and c-Met, and also only ZINC had a higher binding free energy than crystal ligands, suggesting that ZINC was the most likely potential VEGFR2/c-Met dual-target inhibitor. This finding provides a promising starting point for the development of VEGFR2/c-Met dual-target inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jiali Xie
- College of Pharmacy, Chongqing Medical University, Chongqing, China
- Chongqing Research Center for Pharmaceutical Engineering, Chongqing, China
- Chongqing Key Research Laboratory for Quality Evaluation and Safety Research of APIs, Chongqing, China
| | - Xiaoxuan Zhang
- College of Pharmacy, Chongqing Medical University, Chongqing, China
- Chongqing Research Center for Pharmaceutical Engineering, Chongqing, China
- Chongqing Key Research Laboratory for Quality Evaluation and Safety Research of APIs, Chongqing, China
| | - Dan Meng
- College of Pharmacy, Chongqing Medical University, Chongqing, China
- Chongqing Research Center for Pharmaceutical Engineering, Chongqing, China
- Chongqing Key Research Laboratory for Quality Evaluation and Safety Research of APIs, Chongqing, China
| | - Yihao Li
- College of Pharmacy, Chongqing Medical University, Chongqing, China
| | - Ping Deng
- College of Pharmacy, Chongqing Medical University, Chongqing, China
- Chongqing Research Center for Pharmaceutical Engineering, Chongqing, China
- Chongqing Key Research Laboratory for Quality Evaluation and Safety Research of APIs, Chongqing, China
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da Costa RA, da Costa ADSS, da Rocha JAP, Lima MRDC, da Rocha ECM, Nascimento FCDA, Gomes AJB, do Rego JDAR, Brasil DDSB. Exploring Natural Alkaloids from Brazilian Biodiversity as Potential Inhibitors of the Aedes aegypti Juvenile Hormone Enzyme: A Computational Approach for Vector Mosquito Control. Molecules 2023; 28:6871. [PMID: 37836714 PMCID: PMC10574778 DOI: 10.3390/molecules28196871] [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: 07/11/2023] [Revised: 08/26/2023] [Accepted: 09/02/2023] [Indexed: 10/15/2023] Open
Abstract
This study explores the potential inhibitory activity of alkaloids, a class of natural compounds isolated from Brazilian biodiversity, against the mJHBP enzyme of the Aedes aegypti mosquito. This mosquito is a significant vector of diseases such as dengue, zika, and chikungunya. The interactions between the ligands and the enzyme at the molecular level were evaluated using computational techniques such as molecular docking, molecular dynamics (MD), and molecular mechanics with generalized Born surface area (MMGBSA) free energy calculation. The findings suggest that these compounds exhibit a high binding affinity with the enzyme, as confirmed by the binding free energies obtained in the simulation. Furthermore, the specific enzyme residues that contribute the most to the stability of the complex with the compounds were identified: specifically, Tyr33, Trp53, Tyr64, and Tyr129. Notably, Tyr129 residues were previously identified as crucial in the enzyme inhibition process. This observation underscores the significance of the research findings and the potential of the evaluated compounds as natural insecticides against Aedes aegypti mosquitoes. These results could stimulate the development of new vector control agents that are more efficient and environmentally friendly.
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Affiliation(s)
- Renato Araújo da Costa
- Laboratory of Biosolutions and Bioplastics of the Amazon, Graduate Program in Science and Environment, Institute of Exact and Natural Sciences, Federal University of Pará (UFPA), Belém 66075-110, PA, Brazil; (A.d.S.S.d.C.); (F.C.d.A.N.); (J.d.A.R.d.R.); (D.d.S.B.B.)
