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Logo of nihpaAbout Author manuscriptsSubmit a manuscriptHHS Public Access; Author Manuscript; Accepted for publication in peer reviewed journal;
Curr Top Med Chem. Author manuscript; available in PMC 2010 July 23.
Published in final edited form as:
PMCID: PMC2909000

The Identification, Characterization and Optimization of Small Molecule Probes of Cysteine Proteases: Experiences of the Penn Center for Molecular Discovery with Cathepsin B and Cathepsin L


During the pilot phase of the NIH Molecular Library Screening Network, the Penn Center for Molecular Discovery focused on a series of projects aimed at high throughput screening and the development of probes of a variety of protease targets. This review provides our medicinal chemistry experience with two such targets – cathepsin B and cathepsin L. We describe our approach for hit validation, characterization and triage that led to a critical understanding of the nature of hits from the cathepsin B project. In addition, we detail our experience at hit identification and optimization that led to the development of a novel thiocarbazate probe of cathepsin L.

Keywords: cathepsin B, cathepsin L, cysteine proteases, DTT, false positives, hit validation, hit triage, redox cycling, thiocarbazates


As part of the Molecular Libraries Screening Center Network (MLSCN),i,ii the Penn Center for Molecular Discovery (PCMD)iii undertook a series of high throughput screening (HTS) campaigns targeting a variety of proteases, particularly members of the papain-class of cysteine proteases. Completion of the screens was followed by hit evaluation, characterization and triage, and when appropriate, medicinal chemistry optimization to improve potency and/or properties to develop small molecule probes of these proteases. This effort had several goals. First, our work would produce a sizeable data set thoroughly profiling a large compound library in a wide number of protease assays. While numerous inhibitors of proteases have been described in the literature,iv the published data on these compounds typically includes the specific target activity along with selectivity against a handful of genomically-related or pharmacologically and toxicologically relevant enzymes. Second, this effort would contribute to the NIH Roadmap Initiative to annotate the NIH Small Molecule Repository (NIH SMR), by making data from high throughput screening campaigns on biomedical targets, physicochemical characterization assays, and toxicity profiling publicly available via PubChem.v Finally, we were particularly interested in following up reports on the essential roles that cathepsin B and L play in allowing entry of SARS-coronavirus and Ebola viruses into host We sought potent, selective, cell-permeable inhibitors that would allow further elucidation of this mechanism, and might serve as starting points for drug discovery efforts. In this review, we describe the PCMD’s medicinal chemistry experience in identification, characterization and triage of hits from high throughput screens of the NIH SMR for inhibitors of cathepsin B and cathepsin L, as well as the successful development of novel, potent and selective probes of cathepsin L.

Cathepsin B

Cathepsin B is a lysosomal cysteine protease that has been implicated in a number of pathological conditionsvii such as cancer,viii immunological and inflammatory disorders,ix,x Alzheimer’s disease,xi and infectious As such, the identification of peptidic and small molecule inhibitors of Cathepsin B has been an active area of research, however, to date, no compounds have been clinically approved as therapeutics.ivc,xii

High Throughput Screen and Triage of Cathepsin B Hits: Pyrimidotriazine-diones and Pyrazole sulfonamides

The PCMD screened approximately 63,000 NIH SMR samples for inhibition of human liver cathepsin B. The assay incorporated a modified aminomethylcoumarin dipeptide substrate, which upon cleavage by cathepsin B generated a fluorescent signal. Seventy-five (75) compounds inhibited cathepsin B by at least 20% at 10 μM and were characterized as “primary hits.”xiii Upon re-testing using fresh samples, 37 of the initial 75 hits were confirmed in a dose-response assay.


