Potential natural products that target the SARS-CoV-2 spike protein identified by structure-based virtual screening, isothermal titration calorimetry and lentivirus particles pseudotyped (Vpp) infection assay

Guan-Yu Chen; Yi-Cheng Pan; Tung-Ying Wu; Tsung-You Yao; Wei-Jan Wang; Wan-Jou Shen; Azaj Ahmed; Shu-Ting Chan; Chih-Hsin Tang; Wei-Chien Huang; Mien-Chie Hung; Juan-Cheng Yang; Yang-Chang Wu

doi:10.1016/j.jtcme.2021.09.002

Potential natural products that target the SARS-CoV-2 spike protein identified by structure-based virtual screening, isothermal titration calorimetry and lentivirus particles pseudotyped (Vpp) infection assay

J Tradit Complement Med. 2022 Jan;12(1):73-89. doi: 10.1016/j.jtcme.2021.09.002. Epub 2021 Sep 16.

Authors

Guan-Yu Chen¹, Yi-Cheng Pan^{1

2}, Tung-Ying Wu³, Tsung-You Yao^{1

4}, Wei-Jan Wang⁵, Wan-Jou Shen⁶, Azaj Ahmed¹, Shu-Ting Chan⁷, Chih-Hsin Tang^{8

9

10}, Wei-Chien Huang^{1

9

10}, Mien-Chie Hung^{1

5

6

10}, Juan-Cheng Yang¹, Yang-Chang Wu^{1

10

11}

Affiliations

¹ Chinese Medicine Research and Development Center, Sex Hormone Research Center, Department of Obstetrics and Gynecology, Center for Molecular Medicine, China Medical University Hospital, Taichung, Taiwan.
² Program for Cancer Biology and Drug Discovery, China Medical University and Academia Sinica, Taichung, Taiwan.
³ Department of Biological Science & Technology, Department of Food Science and Nutrition, Meiho University, Pingtung, Taiwan.
⁴ School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung, Taiwan.
⁵ Department of Biological Science and Technology, Research Center for Cancer Biology, New Drug Development Center, China Medical University, Taichung, Taiwan.
⁶ Graduate Institute of Biomedical Sciences, College of Medicine, China Medical University, Taichung, Taiwan.
⁷ TCI Academy, TCI CO., Ltd., Taipei, Taiwan.
⁸ Department of Pharmacology, School of Medicine, China Medical University, Taichung, Taiwan.
⁹ Chinese Medicine Research Center, Drug Development Center, Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan.
¹⁰ Department of Medical Laboratory Science and Biotechnology, College of Medical and Health Science, Asia University, Taichung, Taiwan.
¹¹ Graduate Institute of Integrated Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan.

Abstract

Background and aim: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) enters cells through the binding of the viral spike protein with human angiotensin-converting enzyme 2 (ACE2), resulting in the development of coronavirus disease 2019 (COVID-19). To date, few antiviral drugs are available that can effectively block viral infection. This study aimed to identify potential natural products from Taiwan Database of Extracts and Compounds (TDEC) that may prevent the binding of viral spike proteins with human ACE2 proteins.

Methods: The structure-based virtual screening was performed using the AutoDock Vina program within PyRX software, the binding affinities of compounds were verified using isothermal titration calorimetry (ITC), the inhibitions of SARS-CoV-2 viral infection efficacy were examined by lentivirus particles pseudotyped (Vpp) infection assay, and the cell viability was tested by 293T cell in MTT assay.

Results and conclusion: We identified 39 natural products targeting the viral receptor-binding domain (RBD) of the SARS-CoV-2 spike protein in silico. In ITC binding assay, dioscin, celastrol, saikosaponin C, epimedin C, torvoside K, and amentoflavone showed dissociation constant (K _d) = 0.468 μM, 1.712 μM, 6.650 μM, 2.86 μM, 3.761 μM and 4.27 μM, respectively. In Vpp infection assay, the compounds have significantly and consistently inhibition with the 50-90% inhibition of viral infection efficacy. In cell viability, torvoside K, epimedin, amentoflavone, and saikosaponin C showed IC₅₀ > 100 μM; dioscin and celastrol showed IC₅₀ = 1.5625 μM and 0.9866 μM, respectively. These natural products may bind to the viral spike protein, preventing SARS-CoV-2 from entering cells.

Section 1: Natural Products.

Taxonomy classification by evise: SARS-CoV-2, Structure-Based Virtual Screening, Isothermal Titration Calorimetry and Lentivirus Particles Pseudotyped (Vpp) Infection Assay, in silico and in vitro study.

Keywords: Isothermal titration calorimetry; Lentivirus particles pseudotyped (Vpp) infection assay; SARS-CoV-2; Spike protein; Virtual screening.