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Singh S, Prajapati VK. Exploring actinomycetes natural products to identify potential multi-target inhibitors against Leishmania donovani. 3 Biotech 2022; 12:235. [PMID: 35999912 PMCID: PMC9392678 DOI: 10.1007/s13205-022-03304-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 08/09/2022] [Indexed: 12/16/2022] Open
Abstract
Visceral leishmaniasis (VL) is a neglected tropical disease that mainly affects the poor population of the Indian, African, and South American subcontinent. The increasing resistance to antimonial and miltefosine and frequent toxicity of amphotericin B drives an urgent need to develop an anti-leishmanial drug with excellent efficacy and safety profile. In this study, three sequential docking protocols (HTVS, SP, and XP) were performed to screen the secondary metabolites (n = 6519) from the actinomycetes source against five key proteins involved in the metabolic pathway of Leishmania donovani. Those proteins were adenine phosphoribosyltransferase (PDB ID: 1QB7), trypanothione reductase (PDB ID: 2JK6), N-myristoyl transferase (PDB ID: 2WUU), pteridine reductase (PDB ID: 2XOX), and MAP kinase (PDB ID: 4QNY). Although the binding energy of top ligands was predicted using the MM-GBSA module of the Schrödinger suite. SP and XP docking mode resulted in 55 multi-targeted ligands against L donovani. MM-GBSA analysis selected the top 18 ligands with good-binding affinity and the binding-free energy for four proteins, as mentioned earlier, when compared with the miltefosine, paromomycin, and a reference ligand selected for each target. Finally, molecular dynamics simulation, post-MD-binding-free energy (MM-PBSA), and principal component analysis (PCA) proposed three best ligands (Adenosine pentaphosphate, Atetra P, and GDP-4-keto-6-deoxymannose) qualifying the above screening parameters and confirmed as a potential drug candidate to fight against Leishmania donovani parasites.
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Affiliation(s)
- Satyendra Singh
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, NH-8, Bandarsindri, Kishangarh, Ajmer, Rajasthan 305817 India
| | - Vijay Kumar Prajapati
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, NH-8, Bandarsindri, Kishangarh, Ajmer, Rajasthan 305817 India
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Kashapova NE, Kashapov RR, Ziganshina AY, Amerhanova SK, Lyubina AP, Voloshina AD, Salnikov VV, Zakharova LY. Self-assembling nanoparticles based on acetate derivatives of calix[4]resorcinol and octenidine dihydrochloride for tuning selectivity in cancer cells. Colloids Surf A Physicochem Eng Asp 2022. [DOI: 10.1016/j.colsurfa.2022.130087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Bui ATN, Son H, Park S, Oh S, Kim JS, Cho JH, Hwang HJ, Kim JH, Yi GS, Chi SW. Artificial intelligence-based identification of octenidine as a Bcl-xL inhibitor. Biochem Biophys Res Commun 2021; 588:97-103. [PMID: 34953212 DOI: 10.1016/j.bbrc.2021.12.061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 12/16/2021] [Indexed: 11/18/2022]
Abstract
Apoptosis plays an essential role in maintaining cellular homeostasis and preventing cancer progression. Bcl-xL, an anti-apoptotic protein, is an important modulator of the mitochondrial apoptosis pathway and is a promising target for anticancer therapy. In this study, we identified octenidine as a novel Bcl-xL inhibitor through structural feature-based deep learning and molecular docking from a library of approved drugs. The NMR experiments demonstrated that octenidine binds to the Bcl-2 homology 3 (BH3) domain-binding hydrophobic region that consists of the BH1, BH2, and BH3 domains in Bcl-xL. A structural model of the Bcl-xL/octenidine complex revealed that octenidine binds to Bcl-xL in a similar manner to that of the well-known Bcl-2 family protein antagonist ABT-737. Using the NanoBiT protein-protein interaction system, we confirmed that the interaction between Bcl-xL and Bak-BH3 domains within cells was inhibited by octenidine. Furthermore, octenidine inhibited the proliferation of MCF-7 breast and H1299 lung cancer cells by promoting apoptosis. Taken together, our results shed light on a novel mechanism in which octenidine directly targets anti-apoptotic Bcl-xL to trigger mitochondrial apoptosis in cancer cells.
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Affiliation(s)
- Anh Thi Ngoc Bui
- Disease Target Structure Research Center, KRIBB, Daejeon, 31441, Republic of Korea
| | - Hyojin Son
- Department of Bio and Brain Engineering, KAIST, Daejeon, 34141, Republic of Korea
| | - Seulki Park
- Disease Target Structure Research Center, KRIBB, Daejeon, 31441, Republic of Korea
| | - Sohee Oh
- Disease Target Structure Research Center, KRIBB, Daejeon, 31441, Republic of Korea
| | - Jin-Sik Kim
- Disease Target Structure Research Center, KRIBB, Daejeon, 31441, Republic of Korea
| | - Jin Hwa Cho
- Disease Target Structure Research Center, KRIBB, Daejeon, 31441, Republic of Korea
| | - Hye-Jin Hwang
- Disease Target Structure Research Center, KRIBB, Daejeon, 31441, Republic of Korea; Department of Proteome Structural Biology, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Jeong-Hoon Kim
- Disease Target Structure Research Center, KRIBB, Daejeon, 31441, Republic of Korea; Department of Bioscience, University of Science and Technology, Daejeon, 34113, Republic of Korea; Graduate School of New Drug Discovery and Development, Chungnam National University, Republic of Korea.
| | - Gwan-Su Yi
- Department of Bio and Brain Engineering, KAIST, Daejeon, 34141, Republic of Korea.
| | - Seung-Wook Chi
- Disease Target Structure Research Center, KRIBB, Daejeon, 31441, Republic of Korea; Department of Proteome Structural Biology, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon, 34113, Republic of Korea.
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