Peptidomimetic Small-Molecule Inhibitors of 3CLPro Activity and Spike-ACE2 Interaction: Toward Dual-Action Molecules against Coronavirus Infections

Peptidomimetics based on thiacalixarene with L-tyrosine moieties: Antibacterial activity against methicillin-resistant Staphylococcus aureus and degradation induced by binding to α-chymotrypsin

The design of new antimicrobial agents is an important challenge due to the growing resistance of microorganisms to existing antibiotics. In recent years, the trend towards the development of compounds and materials with (bio)degradable properties has emerged. In this work, we propose and develop a method for the synthesis of new peptidomimetics, i.e., water-soluble macrocyclic quaternary ammonium salts containing L-tyrosine fragments based on p-tert-butylthiacalix[4]arene in various stereoisomeric forms (cone, partial cone, and 1,3-alternate). These compounds have low cytotoxicity (IC50 = 80-267 μM) and high antibacterial activity (MIC = 0.5-15.6 μM) against Gram-positive bacterial strains including methicillin-resistant Staphylococcus aureus (MRSA). The obtained peptidomimetics can bind α-chymotrypsin with the formation of supramolecular systems and their subsequent degradation. Our results demonstrate the first example of multi-action thiacalixarene derivatives with antibacterial activity, protein binding ability and degradation induced by binding to α-chymotrypsin. The obtained results open the possibility of creating multi-action peptidomimetic systems with antimicrobial and biodegradable effect.

A patent review of anti-coronavirus agents targeting the spike-ACE2 interaction (2019-present)

INTRODUCTION

The Angiotensin-converting enzyme 2 (ACE2) receptor, crucial for coronavirus recognition of host cells, is a key target for therapeutic intervention against SARS-CoV-2 and related coronaviruses. Therefore, thoroughly investigating the interaction mechanism between ACE2 and the Spike protein (S protein), as well as developing targeted inhibitors based on this mechanism, is vital for effectively controlling the spread of SARS-CoV-2 and preventing potential future pandemics caused by other coronaviruses.

AREAS COVERED

This article comprehensively reviews the mechanisms underlying ACE2-S protein interaction that facilitate SARS-CoV-2 entry into host cells. It also analyzes the patent landscape regarding inhibitors targeting the ACE2-S interface since 2019.

EXPERT OPINION

In the 5 years since the outbreak of SARS-CoV-2, numerous methods and design strategies have been employed to develop innovative therapeutics against coronaviruses. Among these approaches, inhibitors targeting both the ACE2 receptor and the S protein have gained significant interest due to their potential in blocking various coronaviruses. Despite facing challenges similar to other protein-protein interaction inhibitors, progress has been made in developing these inhibitors through virtual screening, covalent protein binding, and peptide modification strategies. However, obstacles persist in clinical translation, necessitating a multidisciplinary strategy that integrates state-of-the-art methodologies to optimize S-ACE2 interface-targeted drug discovery.

How many organic small molecules might be used to treat COVID-19? From natural products to synthetic agents

A large scale of pandemic coronavirus disease (COVID-19) in the past five years motivates a great deal of endeavors donating to the exploration on therapeutic drugs against COVID-19 as well as other diseases caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Herein is an overview on the organic small molecules that are potentially employed to treat COVID-19 and other SARS-CoV-2-related diseases. These organic small molecules are accessed from both natural resources and synthetic strategies. Notably, typical natural products presented herein consist of polyphenols, lignans, alkaloids, terpenoids, and peptides, which exert an advantage for the further discovery of novel anti-COVID-19 drugs from plant herbs. On the other hand, synthetic prodrugs are composed of a series of inhibitors towards RNA-dependent RNA polymerase (RdRp), main protease (Mpro), 3-chymotrypsin-like cysteine protease (3CLpro), spike protein, papain-like protease (PLpro) of the SARS-CoV-2 as well as the angiotensin-converting enzyme 2 (ACE2) in the host cells. Synthetic strategies are worth taken into consideration because they are beneficial for designing novel anti-COVID-19 drugs in the coming investigations. Although examples collected herein are just a drop in the bucket, developments of organic small molecules against coronavirus infections are believed to pave a promising way for the discovery of multi-targeted therapeutic drugs against not only COVID-19 but also other virus-mediated diseases.

