Fruit Bromelain-Derived Peptide Potentially Restrains the Attachment of SARS-CoV-2 Variants to hACE2: A Pharmacoinformatics Approach
Before entering the cell, the SARS-CoV-2 spike glycoprotein receptor-binding domain (RBD) binds to the human angiotensin-converting enzyme 2 (hACE2) receptor. Hence, this RBD is a critical target for the development of antiviral agents. Recent studies have discovered that SARS-CoV-2 variants with mu...
| Main Authors: | , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2022-01-01
|
| Series: | Molecules |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1420-3049/27/1/260 |
| _version_ | 1797498167923572736 |
|---|---|
| author | Trina Ekawati Tallei Fatimawali Ahmad Akroman Adam Mona M. Elseehy Ahmed M. El-Shehawi Eman A. Mahmoud Adinda Dwi Tania Nurdjannah Jane Niode Diah Kusumawaty Souvia Rahimah Yunus Effendi Rinaldi Idroes Ismail Celik Md. Jamal Hossain Talha Bin Emran |
| author_facet | Trina Ekawati Tallei Fatimawali Ahmad Akroman Adam Mona M. Elseehy Ahmed M. El-Shehawi Eman A. Mahmoud Adinda Dwi Tania Nurdjannah Jane Niode Diah Kusumawaty Souvia Rahimah Yunus Effendi Rinaldi Idroes Ismail Celik Md. Jamal Hossain Talha Bin Emran |
| author_sort | Trina Ekawati Tallei |
| collection | DOAJ |
| description | Before entering the cell, the SARS-CoV-2 spike glycoprotein receptor-binding domain (RBD) binds to the human angiotensin-converting enzyme 2 (hACE2) receptor. Hence, this RBD is a critical target for the development of antiviral agents. Recent studies have discovered that SARS-CoV-2 variants with mutations in the RBD have spread globally. The purpose of this in silico study was to determine the potential of a fruit bromelain-derived peptide. DYGAVNEVK. to inhibit the entry of various SARS-CoV-2 variants into human cells by targeting the hACE binding site within the RBD. Molecular docking analysis revealed that DYGAVNEVK interacts with several critical RBD binding residues responsible for the adhesion of the RBD to hACE2. Moreover, 100 ns MD simulations revealed stable interactions between DYGAVNEVK and RBD variants derived from the trajectory of root-mean-square deviation (RMSD), radius of gyration (Rg), and root-mean-square fluctuation (RMSF) analysis, as well as free binding energy calculations. Overall, our computational results indicate that DYGAVNEVK warrants further investigation as a candidate for preventing SARS-CoV-2 due to its interaction with the RBD of SARS-CoV-2 variants. |
| first_indexed | 2024-03-10T03:29:35Z |
| format | Article |
| id | doaj.art-0dd52f87b11449f38dea6ac076f20d5e |
| institution | Directory Open Access Journal |
| issn | 1420-3049 |
| language | English |
| last_indexed | 2024-03-10T03:29:35Z |
| publishDate | 2022-01-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Molecules |
| spelling | doaj.art-0dd52f87b11449f38dea6ac076f20d5e2023-11-23T11:59:02ZengMDPI AGMolecules1420-30492022-01-0127126010.3390/molecules27010260Fruit Bromelain-Derived Peptide Potentially Restrains the Attachment of SARS-CoV-2 Variants to hACE2: A Pharmacoinformatics ApproachTrina Ekawati Tallei0Fatimawali1Ahmad Akroman Adam2Mona M. Elseehy3Ahmed M. El-Shehawi4Eman A. Mahmoud5Adinda Dwi Tania6Nurdjannah Jane Niode7Diah Kusumawaty8Souvia Rahimah9Yunus Effendi10Rinaldi Idroes11Ismail Celik12Md. Jamal Hossain13Talha Bin Emran14Department of Biology, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado 95115, IndonesiaThe University Centre of Excellence for Biotechnology and Conservation of Wallacea, Institute for Research and Community Services, Sam Ratulangi University, Manado 95115, IndonesiaDentistry Study Program, Faculty of Medicine, Sam Ratulangi University, Manado 95115, IndonesiaDepartment of Genetics, Faculty of Agriculture, University of Alexandria, Alexandria 21545, EgyptDepartment of Biotechnology, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi ArabiaDepartment of Food Industries, Faculty of Agriculture, Damietta University, Damietta 34511, EgyptPharmacy Study Program, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado 95115, IndonesiaThe University Centre of Excellence for Biotechnology and Conservation of Wallacea, Institute for Research and Community Services, Sam Ratulangi University, Manado 95115, IndonesiaDepartment of Biology, Faculty of Mathematics and Natural Sciences Education, Universitas Pendidikan Indonesia, Bandung 40154, IndonesiaFood Technology Study Program, Department of Food Industrial Technology, Faculty of Agroindustrial Technology, Universitas Padjadjaran, Jatinangor 45363, IndonesiaDepartment of Biology, Faculty of Science and Technology, Al-Azhar Indonesia University, Jakarta 12110, IndonesiaDepartment of Pharmacy, Faculty of Mathematics and Natural Sciences, Universitas Syiah Kuala, Kopelma Darussalam, Banda Aceh 23111, IndonesiaDepartment of Pharmaceutical Chemistry, Faculty of Pharmacy, Erciyes University, Kayseri 38039, TurkeyDepartment of Pharmacy, State University of Bangladesh, 77 Satmasjid