Discovery of Antiviral Cyclic Peptides Targeting the Main Protease of SARS-CoV-2 via mRNA Display

Antivirals that specifically target SARS-CoV-2 are needed to control the COVID-19 pandemic. The main protease (Mpro) is essential for SARS-CoV-2 replication and is an attractive target for antiviral development. Here we report the use of the Random nonstandard Peptide Integrated Discovery (RaPID) mRNA display on a chemically cross-linked SARS-CoV-2 Mpro dimer, which yielded several high-affinity thioether-linked cyclic peptide inhibitors of the protease. Structural analysis of Mpro complexed with a selenoether analogue of the highest-affinity peptide revealed key binding interactions, including glutamine and leucine residues in sites S1 and S2, respectively, and a binding epitope straddling both protein chains in the physiological dimer. Several of these Mpro peptide inhibitors possessed antiviral activity against SARS-CoV-2 in vitro with EC50 values in the low micromolar range. These cyclic peptides serve as a foundation for the development of much needed antivirals that specifically target SARS-CoV-2.

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Structure-Based Design of a Cyclic Peptide Inhibitor of the SARS-CoV-2 Main Protease

10.1101/2020.08.03.234872 ◽

2020 ◽

Author(s):

Adam G. Kreutzer ◽

Maj Krumberger ◽

Chelsea Marie T. Parrocha ◽

Michael A. Morris ◽

Gretchen Guaglianone ◽

...

Keyword(s):

Cleavage Site ◽

First Generation ◽

Cyclic Peptide ◽

Peptide Inhibitors ◽

Human Cells ◽

Peptide Inhibitor ◽

Cells In Culture ◽

Main Protease

ABSTRACTThis paper presents the design and study of a first-in-class cyclic peptide inhibitor against the SARS-CoV-2 main protease (Mpro). The cyclic peptide inhibitor is designed to mimic the conformation of a substrate at a C-terminal autolytic cleavage site of Mpro. Synthesis and evaluation of a first-generation cyclic peptide inhibitor reveals that the inhibitor is active against Mproin vitro and is non-toxic toward human cells in culture. The initial hit described in this manuscript, UCI-1, lays the groundwork for the development of additional cyclic peptide inhibitors against Mpro with improved activities.

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Potent Cyclic Peptide Inhibitors of FXIIa Discovered by mRNA Display with Genetic Code Reprogramming

Journal of Medicinal Chemistry ◽

10.1021/acs.jmedchem.1c00651 ◽

2021 ◽

Author(s):

Daniel J. Ford ◽

Nisharnthi M. Duggan ◽

Sarah E. Fry ◽

Jorge Ripoll-Rozada ◽

Stijn M. Agten ◽

...

Keyword(s):

Genetic Code ◽

Cyclic Peptide ◽

Peptide Inhibitors ◽

Mrna Display

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The Repurposed Drugs Suramin and Quinacrine Cooperatively Inhibit SARS-CoV-2 3CLpro In Vitro

Viruses ◽

10.3390/v13050873 ◽

2021 ◽

Vol 13 (5) ◽

pp. 873

Author(s):

Raphael J. Eberle ◽

Danilo S. Olivier ◽

Marcos S. Amaral ◽

Ian Gering ◽

Dieter Willbold ◽

...

Keyword(s):

Binding Mode ◽

Drug Candidates ◽

Main Protease ◽

Ic50 Values ◽

Repurposed Drugs ◽

Antiparasitic Drugs ◽

Inhibitory Potential ◽

Dynamics Simulations ◽

Micromolar Range

Since the first report of a new pneumonia disease in December 2019 (Wuhan, China) the WHO reported more than 148 million confirmed cases and 3.1 million losses globally up to now. The causative agent of COVID-19 (SARS-CoV-2) has spread worldwide, resulting in a pandemic of unprecedented magnitude. To date, several clinically safe and efficient vaccines (e.g., Pfizer-BioNTech, Moderna, Johnson & Johnson, and AstraZeneca COVID-19 vaccines) as well as drugs for emergency use have been approved. However, increasing numbers of SARS-Cov-2 variants make it imminent to identify an alternative way to treat SARS-CoV-2 infections. A well-known strategy to identify molecules with inhibitory potential against SARS-CoV-2 proteins is repurposing clinically developed drugs, e.g., antiparasitic drugs. The results described in this study demonstrated the inhibitory potential of quinacrine and suramin against SARS-CoV-2 main protease (3CLpro). Quinacrine and suramin molecules presented a competitive and noncompetitive inhibition mode, respectively, with IC50 values in the low micromolar range. Surface plasmon resonance (SPR) experiments demonstrated that quinacrine and suramin alone possessed a moderate or weak affinity with SARS-CoV-2 3CLpro but suramin binding increased quinacrine interaction by around a factor of eight. Using docking and molecular dynamics simulations, we identified a possible binding mode and the amino acids involved in these interactions. Our results suggested that suramin, in combination with quinacrine, showed promising synergistic efficacy to inhibit SARS-CoV-2 3CLpro. We suppose that the identification of effective, synergistic drug combinations could lead to the design of better treatments for the COVID-19 disease and repurposable drug candidates offer fast therapeutic breakthroughs, mainly in a pandemic moment.

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Macrocyclic Peptides as Allosteric Inhibitors of Nicotinamide N-Methyltransferase (NNMT)

10.26434/chemrxiv.12973130 ◽

2020 ◽

Author(s):

Matthijs J. van Haren ◽

Yurui Zhang ◽

Ned Buijs ◽

Vito Thijssen ◽

Davide Sartini ◽

...

