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Lv BM, Tong XY, Quan Y, Liu MY, Zhang QY, Song YF, Zhang HY. Drug Repurposing for Japanese Encephalitis Virus Infection by Systems Biology Methods. Molecules 2018; 23:molecules23123346. [PMID: 30567313 PMCID: PMC6320907 DOI: 10.3390/molecules23123346] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 12/14/2018] [Accepted: 12/14/2018] [Indexed: 12/22/2022] Open
Abstract
Japanese encephalitis is a zoonotic disease caused by the Japanese encephalitis virus (JEV). It is mainly epidemic in Asia with an estimated 69,000 cases occurring per year. However, no approved agents are available for the treatment of JEV infection, and existing vaccines cannot control various types of JEV strains. Drug repurposing is a new concept for finding new indication of existing drugs, and, recently, the concept has been used to discover new antiviral agents. Identifying host proteins involved in the progress of JEV infection and using these proteins as targets are the center of drug repurposing for JEV infection. In this study, based on the gene expression data of JEV infection and the phenome-wide association study (PheWAS) data, we identified 286 genes that participate in the progress of JEV infection using systems biology methods. The enrichment analysis of these genes suggested that the genes identified by our methods were predominantly related to viral infection pathways and immune response-related pathways. We found that bortezomib, which can target these genes, may have an effect on the treatment of JEV infection. Subsequently, we evaluated the antiviral activity of bortezomib using a JEV-infected mouse model. The results showed that bortezomib can lower JEV-induced lethality in mice, alleviate suffering in JEV-infected mice and reduce the damage in brains caused by JEV infection. This work provides an agent with new indication to treat JEV infection.
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Affiliation(s)
- Bo-Min Lv
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.
| | - Xin-Yu Tong
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.
| | - Yuan Quan
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.
| | - Meng-Yuan Liu
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.
| | - Qing-Ye Zhang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.
| | - Yun-Feng Song
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Hong-Yu Zhang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.
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Cruz JN, Costa JFS, Khayat AS, Kuca K, Barros CAL, Neto AMJC. Molecular dynamics simulation and binding free energy studies of novel leads belonging to the benzofuran class inhibitors of Mycobacterium tuberculosis Polyketide Synthase 13. J Biomol Struct Dyn 2018; 37:1616-1627. [PMID: 29633908 DOI: 10.1080/07391102.2018.1462734] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
In this work, the binding mechanism of new Polyketide Synthase 13 (Pks13) inhibitors has been studied through molecular dynamics simulation and free energy calculations. The drug Tam1 and its analogs, belonging to the benzofuran class, were submitted to 100 ns simulations, and according to the results obtained for root mean square deviation, all the simulations converged from approximately 30 ns. For the analysis of backbone flotation, the root mean square fluctuations were plotted for the Cα atoms; analysis revealed that the greatest fluctuation occurred in the residues that are part of the protein lid domain. The binding free energy value (ΔGbind) obtained for the Tam16 lead molecule was of -51.43 kcal/mol. When comparing this result with the ΔGbind values for the remaining analogs, the drug Tam16 was found to be the highest ranked: this result is in agreement with the experimental results obtained by Aggarwal and collaborators, where it was verified that the IC50 for Tam16 is the smallest necessary to inhibit the Pks13 (IC50 = 0.19 μM). The energy decomposition analysis suggested that the residues which most interact with inhibitors are: Ser1636, Tyr1637, Asn1640, Ala1667, Phe1670, and Tyr1674, from which the greatest energy contribution to Phe1670 was particularly notable. For the lead molecule Tam16, a hydrogen bond with the hydroxyl of the phenol not observed in the other analogs induced a more stable molecular structure. Aggarwal and colleagues reported this hydrogen bonding as being responsible for the stability of the molecule, optimizing its physic-chemical, toxicological, and pharmacokinetic properties.
