scholarly journals Structure and inhibition of the SARS-CoV-2 main protease reveal strategy for developing dual inhibitors against Mpro and cathepsin L

2020 ◽  
Vol 6 (50) ◽  
pp. eabe0751 ◽  
Author(s):  
Michael Dominic Sacco ◽  
Chunlong Ma ◽  
Panagiotis Lagarias ◽  
Ang Gao ◽  
Julia Alma Townsend ◽  
...  
Keyword(s):  
Viral Entry ◽  
Cathepsin L ◽  
Antiviral Drug ◽  
Side Chain ◽  
Calpain Inhibitor ◽  
Main Protease ◽  
New Directions ◽  
Dual Inhibitors ◽  
Hydrophilic Residue ◽  
Calpain Inhibitors

The main protease (Mpro) of SARS-CoV-2 is a key antiviral drug target. While most Mpro inhibitors have a γ-lactam glutamine surrogate at the P1 position, we recently found that several Mpro inhibitors have hydrophobic moieties at the P1 site, including calpain inhibitors II and XII, which are also active against human cathepsin L, a host protease that is important for viral entry. In this study, we solved x-ray crystal structures of Mpro in complex with calpain inhibitors II and XII and three analogs of GC-376. The structure of Mpro with calpain inhibitor II confirmed that the S1 pocket can accommodate a hydrophobic methionine side chain, challenging the idea that a hydrophilic residue is necessary at this position. The structure of calpain inhibitor XII revealed an unexpected, inverted binding pose. Together, the biochemical, computational, structural, and cellular data presented herein provide new directions for the development of dual inhibitors as SARS-CoV-2 antivirals.

scholarly journals Structure and inhibition of the SARS-CoV-2 main protease reveals strategy for developing dual inhibitors against Mpro and cathepsin L

2020 ◽  
Author(s):  
Michael Dominic Sacco ◽  
Chunlong Ma ◽  
Panagiotis Lagarias ◽  
Ang Gao ◽  
Julia Alma Townsend ◽  
...  
Keyword(s):  
Viral Entry ◽  
Cathepsin L ◽  
Antiviral Drug ◽  
Binding Mode ◽  
Calpain Inhibitor ◽  
Catalytic Core ◽  
Main Protease ◽  
Dual Inhibitors ◽  
Calpain Inhibitors

AbstractThe main protease (Mpro) of SARS-CoV-2, the pathogen responsible for the COVID-19 pandemic, is a key antiviral drug target. While most SARS-CoV-2 Mpro inhibitors have a γ-lactam glutamine surrogate at the P1 position, we recently discovered several Mpro inhibitors have hydrophobic moieties at the P1 site, including calpain inhibitors II/XII, which are also active against human cathepsin L, a host-protease that is important for viral entry. To determine the binding mode of these calpain inhibitors and establish a structure-activity relationship, we solved X-ray crystal structures of Mpro in complex with calpain inhibitors II and XII, and three analogues of GC-376, one of the most potent Mpro inhibitors in vitro. The structure of Mpro with calpain inhibitor II confirmed the S1 pocket of Mpro can accommodate a hydrophobic methionine side chain, challenging the idea that a hydrophilic residue is necessary at this position. Interestingly, the structure of calpain inhibitor XII revealed an unexpected, inverted binding pose where the P1’ pyridine inserts in the S1 pocket and the P1 norvaline is positioned in the S1’ pocket. The overall conformation is semi-helical, wrapping around the catalytic core, in contrast to the extended conformation of other peptidomimetic inhibitors. Additionally, the structures of three GC-376 analogues UAWJ246, UAWJ247, and UAWJ248 provide insight to the sidechain preference of the S1’, S2, S3 and S4 pockets, and the superior cell-based activity of the aldehyde warhead compared with the α-ketoamide. Taken together, the biochemical, computational, structural, and cellular data presented herein provide new directions for the development of Mpro inhibitors as SARS-CoV-2 antivirals.

scholarly journals Boceprevir, calpain inhibitors II and XII, and GC-376 have broad-spectrum antiviral activity against coronaviruses in cell culture

