Potential inhibitors for SARS-CoV-2 Mpro from marine compounds

被引:9
作者
Tam, Nguyen Minh [1 ,2 ]
Pham, Minh Quan [3 ,4 ]
Nguyen, Huy Truong [5 ]
Hong, Nam Dao [6 ]
Hien, Nguyen Khoa [3 ,7 ]
Quang, Duong Tuan [8 ]
Thu Phung, Huong Thi [9 ]
Ngo, Son Tung [2 ,10 ]
机构
[1] Ton Duc Thang Univ, Computat Chem Res Grp, Ho Chi Minh City, Vietnam
[2] Ton Duc Thang Univ, Fac Appl Sci, Ho Chi Minh City, Vietnam
[3] Vietnam Acad Sci & Technol, Grad Univ Sci & Technol, Hanoi, Vietnam
[4] Vietnam Acad Sci & Technol, Inst Nat Prod Chem, Hanoi, Vietnam
[5] Ton Duc Thang Univ, Fac Pharm, Ho Chi Minh City, Vietnam
[6] Univ Med & Pharm Ho Chi Minh City, Ho Chi Minh City, Vietnam
[7] Vietnam Acad Sci & Technol, Mientrung Inst Sci Res, Hue City, Thua Thien Hue, Vietnam
[8] Hue Univ, Dept Chem, Hue City, Thua Thien Hue, Vietnam
[9] Nguyen Tat Thanh Univ, NTT Hitech Inst, Ho Chi Minh City, Vietnam
[10] Ton Duc Thang Univ, Lab Theoret & Computat Biophys, Ho Chi Minh City, Vietnam
关键词
RESPIRATORY SYNDROME CORONAVIRUS; FREE-ENERGY; MAIN PROTEASE; IN-SILICO; NATURAL-PRODUCTS; BINDING; DRUGS; DYNAMICS; COVID-19; DOCKING;
D O I
10.1039/d1ra03852d
中图分类号
O6 [化学];
学科分类号
0703 ;
摘要
Preventing the biological activity of SARS-CoV-2 main protease using natural compounds is of great interest. In this context, using a combination of AutoDock Vina and fast pulling of ligand simulations, eleven marine fungi compounds were identified that probably play as highly potent inhibitors for preventing viral replication. In particular, four compounds including M15 (3-O-(6-O-alpha-l-arabinopyranosyl)-beta-d-glucopyranosyl-1,4-dimethoxyxanthone), M8 (wailupemycins H), M11 (cottoquinazolines B), and M9 (wailupemycins I) adopted the predicted ligand-binding free energy of -9.87, -9.82, -9.62, and -9.35 kcal mol(-1), respectively, whereas the other adopted predicted ligand-binding free energies in the range from -8.54 to -8.94 kcal mol(-1). The results were obtained using a combination of Vina and FPL simulations. Notably, although, AutoDock4 adopted higher accurate results in comparison with Vina, Vina is proven to be a more suitable technique for rapidly screening ligand-binding affinity with a large database of compounds since it requires much smaller computing resources. Furthermore, FPL is better than Vina to classify inhibitors upon ROC-AUC analysis.
引用
收藏
页码:22206 / 22213
页数:8
相关论文
共 66 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]   Quinolines-Based SARS-CoV-2 3CLpro and RdRp Inhibitors and Spike-RBD-ACE2 Inhibitor for Drug-Repurposing Against COVID-19: Anin silicoAnalysis [J].
Alexpandi, Rajaiah ;
De Mesquita, Joelma Freire ;
Pandian, Shunmugiah Karutha ;
Ravi, Arumugam Veera .
FRONTIERS IN MICROBIOLOGY, 2020, 11
[3]   Motional timescale predictions by molecular dynamics simulations: Case study using proline and hydroxyproline sidechain dynamics [J].
Aliev, Abil E. ;
Kulke, Martin ;
Khaneja, Harmeet S. ;
Chudasama, Vijay ;
Sheppard, Tom D. ;
Lanigan, Rachel M. .
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2014, 82 (02) :195-215
[4]  
[Anonymous], 2021, CHEMICALIZE WAS USED
[5]  
[Anonymous], 2016, ADV VIRUS RES, V96, P59
[6]  
[Anonymous], COVID 19 COR PAND
[7]   The immune control and cell-to-cell spread of human T-lymphotropic virus type 1 [J].
Bangham, CRM .
JOURNAL OF GENERAL VIROLOGY, 2003, 84 :3177-3189
[8]   Natural product and natural product derived drugs in clinical trials [J].
Butler, Mark S. ;
Robertson, Avril A. B. ;
Cooper, Matthew A. .
NATURAL PRODUCT REPORTS, 2014, 31 (11) :1612-1661
[9]   Molecular design of anticancer drugs from marine fungi derivatives [J].
Cao, Duc Tuan ;
Huong Doan, Thi Mai ;
Pham, Van Cuong ;
Minh Le, Thi Hong ;
Chae, Jung-Woo ;
Yun, Hwi-yeol ;
Na, Min-Kyun ;
Kim, Young-Ho ;
Pham, Minh Quan ;
Nguyen, Van Hung .
RSC ADVANCES, 2021, 11 (33) :20173-20179
[10]  
Case D. A., 2018, AMBER