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Molecular docking as a tool for the discovery of novel insight about the role of acid sphingomyelinase inhibitors in SARS- CoV-2 infectivity

Alkafaas et al., BMC Public Health, doi:10.1186/s12889-024-17747-z

Feb 2024

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Fluvoxamine

27th treatment shown to reduce risk in November 2021, now with p = 0.00014 from 21 studies, recognized in 3 countries.

Lower risk for mortality, hospitalization, progression, recovery, and cases.

No treatment is 100% effective. Protocols combine treatments.

5,100+ studies for 109 treatments. c19early.org

In Silico molecular docking analysis evaluating 71 functional inhibitors of acid sphingomyelinase (FIASMAs), showing that FIASMAs may prevent SARS-CoV-2 cell entry and infection via inhibiting ceramide platform formation that facilitates viral uptake. Dilazep, emetine, pimozide, carvedilol, mebeverine, cepharanthine, hydroxyzine, astemizole, sertindole, and bepridil showed higher predicted binding affinity and inhibition potential compared to the candidate drug amiodarone.

4 preclinical studies support the efficacy of fluvoxamine for COVID-19:

2 In Silico studies1,2

2 In Vitro studies2,3

Fluvoxamine may inhibit SARS-CoV-2 cell entry by preventing the formation of ceramide platforms that facilitates viral uptake1 and may help restore autophagic processes disrupted by NSP6, thereby reducing SARS-CoV-2 replication and improving host cellular defenses3.

Important missing comments or errors? Let us know.

1. Alkafaas et al., Molecular docking as a tool for the discovery of novel insight about the role of acid sphingomyelinase inhibitors in SARS- CoV-2 infectivity, BMC Public Health, doi:10.1186/s12889-024-17747-z.biomedcentral.com, doi.org.

2. Abatematteo et al., A conformational rearrangement of the SARS-CoV-2 host protein sigma-1 is required for antiviral activity: insights from a combined in-silico/in-vitro approach, Scientific Reports, doi:10.1038/s41598-023-39662-w.nature.com, doi.org.

3. Zhang et al., SARS-CoV-2 NSP6 reduces autophagosome size and affects viral replication via sigma-1 receptor, Journal of Virology, doi:10.1128/jvi.00754-24.asm.org, doi.org.

Alkafaas et al., 6 Feb 2024, peer-reviewed, 18 authors. Contact: samar.alkafas@science.tanta.edu.eg, samarsamy2017@yahoo.com.

In Silico studies are an important part of preclinical research, however results may be very different in vivo.

This Paper Fluvoxamine All

Molecular docking as a tool for the discovery of novel insight about the role of acid sphingomyelinase inhibitors in SARS- CoV-2 infectivity

Samar Sami Alkafaas, Abanoub Mosaad Abdallah, Mai H Hassan, Aya Misbah Hussien, Sara Samy Elkafas, Samah A Loutfy, Abanoub Mikhail, Omnia G Murad, Mohamed I Elsalahaty, Mohamed Hessien, Rami M Elshazli, Fatimah A Alsaeed, Ahmed Ezzat Ahmed, Hani K Kamal, Wael Hafez, Mohamed T El-Saadony, Khaled A El-Tarabily, Soumya Ghosh

BMC Public Health, doi:10.1186/s12889-024-17747-z

Recently, COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its variants, caused > 6 million deaths. Symptoms included respiratory strain and complications, leading to severe pneumonia. SARS-CoV-2 attaches to the ACE-2 receptor of the host cell membrane to enter. Targeting the SARS-CoV-2 entry may effectively inhibit infection. Acid sphingomyelinase (ASMase) is a lysosomal protein that catalyzes the conversion of sphingolipid (sphingomyelin) to ceramide. Ceramide molecules aggregate/assemble on the plasma membrane to form "platforms" that facilitate the viral intake into the cell. Impairing the ASMase activity will eventually disrupt viral entry into the cell. In this review, we identified the metabolism of sphingolipids, sphingolipids' role in cell signal transduction cascades, and viral infection mechanisms. Also, we outlined ASMase structure and underlying mechanisms inhibiting viral entry 40 with the aid of inhibitors of acid sphingomyelinase (FIASMAs). In silico molecular docking analyses of FIASMAs with inhibitors revealed that dilazep (S = -12.58 kcal/mol), emetine (S = -11.65 kcal/ mol), pimozide (S = -11.29 kcal/mol), carvedilol (S = -11.28 kcal/mol), mebeverine (S = -11.14 kcal/mol), cepharanthine (S = -11.06 kcal/mol), hydroxyzin (S = -10.96 kcal/mol), astemizole (S = -10.81 kcal/mol), sertindole (S = -10.55 kcal/mol), and bepridil (S = -10.47 kcal/mol) have higher inhibition activity than the candidate drug amiodarone (S = -10.43 kcal/mol), making them better options for inhibition.

