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Luthfiana D, Utomo DH. Network pharmacology reveals the potential of Dolastatin 16 as a diabetic wound healing agent. In Silico Pharmacol 2023; 11:23. [PMID: 37719716 PMCID: PMC10504231 DOI: 10.1007/s40203-023-00161-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 08/26/2023] [Indexed: 09/19/2023] Open
Abstract
Dolastatin 16, a marine cyclic depsipeptide, was initially isolated from the sea hare Dolabella Auricularia by Pettit et al. Due to the lack of information regarding its bioactivity, target identification becomes an indispensable strategy for revealing the potential targets and mechanisms of action of Dolastatin 16. Network pharmacology was utilized to identify targets associated with the disease, gene ontology, and KEGG pathways. The results highlighted Matrix Metalloproteinase-9 (MMP9) as a potential target of Dolastatin 16 through network pharmacology analysis. This target was found to be primarily involved in the TNF signaling pathway and in foot ulceration-associated diabetic polyneuropathy. Furthermore, the binding mode and dynamic behavior of the complex were investigated through molecular docking and molecular dynamics studies. In the docking study, a native ligand (a hydroxamate inhibitor) and (R)-ND-336 were employed as ligand controls, demonstrating binding energy values of - 6.6 and - 8.9 kcal/mol, respectively. The Dolastatin 16 complex exhibited a strong affinity for MMP9, with a binding energy value of - 9.7 kcal/mol, indicating its high potential as an inhibitor. Molecular dynamics also confirmed the stability of the MMP9-Dolastatin complex throughout the simulation process. Dolastatin 16 has the potential to act as an MMP9 inhibitor, offering promise for accelerating the wound healing process in diabetic foot conditions. Supplementary Information The online version contains supplementary material available at 10.1007/s40203-023-00161-5.
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Affiliation(s)
- Dewi Luthfiana
- Bioinformatics Research Center, Indonesian Institute of Bioinformatics (INBIO), Malang, Indonesia
| | - Didik Huswo Utomo
- Bioinformatics Research Center, Indonesian Institute of Bioinformatics (INBIO), Malang, Indonesia
- Department of Biology, Faculty of Mathematics and Natural Sciences, Brawijaya University, Malang, East Java Indonesia
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Huang Y, Li WD, Wei YX, Wang L, Dong WK. Structural, theoretical and optical investigations of two lateral twisting trinuclear Co(II) and Ni(II) salamo type complexes. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2022.134194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Syntheses, crystal structure, luminescent properties and Hirshfeld surface of a set of triazole-based salts. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.134980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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Celik I, Çevik UA, Karayel A, Işık A, Kayış U, Gül Ü, Bostancı HE, Konca SF, Özkay Y, Kaplancıklı ZA. Synthesis, Molecular Docking, Dynamics, Quantum-Chemical Computation, and Antimicrobial Activity Studies of Some New Benzimidazole-Thiadiazole Hybrids. ACS OMEGA 2022; 7:47015-47030. [PMID: 36570216 PMCID: PMC9773947 DOI: 10.1021/acsomega.2c06142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
In this study, some new compounds, which are 2-aminothiadiazole derivatives linked by a phenyl bridge to the 2-position of the benzimidazole ring, were designed and synthesized as antimicrobial agents. The structures of the compounds were elucidated by 1H and 13C NMR spectroscopy, high-resolution mass spectrometry, and elemental analysis. The antifungal activities of the synthesized compounds were tested on Candida albicans, Candida krusei, Candida glabrata, and Candida parapsilosis. Compound 5f is more active against C. albicans and C. glabrata than standard fluconazole and varicanazole. Compounds were also evaluated for their counteracting activity against Gram-positive Escherichia coli, Serratia marcescens, Klebsiella pneumoniae, and Pseudomonas aeruginosa and Gram-negative Enterococcus faecalis, Bacillus subtilis, and Staphylococcus aureus. Compounds 5c and 5h had minimum inhibitory concentrations against E. faecalis close to that of the standard azithromycin. Molecular docking studies were performed against Candida species' 14-α demethylase enzyme. 5f was the most active compound against Candida species, which gave the highest docking interaction energy. The stabilities of compounds 5c and 5f with CYP51 were tested using 100 ns molecular dynamics simulations. According to the theoretical ADME calculations, the profiles of the compounds are suitable in terms of limiting rules. HOMO-LUMO analysis showed that 5h is chemically more reactive (represented with the lower ΔE = 3.432 eV) than the other molecules, which is compatible with the highest antibacterial activity result.
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Affiliation(s)
- Ismail Celik
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy, Erciyes University, 38039 Kayseri, Turkey
| | - Ulviye Acar Çevik
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy, Anadolu University, 26470 Eskişehir, Turkey
| | - Arzu Karayel
- Department
of Physics, Faculty of Arts and Science, Hitit University, 19030 Çorum, Turkey
| | - Ayşen Işık
- Department
of Biochemistry, Faculty of Science, Selçuk
University, 42250 Konya, Turkey
| | - Uğur Kayış
- Pazaryeri
Vocational School, Program of Pharmacy Services, Bilecik Şeyh Edebali University, 11230 Bilecik, Turkey
| | - Ülküye
Dudu Gül
- Department
of Bioengineering, Faculty of Engineering, Bilecik Şeyh Edebali University, 11230 Bilecik, Turkey
| | - Hayrani Eren Bostancı
- Department
of Pharmaceutical Basic Sciences, Faculty of Pharmacy, Cumhuriyet University, 58140 Sivas, Turkey
| | - Süheyl Furkan Konca
- Department
of Pharmaceutical Biotechnology, Faculty of Pharmacy, Erciyes University, 38039 Kayseri, Turkey
| | - Yusuf Özkay
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy, Anadolu University, 26470 Eskişehir, Turkey
| | - Zafer Asım Kaplancıklı
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy, Anadolu University, 26470 Eskişehir, Turkey
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One-pot reproducible Sonosynthesis of trans-[Br(NՈN’)Cu(μBr)2Cu(NՈN’)Br] dimer:[H….Br S(9)] synthons, spectral, DFT/XRD/HSA, thermal, docking and novel LOX/COX enzyme inhibition. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.134626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Huang Y, Li X, Li WD, Dong WK. Experimental and theoretical investigation of a new non-symmetric salamo-like ligand and its tri-nuclear Zn(II) and Ni(II) complexes. Inorganica Chim Acta 2022. [DOI: 10.1016/j.ica.2022.121303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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