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Molecules
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Molecules to Fight SARS-CoV-2 Infection
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Molecules to Fight SARS-CoV-2 Infection

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Medicinal Chemistry".

Deadline for manuscript submissions: closed (30 June 2022) | Viewed by 20473

Special Issue Editors

Prof. Dr. Giuseppe Manfroni

E-Mail Website
Guest Editor
Department of Pharmaceutical Sciences, University of Perugia, 06123 Perugia, Italy
Interests: medicinal chemistry; drug design; molecular modeling; heterocyclic chemistry; organic synthesis; antivirals; antitumor agents; antibacterials; anti-inflammatory agents; chemical biology; kinase inhibitors; ionic liquids; enzyme inhibitors; nucleic acids binders; hit-to-lead optimization
Special Issues, Collections and Topics in MDPI journals
Dr. Tommaso Felicetti

E-Mail
Guest Editor
Department of Pharmaceutical Sciences, University of Perugia, 06123 Perugia, Italy
Interests: medicinal chemistry; drug design; heterocyclic chemistry; organic synthesis; antivirals; anticancer agents; antimicrobial agents; hit-to-lead optimization; efflux pump inhibitors
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Previous epidemics caused by viral pathogens had prompted scientists to believe that the next pandemic (disease X) could develop from an RNA virus (pathogen X) through zoonotic transmission. Nowadays, the current COVID-19 pandemic meets the requirements of disease X, likely representing what had been previously hypothesized. The pandemic caused by SARS-CoV-2 is a serious warning for the humankind and it is highlighting the mistake to have underestimated over the years the infectious diseases. The identification of drugs to treat COVID-19 and other coronavirus diseases represents an urgent global need, thus strategies comprising direct-acting agents or host-targeting agents are strongly required.

In this special issue, we aim to collect a series of high-quality reviews and original papers focused on small molecules and peptides from both natural products and synthetic sources, monoclonal antibodies, and tools for chemical biology studies. Drug repositioning studies, virtual screening campaign and design and synthesis of new molecules aimed at identifying new anti-SARS-CoV-2 agents are welcome. However, we discourage the submission of papers focused only on theoretical studies without experimental validation.

We are proud to invite you to submit your own contribute on the special issue: “Molecules to fight SARS-CoV-2 infection”.

Prof. Dr. Giuseppe Manfroni
Dr. Tommaso Felicetti
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Molecules is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • SARS-CoV-2
  • COVID-19
  • Drug-design
  • Drug repurposing
  • Antiviral agents
  • Medicinal chemistry

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Published Papers (3 papers)

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Research

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17 pages, 4669 KiB  
Article
Computational Simulation of HIV Protease Inhibitors to the Main Protease (Mpro) of SARS-CoV-2: Implications for COVID-19 Drugs Design
by Wei Yu, Xiaomin Wu, Yizhen Zhao, Chun Chen, Zhiwei Yang, Xiaochun Zhang, Jiayi Ren, Yueming Wang, Changwen Wu, Chengming Li, Rongfeng Chen, Xiaoli Wang, Weihong Zheng, Huaxin Liao and Xiaohui Yuan
Molecules 2021, 26(23), 7385; https://doi.org/10.3390/molecules26237385 - 5 Dec 2021
Cited by 9 | Viewed by 3523
Abstract
SARS-CoV-2 is highly homologous to SARS-CoV. To date, the main protease (Mpro) of SARS-CoV-2 is regarded as an important drug target for the treatment of Coronavirus Disease 2019 (COVID-19). Some experiments confirmed that several HIV protease inhibitors present the inhibitory effects on the [...] Read more.
SARS-CoV-2 is highly homologous to SARS-CoV. To date, the main protease (Mpro) of SARS-CoV-2 is regarded as an important drug target for the treatment of Coronavirus Disease 2019 (COVID-19). Some experiments confirmed that several HIV protease inhibitors present the inhibitory effects on the replication of SARS-CoV-2 by inhibiting Mpro. However, the mechanism of action has still not been studied very clearly. In this work, the interaction mechanism of four HIV protease inhibitors Darunavir (DRV), Lopinavir (LPV), Nelfinavir (NFV), and Ritonavire (RTV) targeting SARS-CoV-2 Mpro was explored by applying docking, molecular dynamics (MD) simulations, and MM–GBSA methods using the broad-spectrum antiviral drug Ribavirin (RBV) as the negative and nonspecific control. Our results revealed that LPV, RTV, and NFV have higher binding affinities with Mpro, and they all interact with catalytic residues His41 and the other two key amino acids Met49 and Met165. Pharmacophore model analysis further revealed that the aromatic ring, hydrogen bond donor, and hydrophobic group are the essential infrastructure of Mpro inhibitors. Overall, this study applied computational simulation methods to study the interaction mechanism of HIV-1 protease inhibitors with SARS-CoV-2 Mpro, and the findings provide useful insights for the development of novel anti-SARS-CoV-2 agents for the treatment of COVID-19. Full article
(This article belongs to the Special Issue Molecules to Fight SARS-CoV-2 Infection)
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Review

