Recent advances in the synthesis, design and selection of cysteine protease inhibitors

doi:10.1016/S1367-5931(02)00345-9

Current Opinion in Chemical Biology

Volume 6, Issue 4, 1 August 2002, Pages 459-465

https://doi.org/10.1016/S1367-5931(02)00345-9 Get rights and content

Abstract

Inhibition of cysteine proteases is emerging as an important strategy for the treatment of a variety of human diseases. Intense efforts involving structure-based inhibitor design have been directed toward several cysteine proteases, including cathepsin K, calpain, human rhinovirus 3C protease and several parasitic cysteine protease targets. Other successful recent efforts have involved combinatorial synthesis and screening for identification of new inhibitor templates.

Introduction

The cysteine proteases are a large group of enzymes that play roles in a broad range of biological processes 1., 2.. However, imbalances in the normal expression of human cysteine proteases or involvement of parasitic or viral cysteine proteases are associated with a variety of pathological conditions.

Inhibition of cysteine proteases represents a potential strategy for chemotherapy in such cases. Three structurally different classes of cysteine proteases are current targets for drug design: the papain family, the caspases and the picornaviridae family.

Many cysteine protease targets belong to the papain superfamily, including the cysteinyl cathepsins, calpains [3] and parasitic cysteine proteases that are critical to the life cycle or pathogenicity of parasitic protozoans. The caspases are effectors of apoptosis, or programmed cell death [4]. Cells that undergo apoptosis are activated by a series of caspases that cleave critical cellular substrates. The caspases are topologically different from the papain-family cysteine proteases and are characterized by an almost absolute specificity for aspartic acid in the P₁ position next to the cleavage site. Picornaviruses are involved in diseases such as the common cold, poliomyelitis and hepatitis. During maturation of infectious virions, a single polyprotein precursor is cleaved at specific points by cysteine proteases that also originate from this precursor protein. Accordingly, inhibition of picornaviral proteases is regarded as a promising approach to antiviral chemotherapy 5., 6..

This review focuses on the development of low-molecular-weight inhibitors of cysteine proteases reported in 2001 and early 2002. A few papers from late 2000 that have not been previously reviewed have also been included in this brief review.

Section snippets

Cysteine protease inhibitors deriving from library synthesis

Several cysteine protease inhibitors have resulted from efforts involving combinatorial syntheses (Fig. 1). Michael acceptor 1 was developed from a library generated by copper-(II)-catalyzed transamination of solid-supported peptides with glyoxylate. The resulting library of α-ketoamide peptide isosteres was further elaborated by oxime formation, hydride reduction, reductive amination and addition of appropriate acylating agents. Importantly, use of novel oxirane and oxetane-modified

Structure- or mechanism-based design of papain-family cysteine protease inhibitors

Many recent reports focus on the design of inhibitors of specific papain-family cysteine proteases (Fig. 2). These efforts are often guided by X-ray structural information and/or insights deriving from the mechanism and substrate specificities of the enzyme targets. Dipeptidyl dipeptidase is an exopeptidase that is highly expressed in cytotoxic lymphocytes and activates granzymes involved in apoptosis. Peptidyl vinyl sulfone derivatives were found to be irreversible inhibitors of dipeptidyl

Calpain Inhibitors

The peptidyl α-hydroxamate scaffold has been employed for the design of reversible inhibitors of calpain I (Fig. 4). Two groups identified hydroxamate 21 as the most potent compound in the series (IC₅₀ = 6 nM). The N-alkoxy substituent increases the potency by strengthening the hydrogen bonding between the hydroxamate NH of the inhibitor and the S′1 site of calpain 34., 35.. Peptidyl methyl ketone inhibitors bearing leaving groups derived from HOBT (1-hydroxybenzotriazole) and other

Caspase inhibitors

The Pfizer–BASF group reported structure-based design of reversible, non-peptidic inhibitors of caspase-1. Caspase-1 has a role in peripheral inflammatory disorders and apoptosis. The required P₁ aspartic residue was maintained in a series of biphenyl sulfonamides such as 27, which is a low-micromolar-level inhibitor (Fig. 6). Replacement of the biphenyl sulfonamide for the biphenyl ether sulfonamide in 28 (K_i = 0.11 μM) provided a 20-fold increase in activity because of improved hydrophobic

Inhibitors of picornaviral cysteine proteases

Scientists at Merck reported the discovery of 2-methoxystypandrone 30 (Fig. 7) as a time-dependent inhibitor of human rhinovirus (HRV) 3C protease (IC₅₀ = 4.6 μM) [44]. The synthesis and structure–activity relationships of naphtoquinone analogs were also reported.

