Targeting 3CLpro and SARS-CoV-2 RdRp by Amphimedon sp. Metabolites: A Computational Study

被引：6
|
作者：
Shady, Nourhan Hisham [1 ]
Hayallah, Alaa M. [2 ,3 ]
Mohamed, Mamdouh F. A. [4 ]
Ghoneim, Mohammed M. [5 ,6 ]
Chilingaryan, Garri [7 ,8 ]
Al-Sanea, Mohammad M. [9 ]
Fouad, Mostafa A. [10 ]
Kamel, Mohamed Salah [1 ,10 ]
Abdelmohsen, Usama Ramadan [1 ,10 ]
机构：
[1] Deraya Univ, Fac Pharm, Dept Pharmacognosy, New Minia City 61111, Egypt
[2] Assiut Univ, Fac Pharm, Dept Pharmaceut Organ Chem, Assiut 71526, Egypt
[3] Sphinx Univ, Fac Pharm, Pharmaceut Chem Dept, New Assiut 71515, Egypt
[4] Sohag Univ, Fac Pharm, Dept Pharmaceut Chem, Sohag 82524, Egypt
[5] AlMaarefa Univ, Coll Pharm, Dept Pharm Practice, Ad Diriyah 13713, Saudi Arabia
[6] Al Azhar Univ, Fac Pharm, Dept Pharmacognosy, Cairo 11371, Egypt
[7] NAS RA, Inst Mol Biol, Yerevan 0014, Armenia
[8] Russian Armenian Univ, Inst Biomed & Pharm, Yerevan 0051, Armenia
[9] Jouf Univ, Coll Pharm, Dept Pharmaceut Chem, Aljouf 72341, Saudi Arabia
[10] Minia Univ, Fac Pharm, Dept Pharmacognosy, Al Minya 61519, Egypt
来源：
MOLECULES | 2021年 / 26卷 / 12期
关键词：
COVID-19; coronavirus; molecular docking; Amphimedon sp; sponge; ANTICANCER ACTIVITY; NATURAL-PRODUCTS; INHIBITORS; DESIGN; PROTEASE;
D O I：
10.3390/molecules26123775
中图分类号：
Q5 [生物化学]; Q7 [分子生物学];
学科分类号：
071010 ; 081704 ;
摘要：
Since December 2019, novel coronavirus disease 2019 (COVID-19) pandemic has caused tremendous economic loss and serious health problems worldwide. In this study, we investigated 14 natural compounds isolated from Amphimedon sp. via a molecular docking study, to examine their ability to act as anti-COVID-19 agents. Moreover, the pharmacokinetic properties of the most promising compounds were studied. The docking study showed that virtually screened compounds were effective against the new coronavirus via dual inhibition of SARS-CoV-2 RdRp and the 3CL main protease. In particular, nakinadine B (1), 20-hepacosenoic acid (11) and amphimedoside C (12) were the most promising compounds, as they demonstrated good interactions with the pockets of both enzymes. Based on the analysis of the molecular docking results, compounds 1 and 12 were selected for molecular dynamics simulation studies. Our results showed Amphimedon sp. to be a rich source for anti-COVID-19 metabolites.
引用
收藏
页数：15
相关论文
共 50 条
  • [31] A SAR and QSAR study on 3CLpro inhibitors of SARS-CoV-2 using machine learning methods
    Zhang, Y.
    Tian, Y.
    Yan, A.
    SAR AND QSAR IN ENVIRONMENTAL RESEARCH, 2024, 35 (07) : 531 - 563
  • [32] Exploration of chalcones as 3-chymotrypsin-like protease (3CLpro) inhibitors of SARS-CoV-2 using computational approaches
    Thua-Phong Lam
    Dac-Nhan Nguyen
    Tan Thanh Mai
    Thanh-Dao Tran
    Minh-Tri Le
    Phuong Nguyen Hoai Huynh
    Duc-Tuan Nguyen
    Viet-Hung Tran
    Dieu-Thuong Thi Trinh
    Phuong Truong
    Cam-Van T Vo
    Khac-Minh Thai
    STRUCTURAL CHEMISTRY, 2022, 33 (05) : 1707 - 1725
  • [33] Exploration of chalcones as 3-chymotrypsin-like protease (3CLpro) inhibitors of SARS-CoV-2 using computational approaches
    Thua-Phong Lam
    Dac-Nhan Nguyen
    Tan Thanh Mai
    Thanh-Dao Tran
    Minh-Tri Le
    Phuong Nguyen Hoai Huynh
    Duc-Tuan Nguyen
    Viet-Hung Tran
    Dieu-Thuong Thi Trinh
    Phuong Truong
    Cam-Van T. Vo
    Khac-Minh Thai
    Structural Chemistry, 2022, 33 : 1707 - 1725
  • [34] Comparative protein structure network analysis on 3CLpro from SARS-CoV-1 and SARS-CoV-2
    Lata, Surabhi
    Akif, Mohd.
    PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2021, 89 (09) : 1216 - 1225
  • [35] Structural stability of SARS-CoV-2 3CLpro and identification of quercetin as an inhibitor by experimental screening
    Abian, Olga
    Ortega-Alarcon, David
    Jimenez-Alesanco, Ana
    Ceballos-Laita, Laura
    Vega, Sonia
    Reyburn, Hugh T.
    Rizzuti, Bruno
    Velazquez-Campoy, Adrian
    INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES, 2020, 164 : 1693 - 1703
  • [36] Sensitive detection of SARS-CoV-2 main protease 3CLpro with an engineered ribonuclease zymogen
    Wralstad, Evans C.
    Raines, Ronald T.
    PROTEIN SCIENCE, 2024, 33 (04)
  • [37] Discovery of chebulagic acid and punicalagin as novel allosteric inhibitors of SARS-CoV-2 3CLpro
    Du, Ruikun
    Cooper, Laura
    Chen, Zinuo
    Lee, Hyun
    Rong, Lijun
    Cui, Qinghua
    ANTIVIRAL RESEARCH, 2021, 190
  • [38] The main protease 3CLpro of the SARS-CoV-2 virus: how to turn an enemy into a helper
    Belenkaya, Svetlana V.
    Merkuleva, Iuliia A.
    Yarovaya, Olga I.
    Chirkova, Varvara Yu.
    Sharlaeva, Elena A.
    Shanshin, Daniil V.
    Volosnikova, Ekaterina A.
    Vatsadze, Sergey Z.
    Khvostov, Mikhail V.
    Salakhutdinov, Nariman F.
    Shcherbakov, Dmitriy N.
    FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY, 2023, 11
  • [39] The Repurposed Drugs Suramin and Quinacrine Cooperatively Inhibit SARS-CoV-2 3CLpro In Vitro
    Eberle, Raphael J.
    Olivier, Danilo S.
    Amaral, Marcos S.
    Gering, Ian
    Willbold, Dieter
    Arni, Raghuvir K.
    Coronado, Monika A.
    VIRUSES-BASEL, 2021, 13 (05):
  • [40] Inhibition of SARS-CoV-2 3CLpro by chemically modified tyrosinase from Agaricus bisporus
    Aguilera-Rodriguez, David
    Ortega-Alarcon, David
    Vazquez-Calvo, Angela
    Ricci, Veronica
    Abian, Olga
    Velazquez-Campoy, Adrian
    Alcami, Antonio
    Palomo, Jose M.
    RSC MEDICINAL CHEMISTRY, 2024, 15 (12): : 4159 - 4167
12345