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Key Words
- CNPq, National Council for Scientific and Technological Development
- CoA, coenzyme A
- FAS, fatty acid synthase
- GAFF, general amber force field
- GB, generalized born
- HB, hydrogen bonds
- INH, isoniazid
- KatG, catalase-peroxidase
- MD, molecular dynamics
- MDR, multi-drug resistant
- MM/GBSA, molecular mechanics/generalized-born surface area
- NAD, nicotinamide adenine dinucleotide
- NS, nanoseconds
- PCA, acyl carrier protein
- Pks13
- Pks13, polyketide synthase 13
- RESP, restrained electrostatic potential
- RMSD, root mean square deviation
- RMSF, root mean square fluctuations
- TB, tuberculosis
- TE, C-terminal thioesterase
- XDR, extensively drug resistant
- benzofuran
- free energy
- inhibitors
- molecular dynamics
- Δ internal energy
- Δ, Van Der Waals contributions
- Δ, electrostatic contribution
- Δ, electrostatic contributions
- Δ, energy of desolvation
- Δ, energy of the molecular mechanics
- Δ, non-polar contributions
- Δ, polar contributions
- Δ, polar solvation contribution
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Affiliation(s)
- Jorddy N Cruz
- a Laboratory of Preparation and Computation of Nanomaterials , Federal University of Pará , CP 479, 66075-110 Belém , PA , Brazil
| | - José F S Costa
- a Laboratory of Preparation and Computation of Nanomaterials , Federal University of Pará , CP 479, 66075-110 Belém , PA , Brazil
| | - André S Khayat
- b Oncology Research Center , Federal University of Pará , CP 479, 6675-105 Belém , PA , Brazil
| | - Kamil Kuca
- c Biomedical Research Center , University Hospital Hradec Kralove , Sokolska 581, 500 05 Hradec Kralove , Czech Republic
| | - Carlos A L Barros
- d Department of Pharmacy , Federal University of Pará , CP 479, 66050-160 Belém , PA , Brazil
| | - A M J C Neto
- a Laboratory of Preparation and Computation of Nanomaterials , Federal University of Pará , CP 479, 66075-110 Belém , PA , Brazil
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Quan Y, Liu MY, Liu YM, Zhu LD, Wu YS, Luo ZH, Zhang XZ, Xu SZ, Yang QY, Zhang HY. Facilitating Anti-Cancer Combinatorial Drug Discovery by Targeting Epistatic Disease Genes. Molecules 2018; 23:E736. [PMID: 29570606 PMCID: PMC6017788 DOI: 10.3390/molecules23040736] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 03/15/2018] [Accepted: 03/20/2018] [Indexed: 12/19/2022] Open
Abstract
Due to synergistic effects, combinatorial drugs are widely used for treating complex diseases. However, combining drugs and making them synergetic remains a challenge. Genetic disease genes are considered a promising source of drug targets with important implications for navigating the drug space. Most diseases are not caused by a single pathogenic factor, but by multiple disease genes, in particular, interacting disease genes. Thus, it is reasonable to consider that targeting epistatic disease genes may enhance the therapeutic effects of combinatorial drugs. In this study, synthetic lethality gene pairs of tumors, similar to epistatic disease genes, were first targeted by combinatorial drugs, resulting in the enrichment of the combinatorial drugs with cancer treatment, which verified our hypothesis. Then, conventional epistasis detection software was used to identify epistatic disease genes from the genome wide association studies (GWAS) dataset. Furthermore, combinatorial drugs were predicted by targeting these epistatic disease genes, and five combinations were proven to have synergistic anti-cancer effects on MCF-7 cells through cell cytotoxicity assay. Combined with the three-dimensional (3D) genome-based method, the epistatic disease genes were filtered and were more closely related to disease. By targeting the filtered gene pairs, the efficiency of combinatorial drug discovery has been further improved.
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Affiliation(s)
- Yuan Quan
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.
| | - Meng-Yuan Liu
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.
| | - Ye-Mao Liu
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.
| | - Li-Da Zhu
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.
| | - Yu-Shan Wu
- School of Life Sciences, Shandong University of Technology; No. 12 Zhangzhou Road, Zibo 255049, China.
| | - Zhi-Hui Luo
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.
| | - Xiu-Zhen Zhang
- School of Life Sciences, Shandong University of Technology; No. 12 Zhangzhou Road, Zibo 255049, China.
| | - Shi-Zhong Xu
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA.
| | - Qing-Yong Yang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.
| | - Hong-Yu Zhang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.
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