Viral proteases: Structure, mechanism and inhibition

Zephyr, J.; Yilmaz, Neşe Kurt; Schiffer, Celia A.

doi:10.1016/bs.enz.2021.09.004

Cited by 57 publications

(39 citation statements)

References 137 publications

(172 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Nirmatrelvir is the first oral SARS-CoV-2 (3CLpro) protease inhibitor developed for the treatment of COVID-19. Highly potent protease inhibitors have also been developed against HIV and HCV [26]. To avoid resistance development, HIV and HCV protease inhibitors are being used, with great success, in fixed dose combinations with other directly acting antiviral drugs that have a different mechanism of action.…”

Section: Discussionmentioning

confidence: 99%

The substitutions L50F, E166A and L167F in SARS-CoV-2 3CLpro are selected by a protease inhibitorin vitroand confer resistance to nirmatrelvir

Jochmans

Liu²,

Donckers

et al. 2022

Preprint

View full text Add to dashboard Cite

The SARS-CoV-2 main protease (3CLpro) has an indispensable role in the viral life cycle and is a therapeutic target for the treatment of COVID-19. The potential of 3CLpro-inhibitors to select for drug-resistant variants needs to be established. Therefore SARS-CoV-2 was passaged in vitro in the presence of increasing concentrations of ALG-097161, a probe compound designed in the context of a 3CLpro drug discovery program. We identified a combination of amino acid substitutions in 3CLpro (L50F E166A L167F) that is associated with > 20x increase in EC50 values for ALG-097161, nirmatrelvir (PF-07321332) and PF-00835231. While two of the single substitutions (E166A and L167F) provide low-level resistance to the inhibitors in a biochemical assay, the triple mutant results in the highest levels of resistance (6- to 72-fold). All substitutions are associated with a significant loss of enzymatic 3CLpro activity, suggesting a reduction in viral fitness. Structural biology analysis indicates that the different substitutions reduce the number of inhibitor/enzyme interactions while the binding of the substrate is maintained. These observations will be important for the interpretation of resistance development to 3CLpro inhibitors in the clinical setting.

show abstract

Section: Discussionmentioning

confidence: 99%

The substitutions L50F, E166A and L167F in SARS-CoV-2 3CLpro are selected by a protease inhibitorin vitroand confer resistance to nirmatrelvir

Jochmans

Liu²,

Donckers

et al. 2022

Preprint

View full text Add to dashboard Cite

show abstract

“…To date, thousands of candidate SARS-CoV-2 Mpro inhibitor compounds have been screened so far in order to identify potent drug candidates [ 64 ], but many of them were shown to have no or only limited clinical potential since high concentration was usually required to achieve significant inhibition. Actually, most of the investigational 3CLpro inhibitors are of similar peptidomimetic scaffolds [ 65 ].…”

Section: Proteases Inhibitors and Mutationsmentioning

confidence: 99%

“…Some of these positions are more variable (e.g., M49) and thus may be correlated to resistance development, while E166 is conserved due to its importance in the dimerization of the Mpro [ 87 ]. As in the case of HIV-1 PIs, the substrate envelope hypothesis may be a promising strategy of drug design [ 65 ] in order to avoid resistance against SARS-CoV-2 Mpro inhibitors.…”

Section: Proteases Inhibitors and Mutationsmentioning

confidence: 99%

Potential Resistance of SARS-CoV-2 Main Protease (Mpro) against Protease Inhibitors: Lessons Learned from HIV-1 Protease

Mótyán

Mahdi

Hoffka

et al. 2022

IJMS

View full text Add to dashboard Cite

Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome 2 (SARS-CoV-2), has been one of the most devastating pandemics of recent times. The lack of potent novel antivirals had led to global health crises; however, emergence and approval of potent inhibitors of the viral main protease (Mpro), such as Pfizer’s newly approved nirmatrelvir, offers hope not only in the therapeutic front but also in the context of prophylaxis against the infection. By their nature, RNA viruses including human immunodeficiency virus (HIV) have inherently high mutation rates, and lessons learnt from previous and currently ongoing pandemics have taught us that these viruses can easily escape selection pressure through mutation of vital target amino acid residues in monotherapeutic settings. In this paper, we review nirmatrelvir and its binding to SARS-CoV-2 Mpro and draw a comparison to inhibitors of HIV protease that were rendered obsolete by emergence of resistance mutations, emphasizing potential pitfalls in the design of inhibitors that may be of important relevance to the long-term use of novel inhibitors against SARS-CoV-2.

show abstract

“…A crucial point in the replicative cycle of retroviruses is the successful transition from a non-infective virus particles to an infective virion, and the viral retropepsin (PR), a homodimeric aspartic protease, is the main actor involved in this process [13]. Given the biological importance of PR in the viral replication mechanism, the pharmacological use of specific inhibitors of proteolytic activity constitutes a therapeutic strategy with potential clinical impacts [14]. In fact, the PR of Human immunodeficency virus (HIV) is one of the main targets of antiretroviral drugs, and several inhibitors are currently used in the antiviral pharmacological treatment [13,15,16].…”

Section: Introductionmentioning

confidence: 99%

Kinetics of Bovine leukemia virus aspartic protease reveals its dimerization and conformational change

Fló

Carrión²,

Olivero-Deibe³

et al. 2022

PLoS ONE

View full text Add to dashboard Cite

The retropepsin (PR) of the Bovine leukemia virus (BLV) plays, as in other retroviruses, a crucial role in the transition from the non-infective viral particle to the infective virion by processing the polyprotein Gag. PR is expressed as an immature precursor associated with Gag, after an occasional −1 ribosomal frameshifting event. Self-hydrolysis of PR at specific N- and C-terminal sites releases the monomer that dimerizes giving rise to the active protease. We designed a strategy to express BLV PR in E. coli as a fusion protein with maltose binding protein, with a six-histidine tag at its N-terminal end, and bearing a tobacco etch virus protease hydrolysis site. This allowed us to obtain soluble and mature recombinant PR in relatively good yields, with exactly the same amino acid composition as the native protein. As PR presents relative promiscuity for the hydrolysis sites we designed four fluorogenic peptide substrates based on Förster resonance energy transfer (FRET) in order to characterize the activity of the recombinant enzyme. These substrates opened the way to perform kinetic studies, allowing us to characterize the dimer-monomer equilibrium. Furthermore, we obtained kinetic evidence for the existence of a conformational change that enables the interaction with the substrate. These results constitute a starting point for the elucidation of the kinetic properties of BLV-PR, and may be relevant not only to improve the chemical warfare against this virus but also to better understand other viral PRs.

show abstract

Viral proteases: Structure, mechanism and inhibition

Cited by 57 publications

References 137 publications

The substitutions L50F, E166A and L167F in SARS-CoV-2 3CLpro are selected by a protease inhibitorin vitroand confer resistance to nirmatrelvir

The substitutions L50F, E166A and L167F in SARS-CoV-2 3CLpro are selected by a protease inhibitorin vitroand confer resistance to nirmatrelvir

Potential Resistance of SARS-CoV-2 Main Protease (Mpro) against Protease Inhibitors: Lessons Learned from HIV-1 Protease

Kinetics of Bovine leukemia virus aspartic protease reveals its dimerization and conformational change

Contact Info

Product

Resources

About