- Laboratory of Molecular Biology, Evolution and Microbiology, Federal Institute of Education, Science and Technology of Pará (IFPA) Campus Abaetetuba, Abaetetuba 68440-000, PA, Brazil; (M.R.d.C.L.); (A.J.B.G.)
| | - Andréia do Socorro Silva da Costa
- Laboratory of Biosolutions and Bioplastics of the Amazon, Graduate Program in Science and Environment, Institute of Exact and Natural Sciences, Federal University of Pará (UFPA), Belém 66075-110, PA, Brazil; (A.d.S.S.d.C.); (F.C.d.A.N.); (J.d.A.R.d.R.); (D.d.S.B.B.)
| | - João Augusto Pereira da Rocha
- Graduate Program in Chemistry, Federal University of Pará (UFPA), Belém 66075-110, PA, Brazil; (J.A.P.d.R.); (E.C.M.d.R.)
| | - Marlon Ramires da Costa Lima
- Laboratory of Molecular Biology, Evolution and Microbiology, Federal Institute of Education, Science and Technology of Pará (IFPA) Campus Abaetetuba, Abaetetuba 68440-000, PA, Brazil; (M.R.d.C.L.); (A.J.B.G.)
| | | | - Fabiana Cristina de Araújo Nascimento
- Laboratory of Biosolutions and Bioplastics of the Amazon, Graduate Program in Science and Environment, Institute of Exact and Natural Sciences, Federal University of Pará (UFPA), Belém 66075-110, PA, Brazil; (A.d.S.S.d.C.); (F.C.d.A.N.); (J.d.A.R.d.R.); (D.d.S.B.B.)
| | - Anderson José Baia Gomes
- Laboratory of Molecular Biology, Evolution and Microbiology, Federal Institute of Education, Science and Technology of Pará (IFPA) Campus Abaetetuba, Abaetetuba 68440-000, PA, Brazil; (M.R.d.C.L.); (A.J.B.G.)
| | - José de Arimatéia Rodrigues do Rego
- Laboratory of Biosolutions and Bioplastics of the Amazon, Graduate Program in Science and Environment, Institute of Exact and Natural Sciences, Federal University of Pará (UFPA), Belém 66075-110, PA, Brazil; (A.d.S.S.d.C.); (F.C.d.A.N.); (J.d.A.R.d.R.); (D.d.S.B.B.)
| | - Davi do Socorro Barros Brasil
- Laboratory of Biosolutions and Bioplastics of the Amazon, Graduate Program in Science and Environment, Institute of Exact and Natural Sciences, Federal University of Pará (UFPA), Belém 66075-110, PA, Brazil; (A.d.S.S.d.C.); (F.C.d.A.N.); (J.d.A.R.d.R.); (D.d.S.B.B.)
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Bouzina A, Bouone YO, Sekiou O, Aissaoui M, Ouk TS, Djemel A, Mansouri R, Ibrahim-Ouali M, Bouslama Z, Aouf NE. In vitro antitumor activity, molecular dynamics simulation, DFT study, ADME prediction, and Eg5 binding of enastron analogues. RSC Adv 2023; 13:19567-19584. [PMID: 37388149 PMCID: PMC10301704 DOI: 10.1039/d3ra02904b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 06/16/2023] [Indexed: 07/01/2023] Open
Abstract
The objective of this study is to evaluate a series of molecules based on cyclosulfamide as potential anticancer agents. Additionally, the study aims to analyze the obtained results through in silico studies; by conducting experiments and utilizing theoretical methods. In this context, we investigated the cytotoxic activity of enastron analogues on three human cell lines PRI (lymphoblastic cell line) derived from B-cell lymphoma. JURKAT (ATCC TIB-152) acute T cell leukaemia and K562 (ATCC CLL-243) is a chronic myelogenous leukaemia. Most of the tested compounds showed good inhibitory activity compared with the reference ligand (chlorambucil). The 5a derivative demonstrated the strongest effect against all cancer cells used. Furthermore, molecular docking simulations of the Eg5-enastron analogue complex revealed that studied molecules have the ability to inhibit the Eg5 enzyme, as evidenced by their calculated docking score. Following the promising results from the molecular docking study, the complex Eg5-4a underwent a 100 ns molecular dynamics simulation using Desmond. During the simulation, the receptor-ligand pairing demonstrated substantial stability after the initial 70 ns. In addition, we used DFT calculations to analyze the electronic and geometric characteristics of the studied compounds. The HOMO and LUMO band gap energies, and the molecular electrostatic potential surface were also deducted for the stable structure of each compound. Also, we studied the prediction of absorption, distribution, metabolism and excretion (ADME) of the compounds.
