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Recent Advances in the Discovery and Development of Biomolecules as...
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Recent Advances in the Discovery and Development of Biomolecules as Antiviral Drugs

A special issue of Pharmaceuticals (ISSN 1424-8247). This special issue belongs to the section "Biopharmaceuticals".

Deadline for manuscript submissions: closed (31 January 2022) | Viewed by 19118

Special Issue Editor

Prof. Dr. Jose M. Palomo

E-Mail Website
Guest Editor
Group of Chemical Biology and Biocatalysis, Department of Biocatalysis, Instituto de Catalisis and Petroleoquimica (ICP-CSIC), Marie Curie 2, 28049 Madrid, Spain
Interests: nanotechnology; nanobiotechnology; nanocatalysis; biocatalysis; protein chemistry; medicinal chemistry; chemical biology; chemical technology; organic chemistry
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Viruses are among the most infectious pathogens, responsible for the highest number of deaths worldwide. Although the pathogenic mechanisms of viruses are diverse, all existing viruses need a host to maintain their existence. Viral infections result in millions of deaths and huge economic losses annually. Some important examples from recent years are the viruses Ebola, Zika, SARS, MERS, or, more recently, the pandemic caused by SARS-CoV-2 coronavirus, which has infected more than 140 million and killed more than 3 million people so far (data from April 2021). Although, in most cases, the development of drugs or vaccines has made it possible to control diseases, in some cases, the lack of effective clinical drugs emphasizes the need for the development of new strategies to combat pathogens. As such, biomolecules such as proteins, peptides, or polymers are a new type of drug that can potentially be used, and which is both effective and with low toxicity.

This Special Issue will be focused on innovative and novel research on the synthesis and application of biomolecules as antiviral drugs.

Prof. Dr. Jose Palomo
Guest Editor

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. Pharmaceuticals is an international peer-reviewed open access monthly 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 2900 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

  • proteins
  • peptides
  • polymers
  • antiviral activity
  • drugs
  • pharmaceuticals
  • Zika
  • SARS-CoV-2
  • hepatitis C
  • influenza

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Published Papers (5 papers)