Of the 37 confirmed hits, three structurally related analogs, CID 653297, CID 64750 and CID 66541/Toxoflavin (Figure 1) displayed significantly more potent activity than others. These three exhibited IC50’s of 72nM, 71nM and 46nM, respectively. However, the relatively flat structure of the pyrimidotriazine-diones raised concerns, as did the lack of any structural similarity to other prototypical cysteine protease inhibitors. An analysis of the compounds’ biological activity in Pubchem raised further flags. At the time of this work, according to Pubchem, these compounds had been assayed in thirteen MLSCN assays and were designated “active” in half of them. Most, but not all, of these assays targeted phosphatases; a second common factor was the presence of Dithiothreitol (DTT) in the assay medium, most probably to maintain the enzyme targets in a reduced, active state. Further literature searching led to reports describing pyrimidotriazines’ indirect mechanism of inhibition of caspasesxiv and phosphatases.xv The authors demonstrated that compounds of this class exert their activity through reaction with the reducing agent (e.g., DTT) present in the assay medium, rather than via direct binding and inhibition of the enzyme. Reaction of the putative inhibitors with DTT generated hydrogen peroxide (H2O2), which oxidized the active site cysteine and caused apparent inhibition.

Figure 1
Structures of CID653297, CID647501 and CID66541

To confirm the hypothesis that these hits were acting through a false positive mechanism, the cathepsin B assay was performed using cysteine, a less powerful reductant, in place of DTT. Under these new conditions, the pyrimidotriazine-diones, along with several structurally unrelated compounds, were inactive.xvi This result confirmed that these compounds were acting through a DTT-dependent redox cycling mechanism, rather than through direct inhibition of the enzyme. While there have been sporadic reports describing redox cycling as a mechanism of false positives in enzyme assays, this promiscuous activity has only recently garnered further attention with several groups developing high throughput assays to detect compounds which act through this mechanism.xvii,xviii It is hoped that the availability of these assays, in conjunction with those to detect other undesirable or false positive mechanisms of action such as aggregation,xix fluorescence interferencexx and chemical reactivityxxi will significantly improve the efficiency of the HTS triage process and perhaps allow the development of predictive models of false positive behavior.xixa, xxii

This pyrimidotriazine-dione class of compounds appears to be generally promiscuous through redox cycling, and perhaps through other, as yet unknown, mechanisms. It has also been reported to interfere with fluorescence detection methods.xxa According to Pubchem, as of July 2009, CID 653297 has been designated as “active” in 81 out of the 276 assays in which it has been evaluated. While many of these assays include DDT or other reductants as part of the media, some do not, suggesting additional mechanisms of promiscuity. This collective data supports the removal of these compounds from small molecule screening libraries, or at least their careful and complete characterization when designated as “active.”

Pyrazole sulfonamides

After elimination of redox-active false positives, and other nuisance compounds, a class of pyrazole sulfonamides of general structure 1 (Figure 2) appeared initially promising as cathepsin B inhibitors. Eight analogs in the screening library exhibited inhibitory activity ranging from 250nM to 2 μM, suggesting a relationship between structure and potency. Furthermore the compounds were deemed “drug-like” and had acceptable Lipinski parametersxxiii (MW ~350–380, logP~3, HBD=2, HBA = 6–9). We postulated that if appropriately reactive, the ester carbonyl in 1 could provide an electrophilic site for reaction with the active site cysteine in cathepsin B, in analogy to most other known warhead-containing cathepsin inhibitors.iva We pursed this series further based on its potency and excellent properties, as well as the potential to identify novel chemotypes that inhibit cathepsin B.

Figure 2
General structure of pyrazole sulfonamides (1)

As is our practice, we synthesized a representative set of the actives in order to assure that the structure depicted in the NIH SMR was correctly assigned, and to provide sufficient material for follow-up studies. The synthesis, shown in general terms in Scheme 1,xxiv was based on several literature reportsxxv, xxvi, xxvii, xxviii and proceeded over three steps and in moderate yields. The spectroscopic characteristics were identical to those of the original screening samples, and the structure of 1 (R1=p- fluorophenyl; R2=2-thiophene) was confirmed by x-ray crystallography. The newly prepared samples were then re-tested in the cathepsin B assay and their activity confirmed.