Declarations Ethics approval and consent to participate Not applicable. Consent for publication Not applicable. Financial interest All authors declare that they have no financial or non-financial interests that are directly or indirectly related to the work submitted for publication. Competing interests The authors declare no competing interests. Publisher's Note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

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Symptoms included respiratory strain and complications, leading to severe ' 'pneumonia. SARS-CoV-2 attaches to the ACE-2 receptor of the host cell membrane to enter. ' 'Targeting the SARS-CoV-2 entry may effectively inhibit infection. Acid sphingomyelinase ' '(ASMase) is a lysosomal protein that catalyzes the conversion of sphingolipid (sphingomyelin) ' 'to ceramide. Ceramide molecules aggregate/assemble on the plasma membrane to form “platforms” ' 'that facilitate the viral intake into the cell. Impairing the ASMase activity will eventually ' 'disrupt viral entry into the cell. In this review, we identified the metabolism of ' "sphingolipids, sphingolipids' role in cell signal transduction cascades, and viral infection " 'mechanisms. Also, we outlined ASMase structure and underlying mechanisms inhibiting viral ' 'entry 40 with the aid of inhibitors of acid sphingomyelinase (FIASMAs). In silico molecular ' 'docking analyses of FIASMAs with inhibitors revealed that dilazep (S\u2009=\u2009−\u200912.58 ' 'kcal/mol), emetine (S\u2009=\u2009−\u200911.65 kcal/mol), pimozide (S\u2009=\u2009−\u2009' '11.29 kcal/mol), carvedilol (S\u2009=\u2009−\u200911.28 kcal/mol), mebeverine (S\u2009=\u2009' '−\u200911.14 kcal/mol), cepharanthine (S\u2009=\u2009−\u200911.06 kcal/mol), hydroxyzin ' '(S\u2009=\u2009−\u200910.96 kcal/mol), astemizole (S\u2009=\u2009−\u200910.81 kcal/mol), ' 'sertindole (S\u2009=\u2009−\u200910.55 kcal/mol), and bepridil (S\u2009=\u2009−\u200910.47 ' 'kcal/mol) have higher inhibition activity than the candidate drug amiodarone (S\u2009=\u2009' '−\u200910.43 kcal/mol), making them better options for inhibition.', 'DOI': '10.1186/s12889-024-17747-z', 'type': 'journal-article', 'created': {'date-parts': [[2024, 2, 6]], 'date-time': '2024-02-06T15:03:35Z', 'timestamp': 1707231815000}, 'update-policy': 'http://dx.doi.org/10.1007/springer_crossmark_policy', 'source': 'Crossref', 'is-referenced-by-count': 0, 'title': 'Molecular docking as a tool for the discovery of novel insight about the role of acid ' 'sphingomyelinase inhibitors in SARS- CoV-2 infectivity', 'prefix': '10.1186', 'volume': '24', 'author': [ {'given': 'Samar Sami', 'family': 'Alkafaas', 'sequence': 'first', 'affiliation': []}, {'given': 'Abanoub Mosaad', 'family': 'Abdallah', 'sequence': 'additional', 'affiliation': []}, {'given': 'Mai H.', 'family': 'Hassan', 'sequence': 'additional', 'affiliation': []}, {'given': 'Aya Misbah', 'family': 'Hussien', 'sequence': 'additional', 'affiliation': []}, {'given': 'Sara Samy', 'family': 'Elkafas', 'sequence': 'additional', 'affiliation': []}, {'given': 'Samah A.', 'family': 'Loutfy', 'sequence': 'additional', 'affiliation': []}, {'given': 'Abanoub', 'family': 'Mikhail', 'sequence': 'additional', 'affiliation': []}, {'given': 'Omnia G.', 'family': 'Murad', 'sequence': 'additional', 'affiliation': []}, {'given': 'Mohamed I.', 'family': 'Elsalahaty', 'sequence': 'additional', 'affiliation': []}, {'given': 'Mohamed', 'family': 'Hessien', 'sequence': 'additional', 'affiliation': []}, {'given': 'Rami M.', 'family': 'Elshazli', 'sequence': 'additional', 'affiliation': []}, {'given': 'Fatimah A.', 'family': 'Alsaeed', 'sequence': 'additional', 'affiliation': []}, {'given': 'Ahmed Ezzat', 'family': 'Ahmed', 'sequence': 'additional', 'affiliation': []}, {'given': 'Hani K.', 'family': 'Kamal', 'sequence': 'additional', 'affiliation': []}, {'given': 'Wael', 'family': 'Hafez', 'sequence': 'additional', 'affiliation': []}, {'given': 'Mohamed T.', 'family': 'El-Saadony', 'sequence': 'additional', 'affiliation': []}, {'given': 'Khaled A.', 'family': 'El-Tarabily', 'sequence': 'additional', 'affiliation': []}, {'given': 'Soumya', 'family': 'Ghosh', 'sequence': 'additional', 'affiliation': []}], 'member': '297', 'published-online': {'date-parts': [[2024, 2, 6]]}, 'reference': [ { 'issue': '9', 'key': '17747_CR1', 'doi-asserted-by': 'publisher', 'first-page': '1417', 'DOI': '10.1038/s41591-020-1001-6', 'volume': '26', 'author': 'N Hoertel', 'year': '2020', 'unstructured': 'Hoertel N, Blachier M, Blanco C, Olfson M, Massetti M, Rico MS, Limosin ' 'F, Leleu H. 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