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Research

19 pages, 6683 KiB  
Article
Identifying HSV-1 Inhibitors from Natural Compounds via Virtual Screening Targeting Surface Glycoprotein D
by Jiadai Wu, Helen Power, Monica Miranda-Saksena, Peter Valtchev, Aaron Schindeler, Anthony L. Cunningham and Fariba Dehghani
Pharmaceuticals 2022, 15(3), 361; https://doi.org/10.3390/ph15030361 - 16 Mar 2022
Cited by 5 | Viewed by 3134
Abstract
Herpes simplex virus (HSV) infections are a worldwide health problem in need of new effective treatments. Of particular interest is the identification of antiviral agents that act via different mechanisms compared to current drugs, as these could interact synergistically with first-line antiherpetic agents [...] Read more.
Herpes simplex virus (HSV) infections are a worldwide health problem in need of new effective treatments. Of particular interest is the identification of antiviral agents that act via different mechanisms compared to current drugs, as these could interact synergistically with first-line antiherpetic agents to accelerate the resolution of HSV-1-associated lesions. For this study, we applied a structure-based molecular docking approach targeting the nectin-1 and herpesvirus entry mediator (HVEM) binding interfaces of the viral glycoprotein D (gD). More than 527,000 natural compounds were virtually screened using Autodock Vina and then filtered for favorable ADMET profiles. Eight top hits were evaluated experimentally in African green monkey kidney cell line (VERO) cells, which yielded two compounds with potential antiherpetic activity. One active compound (1-(1-benzofuran-2-yl)-2-[(5Z)-2H,6H,7H,8H-[1,3] dioxolo[4,5-g]isoquinoline-5-ylidene]ethenone) showed weak but significant antiviral activity. Although less potent than antiherpetic agents, such as acyclovir, it acted at the viral inactivation stage in a dose-dependent manner, suggesting a novel mode of action. These results highlight the feasibility of in silico approaches for identifying new antiviral compounds, which may be further optimized by medicinal chemistry approaches. Full article
(This article belongs to the Special Issue Recent Advances in the Discovery and Development of Biomolecules as Antiviral Drugs)
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22 pages, 3478 KiB  
Article
Native RNA Purification Method for Small RNA Molecules Based on Asymmetrical Flow Field-Flow Fractionation
by Alesia A. Levanova, Mirka Lampi, Kiira Kalke, Veijo Hukkanen, Minna M. Poranen and Katri Eskelin
Pharmaceuticals 2022, 15(2), 261; https://doi.org/10.3390/ph15020261 - 21 Feb 2022
Cited by 7 | Viewed by 3190
Abstract
RNA molecules provide promising new possibilities for the prevention and treatment of viral infections and diseases. The rapid development of RNA biology and medicine requires advanced methods for the purification of RNA molecules, which allow fast and efficient RNA processing, preferably under non-denaturing [...] Read more.
RNA molecules provide promising new possibilities for the prevention and treatment of viral infections and diseases. The rapid development of RNA biology and medicine requires advanced methods for the purification of RNA molecules, which allow fast and efficient RNA processing, preferably under non-denaturing conditions. Asymmetrical flow field-flow fractionation (AF4) enables gentle separation and purification of macromolecules based on their diffusion coefficients. The aim of the study was to develop an AF4 method for efficient purification of enzymatically produced antiviral small interfering (si)RNA molecules and to evaluate the overall potential of AF4 in the separation of short single-stranded (ss) and double-stranded (ds) RNA molecules. We show that AF4 separates monomeric ssRNA from dsRNA molecules of the same size and monomeric ssRNA from multimeric forms of the same ssRNA. The developed AF4 method enabled the separation of enzymatically produced 27-nt siRNAs from partially digested substrate dsRNA, which is potentially toxic for mammalian cells. The recovery of AF4-purified enzymatically produced siRNA molecules was about 70%, which is about 20% higher than obtained using anion-exchange chromatography. The AF4-purified siRNAs were not toxic for mammalian cells and fully retained their biological activity as confirmed by efficient inhibition of herpes simplex virus 1 replication in cell culture. Our work is the first to develop AF4 methods for the separation of short RNA molecules. Full article
(This article belongs to the Special Issue Recent Advances in the Discovery and Development of Biomolecules as Antiviral Drugs)
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23 pages, 6490 KiB  
Article
Inhibition Ability of Natural Compounds on Receptor-Binding Domain of SARS-CoV2: An In Silico Approach
by Miroslava Nedyalkova, Mahdi Vasighi, Subrahmanyam Sappati, Anmol Kumar, Sergio Madurga and Vasil Simeonov
Pharmaceuticals 2021, 14(12), 1328; https://doi.org/10.3390/ph14121328 - 18 Dec 2021
Cited by 12 | Viewed by 4198
Abstract
The lack of medication to treat COVID-19 is still an obstacle that needs to be addressed by all possible scientific approaches. It is essential to design newer drugs with varied approaches. A receptor-binding domain (RBD) is a key part of SARS-CoV-2 virus, located [...] Read more.