Scheme 1
General synthesis of pyrazole sulfonamides 1

Further biochemical studiesxxiv however, indicated that these compounds were acting as competitive substrates, rather than as conventional inhibitors of the enzyme. Data to support this conclusion included biochemical experiments that demonstrated the inhibition to be competitive and reversible. This characterization differs from most known cathepsin B inhibitors, which are irreversible or only slowly reversible.ivc Most compelling, however, were the results of studies that monitored the products of a stoichiometric reaction between cathepsin B and Compound 1a (Scheme 2). After 15 minutes under those conditions, 0% of Compound 1a remained; only the hydrolysis product, pyrazalone 4a, was detected.xxiv

Scheme 2
Stoichiometric reaction of 1a with cathepsin B

Limited efforts to convert this substrate into a competitive inhibitor by eliminating the ester function were pursued. Towards that end, the pyrazaolone 4 (R1= p-methoxyphenyl) was used as a pivotal intermediate to generate compounds such as ether 5 and sulfonate 6 (Figure 3). Both compounds were inactive in the cathepsin B assay, indicating that reactivity of the ester function group, and stability of the pyrazolone product, rather than binding energy was the major contributor to apparent potency.xxiv

Figure 3
Non-ester analogs of pyrazole sulfonate 1

In the course of evaluating how modifications of the ester substitutent (R2) in analogs of 1 (Figure 4) affected potency and kinetic properties, we obtained a series of perplexing results. First, during biochemical time course experiments, a decrease in potency was noted with increasing pre-incubation times. Second, while a number of compounds containing heterocylic and aromatic groups such as 2-thienyl (7), 2- furyl (8) and substituted aryl (9) at the R2 position exhibited apparent potent inhibitory activity; other closely related derivatives such as the pyridine ester (10) were inactive. As a reactive carbonyl was presumed to be the primary determinant of activity, the inactivity of this highly electrophilic ester was puzzling. Further studies showed that the presence of DTT in the assay medium caused these confounding results. In this instance however, the nucleophilic character of DTT, rather than its reducing properties, was the culprit.xxiv

Figure 4
Ester analogs

A series of experiments showed that upon incubation of 7 (R1=phenyl) in the DTT-containing assay medium, DTT reacted with the ester carbonyl to generate pyrazolone 4a and a DTT–adduct 11 (Scheme 3). After 2 hours incubation, 80% of 7 was converted to 4a. This transesterification reaction occurred in all analogs of 1 tested, however the rates of reaction varied and were dependent on the nature of R2. For example, complete conversion (>99%) of Compound 10 (R1=p-methoxyphenyl) occurred with only a 1 hour incubation time. This result explained the apparent “inactivity” of certain compounds: only small amounts of the ester were present during the assays, as they were completely converted to the corresponding inactive pyrazalone and DTT- adduct. In this case, replacement of DTT with cysteine did not solve the instability issue as the transesterification occurred in the presence of cysteine as well.xxiv

Scheme 3
Reaction of DTT with pyrazole sulfonamides

It is interesting to note that another MLSCN Center identified members of this series as inhibitors of the two component NS2B-NS3 Proteinase of West Nile Virus.xxix,xxx CID 655490 (R1=p-methoxyphenyl; R2=phenyl) was characterized as a slow-binding, reversible, non-competitive inhibitor. Similar to our observations, instability of the compounds was observed under the conditions of this assay. However, in this case, neither DTT nor cysteine was present. We speculate that Tris in the NS2B-NS3 assay protocol could be responsible for hydrolysis of the ester, and that this series of pyrazole sulfonamides is particularly prone to hydrolysis and degradation.