The Agouron–Pfizer groups have reported their latest efforts in the design and optimization of tripeptidyl C-terminal α,β-unsaturated esters as irreversible inhibitors of HRV 3C protease. Michael acceptor inhibitors 31 with an ester

Conclusions

Cysteine proteases are the focus of numerous efforts to develop new chemotherapeutic strategies for a variety of diseases. The potential of the design of inhibitor libraries suitable for on-bead screening in identification of new leads and the intense activity on development of potent peptidomimetic inhibitors of cathepsin K, calpain I and HRV 3C protease augur well for significant future advances in this field. The identification of new non-peptidic inhibitor templates has allowed the

Acknowledgements

We gratefully acknowledge research support provided by the National Institutes of Health (Program Project Grant AI 35707).

References and recommended reading

Papers of particular interest, published within the annual period of review, have been highlighted as:

• of special interest
•• of outstanding interest

References (46)

M.G. Grütter
Caspases: key players in programmed cell death
Curr Opin Struct Biol
(2000)
J. Seipelt et al.
The structures of picornaviral proteinases
Virus Res
(1999)
M.A. McKinlay
Recent advances in the treatment of rhinovirus infections
Curr Opin Pharm
(2001)
M. Nakamura et al.
A two-step, one-pot synthesis of diverse N-pyruvoyl amino acid derivatives using the Ugi reaction
Bioorg Med Chem Lett
(2000)
G.E. Korver et al.
Dipeptide vinyl sulfones suitable for intracellular inhibition of dipeptidyl peptidase I
Int Immunopharm
(2001)
W.R. Roush et al.
Potent second generation vinyl sulfonamide inhibitors of the trypanosomal cysteine protease cruzain
Bioorg Med Chem Lett
(2001)
A.E. Fenwick et al.
Solid-phase synthesis of cyclic alkoxyketones, inhibitors of the cysteine protease cathepsin K
Bioorg Med Chem Lett
(2001)
A.E. Fenwick et al.
Diastereoselective synthesis, activity and chiral stability of cyclic alkoxyketone inhibitors of cathepsin K
Bioorg Med Chem Lett
(2001)
I.E. James et al.
Potent and selective cathepsin l inhibitors do not inhibit human osteoclast resorption in vitro
J Biol Chem
(2001)
R.A. Smith et al.
Discovery and parallel synthesis of a new class of cathepsin K inhibitors
Bioorg Med Chem Lett
(2001)

S.B. Singh et al.

Discovery, total synthesis, HRV 3C-protease inhibitory activity, and structure-activity relationships of 2-methoxystypandrone and its analogues

Bioorg Med Chem Lett

(2001)

Cited by (76)

