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Hassan HHA, Ismail MI, Abourehab MAS, Boeckler FM, Ibrahim TM, Arafa RK. In Silico Targeting of Fascin Protein for Cancer Therapy: Benchmarking, Virtual Screening and Molecular Dynamics Approaches. Molecules 2023; 28:molecules28031296. [PMID: 36770963 PMCID: PMC9921211 DOI: 10.3390/molecules28031296] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/12/2023] [Accepted: 01/15/2023] [Indexed: 01/31/2023] Open
Abstract
Fascin is an actin-bundling protein overexpressed in various invasive metastatic carcinomas through promoting cell migration and invasion. Therefore, blocking Fascin binding sites is considered a vital target for antimetastatic drugs. This inspired us to find new Fascin binding site blockers. First, we built an active compound set by collecting reported small molecules binding to Fascin's binding site 2. Consequently, a high-quality decoys set was generated employing DEKOIS 2.0 protocol to be applied in conducting the benchmarking analysis against the selected Fascin structures. Four docking programs, MOE, AutoDock Vina, VinaXB, and PLANTS were evaluated in the benchmarking study. All tools indicated better-than-random performance reflected by their pROC-AUC values against the Fascin crystal structure (PDB: ID 6I18). Interestingly, PLANTS exhibited the best screening performance and recognized potent actives at early enrichment. Accordingly, PLANTS was utilized in the prospective virtual screening effort for repurposing FDA-approved drugs (DrugBank database) and natural products (NANPDB). Further assessment via molecular dynamics simulations for 100 ns endorsed Remdesivir (DrugBank) and NANPDB3 (NANPDB) as potential binders to Fascin binding site 2. In conclusion, this study delivers a model for implementing a customized DEKOIS 2.0 benchmark set to enhance the VS success rate against new potential targets for cancer therapies.
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Affiliation(s)
- Heba H. A. Hassan
- Drug Design and Discovery Laboratory, Zewail City of Science and Technology, October Gardens, 6th of October City, Giza 12578, Egypt
| | - Muhammad I. Ismail
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, The British University in Egypt, Al-Sherouk City, Cairo-Suez Desert Road, Cairo 11837, Egypt
| | - Mohammed A. S. Abourehab
- Department of Pharmaceutics, College of Pharmacy, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Frank M. Boeckler
- Lab for Molecular Design and Pharmaceutical Biophysics, Department of Pharmacy and Biochemistry, Institute of Pharmaceutical Sciences, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Tamer M. Ibrahim
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh 33516, Egypt
- Correspondence: or (T.M.I.); (R.K.A.)
| | - Reem K. Arafa
- Drug Design and Discovery Laboratory, Zewail City of Science and Technology, October Gardens, 6th of October City, Giza 12578, Egypt
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, October Gardens, 6th of October City, Giza 12578, Egypt
- Correspondence: or (T.M.I.); (R.K.A.)
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Combined Naïve Bayesian, Chemical Fingerprints and Molecular Docking Classifiers to Model and Predict Androgen Receptor Binding Data for Environmentally- and Health-Sensitive Substances. Int J Mol Sci 2021; 22:ijms22136695. [PMID: 34206613 PMCID: PMC8267747 DOI: 10.3390/ijms22136695] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 06/18/2021] [Accepted: 06/20/2021] [Indexed: 12/15/2022] Open
Abstract
Many chemicals that enter the environment, food chain, and the human body can disrupt androgen-dependent pathways and mimic hormones and therefore, may be responsible for multiple diseases from reproductive to tumor. Thus, modeling and predicting androgen receptor activity is an important area of research. The aim of the current study was to find a method or combination of methods to predict compounds that can bind to and/or disrupt the androgen receptor, and thereby guide decision making and further analysis. A stepwise procedure proceeded from analysis of protein structures from human, chimp, and rat, followed by docking and subsequent ligand, and statistics based techniques that improved classification gradually. The best methods used multivariate logistic regression of combinations of chimpanzee protein structural docking scores, extended connectivity fingerprints, and naïve Bayesians of known binders and non-binders. Combination or consensus methods included data from a variety of procedures to improve the final model accuracy.
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Lin L, Lin K, Wu X, Liu J, Cheng Y, Xu LY, Li EM, Dong G. Potential Inhibitors of Fascin From A Database of Marine Natural Products: A Virtual Screening and Molecular Dynamics Study. Front Chem 2021; 9:719949. [PMID: 34692638 PMCID: PMC8529705 DOI: 10.3389/fchem.2021.719949] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 09/17/2021] [Indexed: 02/05/2023] Open
Abstract
Marine nature products are unique compounds that are produced by the marine environment including plants, animals, and microorganisms. The wide diversity of marine natural products have great potential and are versatile in terms of drug discovery. In this paper, we use state-of-the-art computational methods to discover inhibitors from marine natural products to block the function of Fascin, an overexpressed protein in various cancers. First, virtual screening (pharmacophore model and molecular docking) was carried out based on a marine natural products database (12015 molecules) and provided eighteen molecules that could potentially inhibit the function of Fascin. Next, molecular mechanics generalized Born surface area (MM/GBSA) calculations were conducted and indicated that four molecules have higher binding affinities than the inhibitor NP-G2-029, which was validated experimentally. ADMET analyses of pharmacokinetics demonstrated that one of the four molecules does not match the criterion. Finally, ligand Gaussian accelerated molecular dynamics (LiGaMD) simulations were carried out to validate the three inhibitors binding to Fascin stably. In addition, dynamic interactions between protein and ligands were analyzed systematically. Our study will accelerate the development of the cancer drugs targeting Fascin.
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Affiliation(s)
- Lirui Lin
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, China
- Medical Informatics Research Center, Shantou University Medical College, Shantou, China
| | - Kai Lin
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, China
- Medical Informatics Research Center, Shantou University Medical College, Shantou, China
| | - Xiaodong Wu
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, China
| | - Jia Liu
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, China
| | - Yinwei Cheng
- Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, China
- Cancer Research Center, Shantou University Medical College, Shantou, China
| | - Li-Yan Xu
- Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, China
- Cancer Research Center, Shantou University Medical College, Shantou, China
- *Correspondence: Li-Yan Xu, ; En-Min Li, ; Geng Dong,
| | - En-Min Li
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, China
- Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, China
- *Correspondence: Li-Yan Xu, ; En-Min Li, ; Geng Dong,
| | - Geng Dong
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, China
- Medical Informatics Research Center, Shantou University Medical College, Shantou, China
- *Correspondence: Li-Yan Xu, ; En-Min Li, ; Geng Dong,
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