Transformation of peptides to small molecules in medicinal chemistry: Challenges and opportunities

Peptides are native binders involved in numerous physiological life procedures, such as cellular signaling, and serve as ready-made regulators of biochemical processes. Meanwhile, small molecules compose many drugs owing to their outstanding advantages of physiochemical properties and synthetic convenience. A novel field of research is converting peptides into small molecules, providing a convenient portable solution for drug design or peptidomic research. Endowing properties of peptides onto small molecules can evolutionarily combine the advantages of both moieties and improve the biological druggability of molecules. Herein, we present eight representative recent cases in this conversion and elaborate on the transformation process of each case. We discuss the innovative technological methods and research approaches involved, and analyze the applicability conditions of the approaches and methods in each case, guiding further modifications of peptides to small molecules. Finally, based on the aforementioned cases, we summarize a general procedure for peptide-to-small molecule modifications, listing the technological methods available for each transformation step and providing our insights on the applicable scenarios for these methods. This review aims to present the progress of peptide-to-small molecule modifications and propose our thoughts and perspectives for future research in this field.

Establishment of in-house assay for screening of anti-SARS-CoV-2 protein inhibitors

Developing a potent antiviral agent to combat Coronavirus Disease-19 (COVID-19) is of critical importance as we may be at risk of the emergence of new virus strains or another pandemic recurrence. The interaction between the SARS-CoV-2 spike protein and Angiotensin Converting Enzyme 2 (ACE2) is the main protein-protein interaction (PPI) implicated in the virus entry into the host cells. Spike-ACE2 PPI represents a major target for drug intervention. We have repurposed a previously described protein-protein interaction detection method to be utilized as a drug screening assay. The assay was standardized using Chitosan nanoparticles (CNPs) as the drug and SARS-CoV-2 spike-ACE2 interaction as the PPI model. The assay was then used to screen four natural bioactive compounds: Curcumin (Cur), Gallic acid (GA), Quercetin (Q), and Silymarin (Sil), and their cytotoxicity was evaluated in vitro. Production of the spike protein and the evaluation of its activity in comparison to a standard commercial protein was part of our work as well. Here we describe a novel simple immunofluorescent screening assay to identify potential SARS-CoV-2 inhibitors that could assess the inhibitory effect of any ligand against any PPI.

Inhibition of SARS-CoV-2 3CLpro by chemically modified tyrosinase from Agaricus bisporus

Antiviral compounds are crucial to controlling the SARS-CoV-2 pandemic. Approved drugs have been tested for their efficacy against COVID-19, and new pharmaceuticals are being developed as a complementary tool to vaccines. In this work, a cheap and fast purification method for natural tyrosinase from Agaricus bisporus (AbTyr) fresh mushrooms was developed to evaluate the potential of this enzyme as a therapeutic protein via the inhibition of SARS-CoV-2 3CLpro protease activity in vitro. AbTyr showed a mild inhibition of 3CLpro. Thus, different variants of this protein were synthesized through chemical modifications, covalently binding different tailor-made glycans and peptides to the amino terminal groups of the protein. These new tyrosinase conjugates were purified and characterized through circular dichroism and fluorescence spectroscopy analyses, and their stability was evaluated under different conditions. Subsequently, all these tyrosinase conjugates were tested for 3CLpro protease inhibition. From them, the conjugate between tyrosinase and a dextran-aspartic acid (6 kDa) polymer showed the highest inhibition, with an IC50 of 2.5 μg ml-1 and IC90 of 5 μg ml-1, with no cytotoxicity activity by polymer insertion. Finally, SARS-CoV-2 virus infection was studied. It was found that this new AbTyr-Dext6000 protein showed an 80% decrease in viral load. These results show the capacity of these tyrosinase bioconjugates as potential therapeutic proteins, opening the possibility of extension and applicability against other different viruses.