2020 ◽  
Author(s):  
Yanmei Hu ◽  
Chunlong Ma ◽  
Tommy Szeto ◽  
Brett Hurst ◽  
Bart Tarbet ◽  
...  
Keyword(s):  
Cell Culture ◽  
Antiviral Activity ◽  
Cathepsin L ◽  
Antiviral Drug ◽  
Antiviral Effect ◽  
Neutralization Assay ◽  
Drug Candidates ◽  
Main Protease ◽  
Human Coronaviruses ◽  
Calpain Inhibitors

AbstractAs the COVID-19 pandemic continues to fold out, the morbidity and mortality are increasing daily. Effective treatment for SARS-CoV-2 is urgently needed. We recently discovered four SARS-CoV-2 main protease (Mpro) inhibitors including boceprevir, calpain inhibitors II and XII and GC-376 with potent antiviral activity against infectious SARS-CoV-2 in cell culture. Despite the weaker enzymatic inhibition of calpain inhibitors II and XII against Mpro compared to GC-376, calpain inhibitors II and XII had more potent cellular antiviral activity. This observation promoted us to hypothesize that the cellular antiviral activity of calpain inhibitors II and XII might also involve the inhibition of cathepsin L in addition to Mpro. To test this hypothesis, we tested calpain inhibitors II and XII in the SARS-CoV-2 pseudovirus neutralization assay in Vero E6 cells and found that both compounds significantly decreased pseudoviral particle entry into cells, indicating their role in inhibiting cathepsin L. The involvement of cathepsin L was further confirmed in the drug time-of-addition experiment. In addition, we found that these four compounds not only inhibit SARS-CoV-2, but also SARS-CoV, MERS-CoV, as well as human coronaviruses (CoVs) 229E, OC43, and NL63. The mechanism of action is through targeting the viral Mpro, which was supported by the thermal shift binding assay and enzymatic FRET assay. We further showed that these four compounds have additive antiviral effect when combined with remdesivir. Altogether, these results suggest that boceprevir, calpain inhibitors II and XII, and GC-376 are not only promising antiviral drug candidates against existing human coronaviruses, but also might work against future emerging CoVs.

An expedited approach towards the rationale design of non-covalent SARS-CoV-2 main protease inhibitors with in vitro antiviral activity

2020 ◽  
Author(s):  
Naoya Kitamura ◽  
Michael Dominic Sacco ◽  
Chunlong Ma ◽  
Yanmei Hu ◽  
Julia Alma Townsend ◽  
...  
Keyword(s):  
Antiviral Activity ◽  
Binding Site ◽  
Antiviral Drug ◽  
Binding Pocket ◽  
Native Mass Spectrometry ◽  
Calpain Inhibitor ◽  
Site Analysis ◽  
Main Protease ◽  
Covalent Inhibitors

AbstractThe main protease (Mpro) of SARS-CoV-2 is a validated antiviral drug target. Several Mpro inhibitors have been reported with potent enzymatic inhibition and cellular antiviral activity, including GC376, boceprevir, calpain inhibitors II and XII, each containing a reactive warhead that covalently modifies the catalytic Cys145. In this study, we report an expedited drug discovery approach by coupling structure-based design and Ugi four-component (Ugi-4CR) reaction methodology to the design of non-covalent Mpro inhibitors. The most potent compound 23R had cellular antiviral activity similar to covalent inhibitors such as GC376. Our designs were guided by overlaying the structure of SARS-CoV Mpro + ML188 (R), a non-covalent inhibitor derived from Ug-4CR, with the X-ray crystal structures of SARS-CoV-2 Mpro + calpain inhibitor XII/GC376/UAWJ247. Binding site analysis suggests a strategy of extending the P2 and P3 substitutions in ML188 (R) to achieve optimal shape complementary with SARS-CoV-2 Mpro. Lead optimization led to the discovery of 23R, which inhibits SARS-CoV-2 Mpro and SARS-CoV-2 viral replication with an IC50 of 0.31 μM and EC50 of 1.27 μM, respectively. The binding and specificity of 23R to SARS-CoV-2 Mpro were confirmed in a thermal shift assay and native mass spectrometry assay. The co-crystal structure of SARS-CoV-2 Mpro with 23R revealed the P2 biphenyl fits snuggly into the S2 pocket and the benzyl group in the α-methylbenzyl faces towards the core of the enzyme, occupying a previously unexplored binding site located in between the S2 and S4 pockets. Overall, this study revealed the most potent non-covalent SARS-CoV-2 Mpro inhibitors reported to date and a novel binding pocket that can be explored for Mpro inhibitor design.