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Affiliation(s)
- Abdeslem Bouzina
- Laboratory of Applied Organic Chemistry, Bioorganic Chemistry Group, Department of Chemistry, Sciences Faculty, Badji Mokhtar Annaba University Box 12 23000 Annaba Algeria
| | - Yousra Ouafa Bouone
- Laboratory of Applied Organic Chemistry, Bioorganic Chemistry Group, Department of Chemistry, Sciences Faculty, Badji Mokhtar Annaba University Box 12 23000 Annaba Algeria
| | - Omar Sekiou
- Environmental Research Center (CRE) 23000 Annaba Algeria
| | - Mohamed Aissaoui
- Laboratory of Applied Organic Chemistry, Bioorganic Chemistry Group, Department of Chemistry, Sciences Faculty, Badji Mokhtar Annaba University Box 12 23000 Annaba Algeria
| | - Tan-Sothea Ouk
- Laboratoire Peirene, EA7500 Université de Limoges 123 Avenue Albert Thomas 87000 Limoges Cedex France
| | - Abdelhak Djemel
- Research Unit in Medicinal Plants, URPM 3000 Laghouat Algeria
- Research Center of Biotechnology, CRBt 25000 Constantine Algeria
| | | | | | - Zihad Bouslama
- Environmental Research Center (CRE) 23000 Annaba Algeria
| | - Nour-Eddine Aouf
- Laboratory of Applied Organic Chemistry, Bioorganic Chemistry Group, Department of Chemistry, Sciences Faculty, Badji Mokhtar Annaba University Box 12 23000 Annaba Algeria
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Jiang Y, Yang W, Wang F, Zhou B. In silico studies of a novel scaffold of benzoxazole derivatives as anticancer agents by 3D-QSAR, molecular docking and molecular dynamics simulations. RSC Adv 2023; 13:14808-14824. [PMID: 37197188 PMCID: PMC10184002 DOI: 10.1039/d3ra01316b] [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: 02/26/2023] [Accepted: 05/01/2023] [Indexed: 05/19/2023] Open
Abstract
The vascular endothelial growth factor receptor-2 kinases (VEGFR-2) expressed on tumor cells and vessels are attractive targets for cancer treatment. Potent inhibitors for the VEGFR-2 receptor are novel strategies to develop anti-cancer drugs. In this work, template ligand-based 3D-QSAR studies were performed on a series of benzoxazole derivatives toward different cell lines (HepG2, HCT-116 and MCF-7). Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) techniques were used to generate 3D-QSAR models. Good predictability was derived for the optimal CoMFA models (HepG2: Rcv2 = 0.509, Rpred2 = 0.5128; HCT-116: Rcv2 = 0.574, Rpred2 = 0.5597; MCF-7: Rcv2 = 0.568, Rpred2 = 0.5057) and CoMSIA models (HepG2: Rcv2 = 0.711, Rpred2 = 0.6198; HCT-116: Rcv2 = 0.531, Rpred2 = 0.5804; MCF-7: Rcv2 = 0.669, Rpred2 = 0.6577). In addition, the contour maps derived from CoMFA and CoMSIA models were also generated to illustrate the relationship between different fields and the inhibitory activities. Moreover, molecular docking and molecular dynamics (MD) simulations were also conducted to understand the binding modes and the potential interactions between the receptor and the inhibitors. Some key residues (Leu35, Val43, Lys63, Leu84, Gly117, Leu180 and Asp191) were pointed out for stabilizing the inhibitors in the binding pocket. The binding free energies for the inhibitors agreed well with the experimental inhibitory activity and indicated that steric, electrostatic and hydrogen bond interactions are the main driving force for inhibitor-receptor binding. Overall, a good consistency between theoretical 3D-SQAR and molecular docking and MD simulation studies would provide directions for the design of new candidates, avoiding time-consuming and costly synthesis and biological evaluations. On the whole, the results derived from this study could expand the understanding of benzoxazole derivatives as anticancer agents and would be of great help in lead optimization for early drug discovery of highly potent anticancer activity targeting VEGFR-2.