The lack of medication to treat COVID-19 is still an obstacle that needs to be addressed by all possible scientific approaches. It is essential to design newer drugs with varied approaches. A receptor-binding domain (RBD) is a key part of SARS-CoV-2 virus, located on its surface, that allows it to dock to ACE2 receptors present on human cells, which is followed by admission of virus into cells, and thus infection is triggered. Specific receptor-binding domains on the spike protein play a pivotal role in binding to the receptor. In this regard, the in silico method plays an important role, as it is more rapid and cost effective than the trial and error methods using experimental studies. A combination of virtual screening, molecular docking, molecular simulations and machine learning techniques are applied on a library of natural compounds to identify ligands that show significant binding affinity at the hydrophobic pocket of the RBD. A list of ligands with high binding affinity was obtained using molecular docking and molecular dynamics (MD) simulations for protein–ligand complexes. Machine learning (ML) classification schemes have been applied to obtain features of ligands and important descriptors, which help in identification of better binding ligands. A plethora of descriptors were used for training the self-organizing map algorithm. The model brings out descriptors important for protein–ligand interactions. Full article
(This article belongs to the Special Issue Recent Advances in the Discovery and Development of Biomolecules as Antiviral Drugs)
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19 pages, 13467 KiB  
Article
Computational and In Vitro Experimental Investigations Reveal Anti-Viral Activity of Licorice and Glycyrrhizin against Severe Acute Respiratory Syndrome Coronavirus 2
by Ahmed M. Tolah, Lamya M. Altayeb, Thamir A. Alandijany, Vivek Dhar Dwivedi, Sherif A. El-Kafrawy and Esam I. Azhar
Pharmaceuticals 2021, 14(12), 1216; https://doi.org/10.3390/ph14121216 - 24 Nov 2021
Cited by 18 | Viewed by 3247
Abstract
Without effective antivirals, the COVID-19 pandemic will likely continue to substantially affect public health. Medicinal plants and phytochemicals are attractive therapeutic options, particularly those targeting viral proteins essential for replication cycle. Herein, a total 179 phytochemicals of licorice (Glycyrrhiza glabra) were screened and [...] Read more.
Without effective antivirals, the COVID-19 pandemic will likely continue to substantially affect public health. Medicinal plants and phytochemicals are attractive therapeutic options, particularly those targeting viral proteins essential for replication cycle. Herein, a total 179 phytochemicals of licorice (Glycyrrhiza glabra) were screened and scrutinized against the SARS-CoV-2 main protease (Mpro) with considerable binding affinities in the range of −9.831 to −2.710 kcal/mol. The top 10 compounds with the best docking scores, licuraside, glucoliquiritin apioside, 7,3′-Dihydroxy-5′-methoxyisoflavone, licuroside, kanzonol R, neoisoliquiritin, licochalcone-A, formononetin, isomucronulatol, and licoricone, were redocked using AutoDock Vina, yielding −8.7 to −7.3 kcal/mol binding energy against Glycyrrhizin (−8.0 kcal/mol) as a reference ligand. Four compounds, licuraside, glucoliquiritin apioside, 7,3′-Dihydroxy-5′-methoxyisoflavone, and licuroside, with glycyrrhizin (reference ligand) were considered for the 100 ns MD simulation and post-simulation analysis which support the stability of docked bioactive compounds with viral protein. In vitro studies demonstrated robust anti-SARS-CoV-2 activity of licorice and glycyrrhizin under different treatment protocols (simulations treatment with viral infection, post-infection treatment, and pre-treatment), suggesting multiple mechanisms for action. Although both compounds inhibited SARS-CoV-2 replication, the half-maximal inhibitory concentration (IC50) of glycyrrhizin was substantially lower than licorice. This study supports proceeding with in vivo experimentation and clinical trials and highlights licorice and glycyrrhizin as potential therapeutics for COVID-19. Full article
(This article belongs to the Special Issue Recent Advances in the Discovery and Development of Biomolecules as Antiviral Drugs)
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12 pages, 3390 KiB  
Article
In Vitro Antiviral Activity of Tyrosinase from Mushroom Agaricus bisporus against Hepatitis C Virus
by David Lopez-Tejedor, Rafael Claveria-Gimeno, Adrian Velazquez-Campoy, Olga Abian and Jose M. Palomo
Pharmaceuticals 2021, 14(8), 759; https://doi.org/10.3390/ph14080759 - 3 Aug 2021
Cited by 5 | Viewed by 4050
Abstract
Tyrosinases from a commercial Agaricus bisporus protein extract and directly isolated from white mushrooms were purified in order to obtaining the well-known tyrosinase from A. bisporus (TyrAB) of 45 kDa and a newly discovered 50 kDa tyrosinase isoform (Tyr50 kDa [...] Read more.
Tyrosinases from a commercial Agaricus bisporus protein extract and directly isolated from white mushrooms were purified in order to obtaining the well-known tyrosinase from A. bisporus (TyrAB) of 45 kDa and a newly discovered 50 kDa tyrosinase isoform (Tyr50 kDa), and tested showing high antiviral activity against the hepatitis C virus for the first time. Cell toxicity and antiviral activity of tyrosinases were determined in cultured Huh 5-2 liver tumor cells transfected with a replicon system (a plasmid that includes all non-structural hepatitis C virus proteins and replicates autonomously). TyrAB was able to inhibit the replication of the hepatitis C virus without inducing toxicity in liver cells. In addition, the post-translational isoform Tyr50 kDa showed higher antiviral capacity than the former (up to 10 times greater), also exhibiting 10 times higher activity than the commercial drug Ribavirin®. This antiviral activity was directly proportional to the enzymatic activity of tyrosinases, as no antiviral capacity was observed in the inactive form of the enzymes. The tyrosinases approach could represent a new antiviral inhibition mechanism, through a plausible catalytic mechanism of selective hydroxylation of the key role of tyrosine residues in viral proteases. Full article
(This article belongs to the Special Issue Recent Advances in the Discovery and Development of Biomolecules as Antiviral Drugs)
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