scholarly journals The dimer-monomer equilibrium of SARS-CoV-2 main protease is affected by small molecule inhibitors

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Lucia Silvestrini ◽  
Norhan Belhaj ◽  
Lucia Comez ◽  
Yuri Gerelli ◽  
Antonino Lauria ◽  
...  
Keyword(s):  
Enzymatic Activity ◽  
Dissociation Constant ◽  
Molecular Mechanisms ◽  
Antiviral Drug ◽  
Structural Features ◽  
Experimental Information ◽  
Detailed Knowledge ◽  
Main Protease ◽  
Equilibrium Dissociation ◽  
Drug Leads

AbstractThe maturation of coronavirus SARS-CoV-2, which is the etiological agent at the origin of the COVID-19 pandemic, requires a main protease Mpro to cleave the virus-encoded polyproteins. Despite a wealth of experimental information already available, there is wide disagreement about the Mpro monomer-dimer equilibrium dissociation constant. Since the functional unit of Mpro is a homodimer, the detailed knowledge of the thermodynamics of this equilibrium is a key piece of information for possible therapeutic intervention, with small molecules interfering with dimerization being potential broad-spectrum antiviral drug leads. In the present study, we exploit Small Angle X-ray Scattering (SAXS) to investigate the structural features of SARS-CoV-2 Mpro in solution as a function of protein concentration and temperature. A detailed thermodynamic picture of the monomer-dimer equilibrium is derived, together with the temperature-dependent value of the dissociation constant. SAXS is also used to study how the Mpro dissociation process is affected by small inhibitors selected by virtual screening. We find that these inhibitors affect dimerization and enzymatic activity to a different extent and sometimes in an opposite way, likely due to the different molecular mechanisms underlying the two processes. The Mpro residues that emerge as key to optimize both dissociation and enzymatic activity inhibition are discussed.

scholarly journals The Anti-Viral Applications of Marine Resources for COVID-19 Treatment: An Overview

Marine Drugs ◽  
2021 ◽  
Vol 19 (8) ◽  
pp. 409
Author(s):  
Sarah Geahchan ◽  
Hermann Ehrlich ◽  
M. Azizur Rahman
Keyword(s):  
Viral Entry ◽  
Marine Sponges ◽  
Sulfated Polysaccharides ◽  
Marine Resources ◽  
Active Metabolites ◽  
Marine Metabolites ◽  
Main Protease ◽  
Novel Drug ◽  
First Time ◽  
Potential Therapeutics

The ongoing pandemic has led to an urgent need for novel drug discovery and potential therapeutics for Sars-CoV-2 infected patients. Although Remdesivir and the anti-inflammatory agent dexamethasone are currently on the market for treatment, Remdesivir lacks full efficacy and thus, more drugs are needed. This review was conducted through literature search of PubMed, MDPI, Google Scholar and Scopus. Upon review of existing literature, it is evident that marine organisms harbor numerous active metabolites with anti-viral properties that serve as potential leads for COVID-19 therapy. Inorganic polyphosphates (polyP) naturally found in marine bacteria and sponges have been shown to prevent viral entry, induce the innate immune response, and downregulate human ACE-2. Furthermore, several marine metabolites isolated from diverse sponges and algae have been shown to inhibit main protease (Mpro), a crucial protein required for the viral life cycle. Sulfated polysaccharides have also been shown to have potent anti-viral effects due to their anionic properties and high molecular weight. Likewise, select marine sponges produce bromotyrosines which have been shown to prevent viral entry, replication and protein synthesis. The numerous compounds isolated from marine resources demonstrate significant potential against COVID-19. The present review for the first time highlights marine bioactive compounds, their sources, and their anti-viral mechanisms of action, with a focus on potential COVID-19 treatment.

scholarly journals COVID-19/SARS-CoV-2 Infection: Lysosomes and Lysosomotropism Implicate New Treatment Strategies and Personal Risks

2020 ◽  
Vol 21 (14) ◽  
pp. 4953 ◽  
Author(s):  
Markus Blaess ◽  
Lars Kaiser ◽  
Martin Sauer ◽  
René Csuk ◽  
Hans-Peter Deigner
Keyword(s):  
Viral Entry ◽  
Cathepsin L ◽  
Treatment Strategies ◽  
Disease Process ◽  
Host Cells ◽  
Cytokine Release ◽  
Early Administration ◽  
Lysosomal Ph ◽  
New Treatment ◽  
Exposure Prophylaxis

