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
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 s...
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| Format: | Article |
| Language: | English English |
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Molecular Diversity Preservation International (MDPI)
2023
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| Online Access: | https://eprints.ums.edu.my/id/eprint/36627/1/ABSTRACT.pdf https://eprints.ums.edu.my/id/eprint/36627/2/FULL%20TEXT.pdf |
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| author | Iqra Ali Muhammad Asif Rasheed Simona Cavalu Kashif Rahim Sana Ijaz Galal Yahya Lucky Poh Wah Goh Mihaela Simona Popoviciu |
| author_facet | Iqra Ali Muhammad Asif Rasheed Simona Cavalu Kashif Rahim Sana Ijaz Galal Yahya Lucky Poh Wah Goh Mihaela Simona Popoviciu |
| author_sort | Iqra Ali |
| collection | UMS |
| description | 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 (∆Gbind −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. |
| first_indexed | 2024-03-06T03:25:08Z |
| format | Article |
| id | ums.eprints-36627 |
| institution | Universiti Malaysia Sabah |
| language | English English |
| last_indexed | 2024-03-06T03:25:08Z |
| publishDate | 2023 |
| publisher | Molecular Diversity Preservation International (MDPI) |
| record_format | dspace |
| spelling | ums.eprints-366272023-09-01T00:53:27Z https://eprints.ums.edu.my/id/eprint/36627/ 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 Iqra Ali Muhammad Asif Rasheed Simona Cavalu Kashif Rahim Sana Ijaz Galal Yahya Lucky Poh Wah Goh Mihaela Simona Popoviciu QA299.6-433 Analysis QR355-502 Virology 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 (∆Gbind −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. Molecular Diversity Preservation International (MDPI) 2023 Article NonPeerReviewed text en https://eprints.ums.edu.my/id/eprint/36627/1/ABSTRACT.pdf text en https://eprints.ums.edu.my/id/eprint/36627/2/FULL%20TEXT.pdf Iqra Ali and Muhammad Asif Rasheed and Simona Cavalu and Kashif Rahim and Sana Ijaz and Galal Yahya and 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. pp. 1-17. https://doi.org/10.3390/biomedicines11030793 |
| spellingShingle | QA299.6-433 Analysis QR355-502 Virology Iqra Ali Muhammad Asif Rasheed Simona Cavalu Kashif Rahim Sana Ijaz Galal Yahya Lucky Poh Wah Goh Mihaela Simona Popoviciu 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 |
| title | 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 |
| title_full | 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 |
| title_fullStr | 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 |
| title_full_unstemmed | 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 |
| title_short | 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 |
| title_sort | 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 |
| topic | QA299.6-433 Analysis QR355-502 Virology |
| url | https://eprints.ums.edu.my/id/eprint/36627/1/ABSTRACT.pdf https://eprints.ums.edu.my/id/eprint/36627/2/FULL%20TEXT.pdf |
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