Calpains for dummies: What you need to know about the calpain family
2021, Biochimica et Biophysica Acta - Proteins and Proteomics
This review was written in memory of our late friend, Dr. Hiroyuki Sorimachi, who, following the steps of his mentor Koichi Suzuki, a pioneer in calpain research, has made tremendous contributions to the field. During his career, Hiro also wrote several reviews on calpain, the last of which, published in 2016, was comprehensive. In this manuscript, we decided to put together a review with the basic information a novice may need to know about calpains. We also tried to avoid similarities with previous reviews and reported the most significant new findings, at the same time highlighting Hiro's contributions to the field. The review will cover a short history of calpain discovery, the presentation of the family, the life of calpain from transcription to activity, human diseases caused by calpain mutations and therapeutic perspectives.
Some thiocarbamoyl based novel anticathepsin agents
2020, Bioorganic Chemistry
Cathepsins have emerged as important targets in various tissues degenerative disorders due to their involvement in degradation of extracellular matrices and endogenous protein turnover. Elevated cathepsins levels vis-à-vis decreased concentration of endogenous inhibitors has been reported at different diseased sites. The design and synthesis of specific potential anti-cathepsin agents is therefore of great significance. Most of potential anti-cathepsin agents developed have peptide based structures with an active warhead. Due to oral instability and immunogenic problems related to peptidyl inhibitors drift the synthesis and evaluation of non-peptide cathepsin inhibitors in last two decades. The present work provides a detailed structure activity relationship for developing potential non-peptide anticathepsin agents based on in-vitro inhibition studies of a library of synthesized thiocarbamoyl- non-peptide inhibitors.
Opportunities and challenges for the development of covalent chemical immunomodulators
2019, Bioorganic and Medicinal Chemistry
Compounds that react irreversibly with cysteines have reemerged as potent and selective tools for altering protein function, serving as chemical probes and even clinically approved drugs. The exquisite sensitivity of human immune cell signaling pathways to oxidative stress indicates the likely, yet still underexploited, general utility of covalent probes for selective chemical immunomodulation. Here, we provide an overview of immunomodulatory cysteines, including identification of electrophilic compounds available to label these residues. We focus our discussion on three protein classes essential for cell signaling, which span the ‘druggability’ spectrum from amenable to chemical probes (kinases), somewhat druggable (proteases), to inaccessible (phosphatases). Using existing inhibitors as a guide, we identify general strategies to guide the development of covalent probes for selected undruggable classes of proteins and propose the application of such compounds to alter immune cell functions.
Cysteine proteases as therapeutic targets: Does selectivity matter? A systematic review of calpain and cathepsin inhibitors
2015, Acta Pharmaceutica Sinica B
Citation Excerpt :
This review will focus on approaches to inhibition of two families of protease enzymes, calpains and cathepsins, of interest in neurodegeneration and cancer therapy and the quixotic pursuit of selectivity. Cathepsin inhibitors have been reviewed recently by Turk et al.2 and earlier by Hernandez and Roush3. A review specific to cathepsin B inhibitors has also been published by Frlan and Gobec4.
Cysteine proteases continue to provide validated targets for treatment of human diseases. In neurodegenerative disorders, multiple cysteine proteases provide targets for enzyme inhibitors, notably caspases, calpains, and cathepsins. The reactive, active-site cysteine provides specificity for many inhibitor designs over other families of proteases, such as aspartate and serine; however, a) inhibitor strategies often use covalent enzyme modification, and b) obtaining selectivity within families of cysteine proteases and their isozymes is problematic. This review provides a general update on strategies for cysteine protease inhibitor design and a focus on cathepsin B and calpain 1 as drug targets for neurodegenerative disorders; the latter focus providing an interesting query for the contemporary assumptions that irreversible, covalent protein modification and low selectivity are anathema to therapeutic safety and efficacy.
In silico modeling and docking studies of Soap Nut Trypsin Inhibitor
2012, Process Biochemistry
Citation Excerpt :
Inhibition of cysteine proteases is emerging as an important strategy for the treatment of a variety of human diseases. Intense efforts involving structure-based inhibitor design have been directed towards several cysteine proteases, including cathepsin K, calpain, human rhinovirus 3C protease and several parasitic cysteine protease targets [27]. Phase II trials of two PIs have recently been reported.
Soap nut trypsin inhibitor (SNTI), an inhibitory protein was isolated and purified from the seeds of Sapindus trifoliatus by ammonium sulphate precipitation followed by ion-exchange and gel filtration chromatographic techniques and was found to be homogenous by PAGE. Using advanced proteomic techniques like MALDI-TOF the inhibitor was sequenced and analyzed using MASCOT software. A refined 3D model of the structure was predicted by in silico technique like homology modeling. The docked interactions between the predicted structure of SNTI and bovine trypsin were studied using ClusPro 2.0. Further docking results indicate that residues within the receptor binding domain include N145, R241, P242, L243, R244, R249, E266 and R275 respectively which play a key role in protein–protein interaction between SNTI and 3MFJ (bovine trypsin). SNTI was also known to exhibit potent anti-fungal activity against dandruff causing fungi. This study provides an insight into the structure of SNTI and also gives an idea about potential sites responsible for inhibitory action that could further be substantiated by experimental investigations.
On the origins of SARS-CoV-2 main protease inhibitors
2023, RSC Medicinal Chemistry

View all citing articles on Scopus

View full text

ReviewRecent advances in the synthesis, design and selection of cysteine protease inhibitors

Abstract

Introduction

Section snippets

Cysteine protease inhibitors deriving from library synthesis

Structure- or mechanism-based design of papain-family cysteine protease inhibitors

Calpain Inhibitors

Caspase inhibitors

Inhibitors of picornaviral cysteine proteases

Conclusions

Acknowledgements

References and recommended reading

Curr Opin Struct Biol

Virus Res

Curr Opin Pharm

Bioorg Med Chem Lett

Int Immunopharm

Bioorg Med Chem Lett

Bioorg Med Chem Lett

Bioorg Med Chem Lett

J Biol Chem

Bioorg Med Chem Lett

Bioorg Med Chem Lett

FEBS Lett

Mol Biochem Parasitol

Bioorg Med Chem Lett

Bioorg Med Chem Lett

Bioorg Med Chem Lett

Bioorg Med Chem Lett

Bioorg Med Chem Lett

Bioorg Med Chem Lett

Bioorg Med Chem

Bioorg Med Chem Lett

Bioorg Med Chem

Bioorg Med Chem Lett

Review
Recent advances in the synthesis, design and selection of cysteine protease inhibitors