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Affiliation(s)
- Yuhan Jiang
- School of Life Science, Linyi University Linyi 276000 China
| | - Wei Yang
- National Clinical Research Center for Infectious Diseases, Shenzhen Third People's Hospital Shenzhen 518112 China
| | - Fangfang Wang
- School of Life Science, Linyi University Linyi 276000 China
| | - Bo Zhou
- State Key Laboratory of Functions and Applications of Medicinal Plants, College of Basic Medical, Guizhou Medical University Guizhou 550004 China
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Phenotypic Discovery of Thiocarbohydrazone with Anticancer Properties and Catalytic Inhibition of Human DNA Topoisomerase IIα. Pharmaceuticals (Basel) 2023; 16:ph16030341. [PMID: 36986441 PMCID: PMC10054454 DOI: 10.3390/ph16030341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/06/2023] [Accepted: 02/21/2023] [Indexed: 02/25/2023] Open
Abstract
Phenotypic screening of α-substituted thiocarbohydrazones revealed promising activity of 1,5-bis(salicylidene)thiocarbohydrazide against leukemia and breast cancer cells. Supplementary cell-based studies indicated an impairment of DNA replication via the ROS-independent pathway. The structural similarity of α-substituted thiocarbohydrazone to previously published thiosemicarbazone catalytic inhibitors targeting the ATP-binding site of human DNA topoisomerase IIα prompted us to investigate the inhibition activity on this target. Thiocarbohydrazone acted as a catalytic inhibitor and did not intercalate the DNA molecule, which validated their engagement with this cancer target. A comprehensive computational assessment of molecular recognition for a selected thiosemicarbazone and thiocarbohydrazone provided useful information for further optimization of this discovered lead compound for chemotherapeutic anticancer drug discovery.
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Galantamine Based Novel Acetylcholinesterase Enzyme Inhibitors: A Molecular Modeling Design Approach. Molecules 2023; 28:molecules28031035. [PMID: 36770702 PMCID: PMC9919016 DOI: 10.3390/molecules28031035] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 12/31/2022] [Accepted: 01/09/2023] [Indexed: 01/22/2023] Open
Abstract
Acetylcholinesterase (AChE) enzymes play an essential role in the development of Alzheimer's disease (AD). Its excessive activity causes several neuronal problems, particularly psychopathies and neuronal cell death. A bioactive pose on the hAChE B site of the human acetylcholinesterase (hAChE) enzyme employed in this investigation, which was obtained from the Protein Data Bank (PDB ID 4EY6), allowed for the prediction of the binding affinity and free binding energy between the protein and the ligand. Virtual screening was performed to obtain structures similar to Galantamine (GNT) with potential hAChE activity. The top 200 hit compounds were prioritized through the use of filters in ZincPharmer, with special features related to the pharmacophore. Critical analyses were carried out, such as hierarchical clustering analysis (HCA), ADME/Tox predictions, molecular docking, molecular simulation studies, synthetic accessibility (SA), lipophilicity, water solubility, and hot spots to confirm the stable binding of the two promising molecules (ZINC16951574-LMQC2, and ZINC08342556-LMQC5). The metabolism prediction, with metabolites M3-2, which is formed by Glutathionation reaction (Phase II), M1-2, and M2-2 formed from the reaction of S-oxidation and Aliphatic hydroxylation (Phase I), were both reactive but with no side effects. Theoretical synthetic routes and prediction of synthetic accessibility for the most promising compounds are also proposed. In conclusion, this study shows that in silico modeling can be used to create new drug candidate inhibitors for hAChE. The compounds ZINC16951574-LMQC2, and ZINC08342556-LMQC5 are particularly promising for oral administration because they have a favorable drug-likeness profile, excellent lipid solubility, high bioavailability, and adequate pharmacokinetics.
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