Identification of Natural Lead Compounds against Hemagglutinin-Esterase Surface Glycoprotein in Human Coronaviruses Investigated via MD Simulation, Principal Component Analysis, Cross-Correlation, H-Bond Plot and MMGBSA

Ali, Iqra; Rasheed, Muhammad Asif; Cavalu, Simona; Rahim, Kashif; Ijaz, Sana; Yahya, Galal; Goh, Lucky Poh Wah; Popoviciu, Mihaela Simona

doi:10.3390/biomedicines11030793

Open AccessArticle

Identification of Natural Lead Compounds against Hemagglutinin-Esterase Surface Glycoprotein in Human Coronaviruses Investigated via MD Simulation, Principal Component Analysis, Cross-Correlation, H-Bond Plot and MMGBSA

by

Iqra Ali

^1,2,*,†

,

Muhammad Asif Rasheed

^1,†,

Simona Cavalu

³

,

Kashif Rahim

⁴,

Sana Ijaz

¹,

Galal Yahya

⁵

,

Lucky Poh Wah Goh

⁶

and

Mihaela Simona Popoviciu

^3,*

¹

Department of Biosciences, COMSATS (Commission on Science and Technology for Sustainable Development in the South) University Islamabad, Sahiwal Campus, Sahiwal 57000, Pakistan

²

Department of Biosciences, COMSATS (Commission on Science and Technology for Sustainable Development in the South) University Islamabad, Islamabad Campus, Islamabad 45550, Pakistan

³

Faculty of Medicine and Pharmacy, University of Oradea, P-ta 1 Decembrie 10, 410087 Oradea, Romania

⁴

Department of Microbiology, Cholistan University of Veterinary and Animal Sciences (CUVAS), Bahawalpur 63100, Pakistan

⁵

Department of Microbiology and Immunology, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt

⁶

Faculty of Science and Natural Resources, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu 88400, Sabah, Malaysia

^*

Authors to whom correspondence should be addressed.

^†

These authors contributed equally to this work.

Biomedicines 2023, 11(3), 793; https://doi.org/10.3390/biomedicines11030793

Submission received: 31 December 2022 / Revised: 22 February 2023 / Accepted: 2 March 2023 / Published: 6 March 2023

(This article belongs to the Special Issue Drug Discovery for Infectious Diseases)

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Abstract

The pandemic outbreak of human coronavirus is a global health concern that affects people of all ages and genders, but there is currently still no effective, approved and potential drug against human coronavirus, as many other coronavirus vaccines have serious side effects while the development of small antiviral inhibitors has gained tremendous attention. For this research, HE was used as a therapeutic target, as the spike protein displays a high binding affinity for both host ACE2 and viral HE glycoprotein. Molecular docking, pharmacophore modelling and virtual screening of 38,000 natural compounds were employed to find out the best natural inhibitor against human coronaviruses with more efficiency and fewer side effects and further evaluated via MD simulation, PCA, DCCR and MMGBSA. The lead compound ‘Calceolarioside B’ was identified on the basis of pharmacophoric features which depict favorable binding (ΔGbind −37.6799 kcal/mol) with the HE(5N11) receptor that describes positive correlation movements in active site residues with better stability, a robust H-bond network, compactness and reliable ADMET properties. The Fraxinus sieboldiana Blume plant containing the Calceolarioside B compound could be used as a potential inhibitor that shows a higher efficacy and potency with fewer side effects. This research work will aid investigators in the testing and identification of chemicals that are effective and useful against human coronavirus.

Keywords: hemagglutinin esterase; human coronaviruses; lead compounds; molecular docking; pharmacophore model; MD simulation; principal component analysis; dynamic cross correlation; energy decomposition; MMGBSA

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MDPI and ACS Style

Ali, I.; Rasheed, M.A.; Cavalu, S.; Rahim, K.; Ijaz, S.; Yahya, G.; Goh, L.P.W.; Popoviciu, M.S. Identification of Natural Lead Compounds against Hemagglutinin-Esterase Surface Glycoprotein in Human Coronaviruses Investigated via MD Simulation, Principal Component Analysis, Cross-Correlation, H-Bond Plot and MMGBSA. Biomedicines 2023, 11, 793. https://doi.org/10.3390/biomedicines11030793

AMA Style

Ali I, Rasheed MA, Cavalu S, Rahim K, Ijaz S, Yahya G, Goh LPW, Popoviciu MS. Identification of Natural Lead Compounds against Hemagglutinin-Esterase Surface Glycoprotein in Human Coronaviruses Investigated via MD Simulation, Principal Component Analysis, Cross-Correlation, H-Bond Plot and MMGBSA. Biomedicines. 2023; 11(3):793. https://doi.org/10.3390/biomedicines11030793

Chicago/Turabian Style

Ali, Iqra, Muhammad Asif Rasheed, Simona Cavalu, Kashif Rahim, Sana Ijaz, Galal Yahya, Lucky Poh Wah Goh, and Mihaela Simona Popoviciu. 2023. "Identification of Natural Lead Compounds against Hemagglutinin-Esterase Surface Glycoprotein in Human Coronaviruses Investigated via MD Simulation, Principal Component Analysis, Cross-Correlation, H-Bond Plot and MMGBSA" Biomedicines 11, no. 3: 793. https://doi.org/10.3390/biomedicines11030793

APA Style

Ali, I., Rasheed, M. A., Cavalu, S., Rahim, K., Ijaz, S., Yahya, G., Goh, L. P. W., & Popoviciu, M. S. (2023). Identification of Natural Lead Compounds against Hemagglutinin-Esterase Surface Glycoprotein in Human Coronaviruses Investigated via MD Simulation, Principal Component Analysis, Cross-Correlation, H-Bond Plot and MMGBSA. Biomedicines, 11(3), 793. https://doi.org/10.3390/biomedicines11030793

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Identification of Natural Lead Compounds against Hemagglutinin-Esterase Surface Glycoprotein in Human Coronaviruses Investigated via MD Simulation, Principal Component Analysis, Cross-Correlation, H-Bond Plot and MMGBSA

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