In line with SARS and MERS, the SARS-CoV-2/COVID-19 pandemic is one of the largest challenges in medicine and health care worldwide. SARS-CoV-2 infection/COVID-19 provides numerous therapeutic targets, each of them promising, but not leading to the success of therapy to date. Neither an antiviral nor an immunomodulatory therapy in patients with SARS-CoV-2 infection/COVID-19 or pre-exposure prophylaxis against SARS-CoV-2 has proved to be effective. In this review, we try to close the gap and point out the likely relationships among lysosomotropism, increasing lysosomal pH, SARS-CoV-2 infection, and disease process, and we deduce an approach for the treatment and prophylaxis of COVID-19, and cytokine release syndrome (CRS)/cytokine storm triggered by bacteria or viruses. Lysosomotropic compounds affect prominent inflammatory messengers (e.g., IL-1B, CCL4, CCL20, and IL-6), cathepsin-L-dependent viral entry of host cells, and products of lysosomal enzymes that promote endothelial stress response in systemic inflammation. As supported by recent clinical data, patients who have already taken lysosomotropic drugs for other pre-existing conditions likely benefit from this treatment in the COVID-19 pandemic. The early administration of a combination of antivirals such as remdesivir and lysosomotropic drugs, such as the antibiotics teicoplanin or dalbavancin, seems to be able to prevent SARS-CoV-2 infection and transition to COVID-19.

scholarly journals Middle East Respiratory Syndrome Coronavirus Spike Protein Is Not Activated Directly by Cellular Furin during Viral Entry into Target Cells

2018 ◽  
Vol 92 (19) ◽  
Author(s):  
Shutoku Matsuyama ◽  
Kazuya Shirato ◽  
Miyuki Kawase ◽  
Yutaka Terada ◽  
Kengo Kawachi ◽  
...  
Keyword(s):  
Middle East ◽  
Viral Entry ◽  
Cathepsin L ◽  
Inhibitory Effect ◽  
Middle East Respiratory Syndrome ◽  
Cell Entry ◽  
Target Cells ◽  
Furin Cleavage ◽  
S Protein ◽  
Entry Assay

ABSTRACT Middle East respiratory syndrome coronavirus (MERS-CoV) utilizes host cellular proteases to enter cells. A previous report shows that furin, which is distributed mainly in the Golgi apparatus and cycled to the cell surface and endosomes, proteolytically activates the MERS-CoV spike (S) protein following receptor binding to mediate fusion between the viral and cellular membranes. In this study, we reexamined furin usage by MERS-CoV using a real-time PCR-based virus cell entry assay after inhibition of cellular proteases. We found that the furin inhibitor dec-RVKR-CMK blocked entry of MERS-CoV harboring an S protein lacking furin cleavage sites; it even blocked entry into furin-deficient LoVo cells. In addition, dec-RVKR-CMK inhibited not only the enzymatic activity of furin but also those of cathepsin L, cathepsin B, trypsin, papain, and TMPRSS2. Furthermore, a virus cell entry assay and a cell-cell fusion assay provided no evidence that the S protein was activated by exogenous furin. Therefore, we conclude that furin does not play a role in entry of MERS-CoV into cells and that the inhibitory effect of dec-RVKR-CMK is specific for TMPRSS2 and cathepsin L rather than furin. IMPORTANCE Previous studies using the furin inhibitor dec-RVKR-CMK suggest that MERS-CoV utilizes a cellular protease, furin, to activate viral glycoproteins during cell entry. However, we found that dec-RVKR-CMK inhibits not only furin but also other proteases. Furthermore, we found no evidence that MERS-CoV uses furin. These findings suggest that previous studies in the virology field based on dec-RVKR-CMK should be reexamined carefully. Here we describe appropriate experiments that can be used to assess the effect of protease inhibitors on virus cell entry.

scholarly journals Potential Binding Efficiency of Antiviral Drug Lopinavir Targeted to the Catalytic Dyad, His41 - Cys145 of SARS CoV -2 Main Protease