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27 pages, 1575 KiB  
Review
Coronavirus Infection-Associated Cell Death Signaling and Potential Therapeutic Targets
by Rittibet Yapasert, Patompong Khaw-on and Ratana Banjerdpongchai
Molecules 2021, 26(24), 7459; https://doi.org/10.3390/molecules26247459 - 9 Dec 2021
Cited by 41 | Viewed by 9237
Abstract
COVID-19 is the name of the disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection that occurred in 2019. The virus–host-specific interactions, molecular targets on host cell deaths, and the involved signaling are crucial issues, which become potential targets for [...] Read more.
COVID-19 is the name of the disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection that occurred in 2019. The virus–host-specific interactions, molecular targets on host cell deaths, and the involved signaling are crucial issues, which become potential targets for treatment. Spike protein, angiotensin-converting enzyme 2 (ACE2), cathepsin L-cysteine peptidase, transmembrane protease serine 2 (TMPRSS2), nonstructural protein 1 (Nsp1), open reading frame 7a (ORF7a), viral main protease (3C-like protease (3CLpro) or Mpro), RNA dependent RNA polymerase (RdRp) (Nsp12), non-structural protein 13 (Nsp13) helicase, and papain-like proteinase (PLpro) are molecules associated with SARS-CoV infection and propagation. SARS-CoV-2 can induce host cell death via five kinds of regulated cell death, i.e., apoptosis, necroptosis, pyroptosis, autophagy, and PANoptosis. The mechanisms of these cell deaths are well established and can be disrupted by synthetic small molecules or natural products. There are a variety of compounds proven to play roles in the cell death inhibition, such as pan-caspase inhibitor (z-VAD-fmk) for apoptosis, necrostatin-1 for necroptosis, MCC950, a potent and specific inhibitor of the NLRP3 inflammasome in pyroptosis, and chloroquine/hydroxychloroquine, which can mitigate the corresponding cell death pathways. However, NF-κB signaling is another critical anti-apoptotic or survival route mediated by SARS-CoV-2. Such signaling promotes viral survival, proliferation, and inflammation by inducing the expression of apoptosis inhibitors such as Bcl-2 and XIAP, as well as cytokines, e.g., TNF. As a result, tiny natural compounds functioning as proteasome inhibitors such as celastrol and curcumin can be used to modify NF-κB signaling, providing a responsible method for treating SARS-CoV-2-infected patients. The natural constituents that aid in inhibiting viral infection, progression, and amplification of coronaviruses are also emphasized, which are in the groups of alkaloids, flavonoids, terpenoids, diarylheptanoids, and anthraquinones. Natural constituents derived from medicinal herbs have anti-inflammatory and antiviral properties, as well as inhibitory effects, on the viral life cycle, including viral entry, replication, assembly, and release of COVID-19 virions. The phytochemicals contain a high potential for COVID-19 treatment. As a result, SARS-CoV-2-infected cell death processes and signaling might be of high efficacy for therapeutic targeting effects and yielding encouraging outcomes. Full article
(This article belongs to the Special Issue Molecules to Fight SARS-CoV-2 Infection)
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24 pages, 1620 KiB  
Review
A Review of Human Coronaviruses’ Receptors: The Host-Cell Targets for the Crown Bearing Viruses
by Aaya Nassar, Ibrahim M. Ibrahim, Fatma G. Amin, Merna Magdy, Ahmed M. Elgharib, Eman B. Azzam, Filopateer Nasser, Kirllos Yousry, Israa M. Shamkh, Samah M. Mahdy and Abdo A. Elfiky
Molecules 2021, 26(21), 6455; https://doi.org/10.3390/molecules26216455 - 26 Oct 2021
Cited by 45 | Viewed by 6602
Abstract
A novel human coronavirus prompted considerable worry at the end of the year 2019. Now, it represents a significant global health and economic burden. The newly emerged coronavirus disease caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is the primary reason for [...] Read more.
A novel human coronavirus prompted considerable worry at the end of the year 2019. Now, it represents a significant global health and economic burden. The newly emerged coronavirus disease caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is the primary reason for the COVID-19 global pandemic. According to recent global figures, COVID-19 has caused approximately 243.3 million illnesses and 4.9 million deaths. Several human cell receptors are involved in the virus identification of the host cells and entering them. Hence, understanding how the virus binds to host-cell receptors is crucial for developing antiviral treatments and vaccines. The current work aimed to determine the multiple host-cell receptors that bind with SARS-CoV-2 and other human coronaviruses for the purpose of cell entry. Extensive research is needed using neutralizing antibodies, natural chemicals, and therapeutic peptides to target those host-cell receptors in extremely susceptible individuals. More research is needed to map SARS-CoV-2 cell entry pathways in order to identify potential viral inhibitors. Full article
(This article belongs to the Special Issue Molecules to Fight SARS-CoV-2 Infection)
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