Road, Dhanmondi, Dhaka 1205, BangladeshDepartment of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, BangladeshBefore entering the cell, the SARS-CoV-2 spike glycoprotein receptor-binding domain (RBD) binds to the human angiotensin-converting enzyme 2 (hACE2) receptor. Hence, this RBD is a critical target for the development of antiviral agents. Recent studies have discovered that SARS-CoV-2 variants with mutations in the RBD have spread globally. The purpose of this in silico study was to determine the potential of a fruit bromelain-derived peptide. DYGAVNEVK. to inhibit the entry of various SARS-CoV-2 variants into human cells by targeting the hACE binding site within the RBD. Molecular docking analysis revealed that DYGAVNEVK interacts with several critical RBD binding residues responsible for the adhesion of the RBD to hACE2. Moreover, 100 ns MD simulations revealed stable interactions between DYGAVNEVK and RBD variants derived from the trajectory of root-mean-square deviation (RMSD), radius of gyration (Rg), and root-mean-square fluctuation (RMSF) analysis, as well as free binding energy calculations. Overall, our computational results indicate that DYGAVNEVK warrants further investigation as a candidate for preventing SARS-CoV-2 due to its interaction with the RBD of SARS-CoV-2 variants.https://www.mdpi.com/1420-3049/27/1/260bromelainpeptideSARS-CoV-2 variantsin silicoreceptor-binding domainRBD mutation |
| spellingShingle | Trina Ekawati Tallei Fatimawali Ahmad Akroman Adam Mona M. Elseehy Ahmed M. El-Shehawi Eman A. Mahmoud Adinda Dwi Tania Nurdjannah Jane Niode Diah Kusumawaty Souvia Rahimah Yunus Effendi Rinaldi Idroes Ismail Celik Md. Jamal Hossain Talha Bin Emran Fruit Bromelain-Derived Peptide Potentially Restrains the Attachment of SARS-CoV-2 Variants to hACE2: A Pharmacoinformatics Approach Molecules bromelain peptide SARS-CoV-2 variants in silico receptor-binding domain RBD mutation |
| title | Fruit Bromelain-Derived Peptide Potentially Restrains the Attachment of SARS-CoV-2 Variants to hACE2: A Pharmacoinformatics Approach |
| title_full | Fruit Bromelain-Derived Peptide Potentially Restrains the Attachment of SARS-CoV-2 Variants to hACE2: A Pharmacoinformatics Approach |
| title_fullStr | Fruit Bromelain-Derived Peptide Potentially Restrains the Attachment of SARS-CoV-2 Variants to hACE2: A Pharmacoinformatics Approach |
| title_full_unstemmed | Fruit Bromelain-Derived Peptide Potentially Restrains the Attachment of SARS-CoV-2 Variants to hACE2: A Pharmacoinformatics Approach |
| title_short | Fruit Bromelain-Derived Peptide Potentially Restrains the Attachment of SARS-CoV-2 Variants to hACE2: A Pharmacoinformatics Approach |
| title_sort | fruit bromelain derived peptide potentially restrains the attachment of sars cov 2 variants to hace2 a pharmacoinformatics approach |
| topic | bromelain peptide SARS-CoV-2 variants in silico receptor-binding domain RBD mutation |
| url | https://www.mdpi.com/1420-3049/27/1/260 |
| work_keys_str_mv | AT trinaekawatitallei fruitbromelainderivedpeptidepotentiallyrestrainstheattachmentofsarscov2variantstohace2apharmacoinformaticsapproach AT fatimawali fruitbromelainderivedpeptidepotentiallyrestrainstheattachmentofsarscov2variantstohace2apharmacoinformaticsapproach AT ahmadakromanadam fruitbromelainderivedpeptidepotentiallyrestrainstheattachmentofsarscov2variantstohace2apharmacoinformaticsapproach AT monamelseehy fruitbromelainderivedpeptidepotentiallyrestrainstheattachmentofsarscov2variantstohace2apharmacoinformaticsapproach AT ahmedmelshehawi fruitbromelainderivedpeptidepotentiallyrestrainstheattachmentofsarscov2variantstohace2apharmacoinformaticsapproach AT emanamahmoud fruitbromelainderivedpeptidepotentiallyrestrainstheattachmentofsarscov2variantstohace2apharmacoinformaticsapproach AT adindadwitania fruitbromelainderivedpeptidepotentiallyrestrainstheattachmentofsarscov2variantstohace2apharmacoinformaticsapproach AT nurdjannahjaneniode fruitbromelainderivedpeptidepotentiallyrestrainstheattachmentofsarscov2variantstohace2apharmacoinformaticsapproach AT diahkusumawaty fruitbromelainderivedpeptidepotentiallyrestrainstheattachmentofsarscov2variantstohace2apharmacoinformaticsapproach AT souviarahimah fruitbromelainderivedpeptidepotentiallyrestrainstheattachmentofsarscov2variantstohace2apharmacoinformaticsapproach AT yunuseffendi fruitbromelainderivedpeptidepotentiallyrestrainstheattachmentofsarscov2variantstohace2apharmacoinformaticsapproach AT rinaldiidroes fruitbromelainderivedpeptidepotentiallyrestrainstheattachmentofsarscov2variantstohace2apharmacoinformaticsapproach AT ismailcelik fruitbromelainderivedpeptidepotentiallyrestrainstheattachmentofsarscov2variantstohace2apharmacoinformaticsapproach AT mdjamalhossain fruitbromelainderivedpeptidepotentiallyrestrainstheattachmentofsarscov2variantstohace2apharmacoinformaticsapproach AT talhabinemran fruitbromelainderivedpeptidepotentiallyrestrainstheattachmentofsarscov2variantstohace2apharmacoinformaticsapproach |