2020 ◽  
Author(s):  
Muthu Raj S ◽  
Manohar M ◽  
Mohan M ◽  
Ganesh P ◽  
Marimuthu K
Keyword(s):  
Antiviral Drug ◽  
Emergency Situation ◽  
Viral Disease ◽  
New Drugs ◽  
Viral Population ◽  
Protease Inhibition ◽  
Main Protease ◽  
Model Drug ◽  
Approved Drugs ◽  
Catalytic Dyad

<p>The spread of SARS CoV 2 across the globe rushed the scientific community to find out the potential inhibitor for controlling the viral disease. The main protease (Mpro) or Chymotrypsin protease (3CLpro) is involved in the cleavage of polyproteins, duplication of intracellular materials and release of nonstructural proteins. Cys-His catalytic dyad is located in the SARS-CoV Mpro which is the substrate-binding site located in domains I and II. There are many approved drugs that have their active protease inhibition capability. The targeting of the active site of the main protease is the better option to fight against the viral population. Lopinavir, ritonavir, Remdesivir and Chloroquine are some of the drug candidates considered to be involved in the treatment of SARS CoV 2 under emergency situation as a trial basis. In the present investigation we used lopinavir as a drug to bind the catalytic dyad His41, Cys145 of main protease. The minimum binding of energy of -11.45 kcal/mol observed with the binding of Cys145 and -10.93 kcal/mol was noted with the residue His41. The inhibition constant was also found to be relevant to the binding efficiency of the drug. This is considered to be a model drug target which is initiating the finding of many new drugs to target the current outbreak created by the virus SARS.CoV - 2.</p>

scholarly journals Effects of a Caspase and a Calpain Inhibitor on Resting Energy Expenditures in Normal and Hypermetabolic Rats: a Pilot Study

2016 ◽  
pp. 537-541 ◽  
Author(s):  
P. G. VANA ◽  
H. M. LAPORTE ◽  
R. H. KENNEDY ◽  
R. L. GAMELLI ◽  
M. MAJETSCHAK
Keyword(s):  
Whole Body ◽  
Calpain Inhibitor ◽  
Protein Loss ◽  
Body Protein ◽  
Physiological Conditions ◽  
Energy Expenditures ◽  
Calpain Inhibitors ◽  
Caspase Cascades ◽  
Observation Period ◽  
Resting Energy

Several diseases induce hypermetabolism, which is characterized by increases in resting energy expenditures (REE) and whole body protein loss. Exaggerated protein degradation is thought to be the driving force underlying this response. The effects of caspase and calpain inhibitors on REE in physiological and hypermetabolic conditions, however, are unknown. Thus, we studied whether MDL28170 (calpain inhibitor) or z-VAD-fmk (caspase inhibitor) affect REE under physiological conditions and during hypermetabolism post-burn. Rats were treated five times weekly and observed for 6 weeks. Treatment was started 2 h (early) or 48 h (late) after burn. In normal rats, MDL28170 transiently increased REE to 130 % of normal during week 2-4. z-VAD-fmk reduced REE by 20-25 % throughout the observation period. Within 14 days after burns, REE increased to 130±5 %. Whereas MDL28170/early treatment did not affect REE, MDL28170/late transiently increased REE to 180±10 % of normal by week 4 post-burn. In contrast, with z-VAD-fmk/early REE remained between 90-110 % of normal post-burn. z-VAD-fmk/late did not affect burn-induced increases in REE. These data suggest that caspase cascades contribute to the development of hypermetabolism and that burn-induced hypermetabolism can be pharmacologically modulated. Our data point towards caspase cascades as possible therapeutic targets to attenuate hypermetabolism after burns, and possibly in other catabolic disease processes.

Computational screening of dual inhibitors from FDA approved antiviral drugs on SARS-CoV-2 spike protein and the main protease using molecular docking approach

2021 ◽  
Vol 65 (02) ◽  
pp. 160-172
Author(s):  
Shanthi Sabarimurugan ◽  
Indu Purushothaman ◽  
Rajarajan Swaminathan ◽  
Arun Dharmarajan ◽  
Sudha Warrier ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Antiviral Drugs ◽  
Spike Protein ◽  
Computational Screening ◽  
Main Protease ◽  
Docking Approach ◽  
Dual Inhibitors
Sign in / Sign up

Export Citation Format

Share Document