Keyword(s):

Cyclic Peptides ◽

Cyclic Peptide ◽

Peptide Inhibitors ◽

Allosteric Inhibitors ◽

Disease States ◽

Potent Inhibition ◽

Macrocyclic Peptides ◽

Diabetes And Obesity ◽

Substrate Competition

Nicotinamide N-methyltransferase (NNMT) methylates nicotinamide to form 1-methylnicotinamide using S-adenosyl-l-methionine (SAM) as the methyl donor. The complexity of the role of NNMT in healthy and disease states is slowly being elucidated and provides indication that NNMT may be an interesting therapeutic target for a variety of diseases including cancer, diabetes, and obesity. Most inhibitors of NNMT described to date are structurally related to one or both of its substrates. In search of structurally diverse NNMT inhibitors, an mRNA display screening technique was used to identify macrocyclic peptides which bind to NNMT. Several of the cyclic peptides identified in this manner show potent inhibition of NNMT with IC50 values as low as 229 nM. Interestingly, substrate competition experiments reveal that these cyclic peptide inhibitors are noncompetitive with either SAM or NA indicating they may be the first allosteric inhibitors reported for NNMT.

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High Affinity Peptide Inhibitors of the Hepatitis C Virus NS3-4A Protease Refractory to Common Resistant Mutants

Journal of Biological Chemistry ◽

10.1074/jbc.m112.393843 ◽

2012 ◽

Vol 287 (46) ◽

pp. 39224-39232 ◽

Cited By ~ 11

Author(s):

Jonas Kügler ◽

Stefan Schmelz ◽

Juliane Gentzsch ◽

Sibylle Haid ◽

Erik Pollmann ◽

...

Keyword(s):

Hepatitis C Virus ◽

Hepatitis C ◽

Peptide Inhibitors ◽

High Affinity ◽

Resistant Mutants ◽

Affinity Peptide

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Disruption of SND1–MTDH Interaction by a High Affinity Peptide Results in SND1 Degradation and Cytotoxicity to Breast Cancer Cells In Vitro and In Vivo

Molecular Cancer Therapeutics ◽

10.1158/1535-7163.mct-20-0130 ◽

2020 ◽

Vol 20 (1) ◽

pp. 76-84

Author(s):

Peng Li ◽

Yunjiao He ◽

Teng Chen ◽

Kit-Ying Choy ◽

Tsun Sing Chow ◽

...

Keyword(s):

Breast Cancer ◽

Cancer Cells ◽

Breast Cancer Cells ◽

High Affinity ◽

Affinity Peptide

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Identification of Novel and Natural High Affinity Peptide Inhibitors of KcsA by Phage-Display Reveals an Unexpected Mechanism of Pore Blockade

Biophysical Journal ◽

10.1016/j.bpj.2016.11.956 ◽

2017 ◽

Vol 112 (3) ◽

pp. 173a

Author(s):

Ruiming Zhao ◽

Hui Dai ◽

Netanel Mendelman ◽

Luis G. Cuello ◽

Jordan H. Chill ◽

...

Keyword(s):

Phage Display ◽

Peptide Inhibitors ◽

High Affinity ◽

Affinity Peptide

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Systemic Antibacterial Activity of Novel Synthetic Cyclic Peptides

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.49.8.3302-3310.2005 ◽

2005 ◽

Vol 49 (8) ◽

pp. 3302-3310 ◽

Cited By ~ 106

Author(s):

Véronique Dartois ◽

Jorge Sanchez-Quesada ◽

Edelmira Cabezas ◽

Ellen Chi ◽

Chad Dubbelde ◽

...

Keyword(s):

Cyclic Peptides ◽

Prolonged Exposure ◽

Cyclic Peptide ◽

Present Report ◽

Bacterial Load ◽

Pharmacokinetic Profile ◽

Therapeutic Window ◽

Infection Model

ABSTRACT Cyclic peptides with an even number of alternating d,l-α-amino acid residues are known to self-assemble into organic nanotubes. Such peptides previously have been shown to be stable upon protease treatment, membrane active, and bactericidal and to exert antimicrobial activity against Staphylococcus aureus and other gram-positive bacteria. The present report describes the in vitro and in vivo pharmacology of selected members of this cyclic peptide family. The intravenous (i.v.) efficacy of six compounds with MICs of less than 12 μg/ml was tested in peritonitis and neutropenic-mouse thigh infection models. Four of the six peptides were efficacious in vivo, with 50% effective doses in the peritonitis model ranging between 4.0 and 6.7 mg/kg against methicillin-sensitive S. aureus (MSSA). In the thigh infection model, the four peptides reduced the bacterial load 2.1 to 3.0 log units following administration of an 8-mg/kg i.v. dose. Activity against methicillin-resistant S. aureus was similar to MSSA. The murine pharmacokinetic profile of each compound was determined following i.v. bolus injection. Interestingly, those compounds with poor efficacy in vivo displayed a significantly lower maximum concentration of the drug in serum and a higher volume of distribution at steady state than compounds with good therapeutic properties. S. aureus was unable to easily develop spontaneous resistance upon prolonged exposure to the peptides at sublethal concentrations, in agreement with the proposed interaction with multiple components of the bacterial membrane canopy. Although additional structure-activity relationship studies are required to improve the therapeutic window of this class of antimicrobial peptides, our results suggest that these amphipathic cyclic d,l-α-peptides have potential for systemic administration and treatment of otherwise antibiotic-resistant infections.

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