Progress in Research on Inhibitors Targeting SARS-CoV-2 Main Protease (Mpro)

Since 2019, the novel coronavirus (SARS-CoV-2) has caused significant morbidity and millions of deaths worldwide. The Coronavirus Disease 2019 (COVID-19), caused by SARS-CoV-2 and its variants, has further highlighted the urgent need for the development of effective therapeutic agents. Currently, the highly conserved and broad-spectrum nature of main proteases (Mpro) renders them of great importance in the field of inhibitor study. In this study, we categorize inhibitors targeting Mpro into three major groups: mimetic, nonmimetic, and natural inhibitors. We then present the research progress of these inhibitors in detail, including their mechanism of action, antiviral activity, pharmacokinetic properties, animal experiments, and clinical studies. This review aims to provide valuable insights and potential avenues for the development of more effective antiviral drugs against SARS-CoV-2.

Development of novel PEX5-PEX14 protein-protein interaction (PPI) inhibitors based on an oxopiperazine template

Protein-protein interactions (PPIs) constitute an important but challenging class of molecular targets for small molecules. The PEX5-PEX14 PPI has been shown to play a critical role in glycosome biogenesis and its disruption impairs the metabolism in Trpanosoma parasites, eventually leading to their death. Therefore, this PPI is a potential molecular target for new drugs against diseases caused by Trypanosoma infections. Here, we report a new class of peptidomimetic scaffolds to target the PEX5-PEX14 PPI. The molecular design was based on an oxopiperazine template for the α-helical mimetics. A structural simplification along with modifications of the central oxopiperazine scaffold and addressing the lipophilic interactions led to the development of peptidomimetics that inhibit PEX5-TbPEX14 PPI and display cellular activity against T. b. brucei. This approach provides an alternative approach towards the development of trypanocidal agents and may be generally useful for the design of helical mimetics as PPI inhibitors.

Identification of a short ACE2-derived stapled peptide targeting the SARS-CoV-2 spike protein

The design and synthesis of a series of peptide derivatives based on a short ACE2 α-helix 1 epitope and subsequent [i - i+4] stapling of the secondary structure resulted in the identification of a 9-mer peptide capable to compete with recombinant ACE2 towards Spike RBD in the micromolar range. Specifically, SARS-CoV-2 Spike inhibitor screening based on colorimetric ELISA assay and structural studies by circular dichroism showed the ring-closing metathesis cyclization being capable to stabilize the helical structure of the 9-mer ³⁴HEAEDLFYQ⁴² epitope better than the triazole stapling via click chemistry. MD simulations showed the stapled peptide being able not only to bind the Spike RBD, sterically interfering with ACE2, but also showing higher affinity to the target as compared to parent epitope.

SARS-CoV-2 main protease inhibitors: What is moving in the field of peptides and peptidomimetics?

The COVID-19 pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is still affecting people worldwide. Despite the good degree of immunological protection achieved through vaccination, there are still severe cases that require effective antivirals. In this sense, two specific pharmaceutical preparations have been marketed already, the RdRp polymerase inhibitor molnupiravir and the main viral protease inhibitor nirmatrelvir (commercialized as Paxlovid, a combination with ritonavir). Nirmatrelvir is a peptidomimetic acting as orally available, covalent, and reversible inhibitor of SARS-CoV-2 main viral protease. The success of this compound has revitalized the search for new peptide and peptidomimetic protease inhibitors. This highlight collects some selected examples among those recently published in the field of SARS-CoV-2.

Overview of Antiviral Drug Therapy for COVID-19: Where Do We Stand?

The vaccine weapon has resulted in being essential in fighting the COVID-19 outbreak, but it is not fully preventing infection due to an alarming spreading of several identified variants of concern. In fact, the recent emergence of variants has pointed out how the SARS-CoV-2 pandemic still represents a global health threat. Moreover, oral antivirals also develop resistance, supporting the need to find new targets as therapeutic tools. However, cocktail therapy is useful to reduce drug resistance and maximize vaccination efficacy. Natural products and metal-drug-based treatments have also shown interesting antiviral activity, representing a valid contribution to counter COVID-19 outbreak. This report summarizes the available evidence which supports the use of approved drugs and further focuses on significant clinical trials that have investigated the safety and efficacy of repurposing drugs and new molecules in different COVID-19 phenotypes. To date, there are many individuals vulnerable to COVID-19 exhibiting severe symptoms, thus characterizing valid therapeutic strategies for better management of the disease is still a challenge.