Discovering New Tyrosinase Inhibitors by Using In Silico Modelling, Molecular Docking, and Molecular Dynamics

被引:2
作者
Oremaldonado, Kevin A. [1 ]
Cuesta, Sebastian A. [2 ,3 ]
Mora, Jose R. [2 ]
Lorono, Marcos A. [1 ]
Paz, Jose L. [4 ]
机构
[1] Univ Nacl Mayor San Marcos, Fac Quim & Ingn Quim, Dept Acad Quim Fisicoquim, Lima 15081, Peru
[2] Univ San Francisco Quito, Dept Ingn Quim, Grp Quim Computac & Teor QCT USFQ, Diego Robles & Via Interocean, Quito 170901, Ecuador
[3] Univ Manchester, Manchester Inst Biotechnol, Dept Chem, Manchester M1 7DN, England
[4] Univ Nacl Mayor San Marcos, Fac Quim & Ingn Quim, Dept Acad Quim Inorgan, Lima 15081, Peru
关键词
tyrosinase; melanoma; QSAR; molecular docking; molecular dynamics; MUSHROOM TYROSINASE; HIGHLY POTENT; MELANIN; PREDICTION; DESIGN; MELANOGENESIS; BRINZOLAMIDE; COMPUTATION; DERIVATIVES; ABSORPTION;
D O I
10.3390/ph18030418
中图分类号
R914 [药物化学];
学科分类号
100701 ;
摘要
Background/Objectives: This study was used in silico modelling to search for potential tyrosinase protein inhibitors from a database of different core structures for IC50 prediction. Methods: Four machine learning algorithms and topographical descriptors were tested for model construction. Results: A model based on multiple linear regression was the most robust, with only six descriptors, and validated by the Tropsha test with statistical parameters R2 = 0.8687, Q2LOO = 0.8030, and Q2ext = 0.9151. From the screening of FDA-approved drugs and natural products, the pIC50 values for 15,424 structures were calculated. The applicability domain analysis covered 100% of the external dataset and 71.22% and 73.26% of the two screening datasets. Fifteen candidates with pIC50 above 7.6 were identified, with five structures proposed as potential tyrosinase enzyme inhibitors, which underwent ADME analysis. Conclusions: The molecular docking analysis was performed for the dataset used in the training-test process and for the fifteen structures from the screening dataset with potential pharmaceutical tyrosinase inhibition, followed by molecular dynamics studies for the top five candidates with the highest predicted pIC50 values. The new use of these five candidates in tyrosinase inhibition is highlighted based on their promising application in melanoma treatment.
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页数:20
相关论文
共 84 条
[1]   Gromacs: High performance molecular simulations through multi-level parallelism from laptops to supercomputers [J].
Abraham, Mark James ;
Murtola, Teemu ;
Schulz, Roland ;
Páll, Szilárd ;
Smith, Jeremy C. ;
Hess, Berk ;
Lindah, Erik .
SoftwareX, 2015, 1-2 :19-25
[2]   A combined experimental and computational study to discover novel tyrosinase inhibitors [J].
Amaral, Luisa M. P. F. ;
Moniz, Tania ;
Leite, Andreia ;
Oliveira, Ana ;
Fernandes, Pedro ;
Ramos, Maria Joao ;
Araujo, Alberto N. ;
Freitas, Marisa ;
Fernandes, Eduarda ;
Rangel, Maria .
JOURNAL OF INORGANIC BIOCHEMISTRY, 2022, 234
[3]  
[Anonymous], 2009, ACM SIGKDD Explorations Newsletter, DOI [10.1145/1656274.1656278, DOI 10.1145/1656274.1656278]
[4]  
[Anonymous], ANALYTICON DISCOVERY
[5]   Flavones as tyrosinase inhibitors: kinetic studies in vitro and in silico [J].
Arroo, Randolph R. J. ;
Sari, Suat ;
Barut, Burak ;
Ozel, Arzu ;
Ruparelia, Ketan C. ;
Sohretoglu, Didem .
PHYTOCHEMICAL ANALYSIS, 2020, 31 (03) :314-321
[6]   Lexicon of lipid nutrition [J].
Beare-Rogers, J ;
Dieffenbacher, A ;
Holm, JV .
PURE AND APPLIED CHEMISTRY, 2001, 73 (04) :685-744
[7]   MOLECULAR-DYNAMICS WITH COUPLING TO AN EXTERNAL BATH [J].
BERENDSEN, HJC ;
POSTMA, JPM ;
VANGUNSTEREN, WF ;
DINOLA, A ;
HAAK, JR .
JOURNAL OF CHEMICAL PHYSICS, 1984, 81 (08) :3684-3690
[8]   The Protein Data Bank [J].
Berman, HM ;
Westbrook, J ;
Feng, Z ;
Gilliland, G ;
Bhat, TN ;
Weissig, H ;
Shindyalov, IN ;
Bourne, PE .
NUCLEIC ACIDS RESEARCH, 2000, 28 (01) :235-242
[9]   The protective role of melanin against UV damage in human skin [J].
Brenner, Michaela ;
Hearing, Vincent J. .
PHOTOCHEMISTRY AND PHOTOBIOLOGY, 2008, 84 (03) :539-549
[10]   In Silico Searching for Alternative Lead Compounds to Treat Type 2 Diabetes through a QSAR and Molecular Dynamics Study [J].
Cabrera, Nicolas ;
Cuesta, Sebastian A. ;
Mora, Jose R. ;
Calle, Luis ;
Marquez, Edgar A. ;
Kaunas, Roland ;
Paz, Jose Luis .
PHARMACEUTICS, 2022, 14 (02)