Our experience with the cathepsin B assay supports the contention that a thorough analysis of high throughput screening data and significant follow up studies need to be carefully considered prior to assigning a compound as “active.” The presence of DTT, a seemingly innocuous and common additive to assay media, can often provide misleading data not only due to its potential to act as a potent reductant and H2O2 generator, but also through its nucleophilic reactivity. In some instances, replacement of DTT with other reductants such as β-mercaptoethanol or cysteine may attenuate the promiscuous reductant activity, and thereby serve as useful replacements. However, when the nucleophilicity of DTT is a confounding factor, these alternatives are similarly problematic. In fact, the general stability of each hit series under the assay conditions should be evaluated as part of the routine hit triage process. In this study, the characterization of the mode of action of the pyrazole sulfonamides was essential to identify issues of instability, as well as to determine the nature of the inhibition as competitive substrates. These data on pyrimidotriazine-diones as well pyrazole sulfonamides such as 1 should be considered before including these or similar compounds in screening libraries or advancing them as hits.

Cathepsin L

Like cathepsin B, cathepsin L is a cysteine protease of the papain-superfamily that plays a variety of roles in physiological function. Cathepsin L, or its inappropriate or overactivity, has also been implicated in a number of pathophysiological conditions such as osteo- and rheumatoid arthritis, cancer, and osteoporosis,vii as well as in viral Furthermore, cathepsin L-like (and cathepsin B-like) proteases have been isolated from and implicated in the replication of parasites such as Plasmodium falciparum, Leishmania major and Trypanosoma brucei and cruzi.xxxi Known inhibitors of cathepsin L include peptide as well as non-peptide analogs.iv

High Throughput Screen, Triage and Identification of Cathepsin L Hits

Our efforts began with screening of approximately 58,000 NIH SMR compoundsxxxii for inhibitors of human liver cathepsin L. After the primary screen, 100 compounds were designated “active” according to the criteria of >45% inhibition at 10 μM; approximately half of those compounds were confirmed in dose-response testing in the presence of cysteine, rather than DTT.xxxiii A series of 5 oxadiazoles of general structure 12 appeared most promising based on their potent activity under the cysteine-assay conditions (IC50 ~200–600nM), excellent selectivity (no other activity noted in PubChem assays) and good predicted physical properties.xxxiv

Completion of an analysis of the purity and integrity of the original library and re-supplied samples indicated the presence of some impurities. A synthesis of oxadiazoles (e.g., 12: R1=H; R2=o-ethylphenyl)xxxiv was developed based on procedures in the literaturexxxv and provided pure materials as determined by LC/MS. However, when this pure sample of 12 (R1=H; R2=o-ethylphenyl) was tested in the cathepsin L assay, no inhibition was observed. Further studies revealed that the impurities present in the original samples were responsible for the biological activity. Those activities were attributed to thiocarbazate 13, the product of hydrolysis of the oxadiazole moiety.xxxiv This chemotype – “CO-NH-NH-CO-S” - had not been previously described in the literature, however it bears resemblance to azapeptides, some of which have been described as papain inhibitors.xxxvi

A general synthesis of thiocarbazates (Scheme 4) was quickly developed, and required three chemical steps starting from an amino acid derived hydrazone (14). Treatment of the hydrazone with thiocarbonyl gas,xxxvii followed by alkylation generated thiocarbazate 15. The N-Boc group was then removed using acid treatment to furnish the free amine 13. This sequence was efficient and proceeded in moderate to good overall yield. When tested, 13 (R1=H, R2=o-ethylphenyl) inhibited cathepsin L with an IC50 of 133nM. Some instability of 13 was noted due to diketopiperazine formation (Scheme 5); thus subsequent analogs retained the N-Boc group. The Boc-protected analogs such as 15 (R1=H, R2=o-ethylphenyl) were more potent (IC50=56nM) then the corresponding free amines.xxiv

Scheme 4
General synthesis of thiocarbazates
Scheme 5
Diketopiperazine formation

Characterization of Thiocarbazate’s Inhibition

Typical cysteine protease inhibitors contain an electrophilic warhead that provides a site for reaction with the active site cysteine. In the case of the thiocarbazates, the reactivity of the C2 carbonyl as evidenced by diketopiperazine formation (Figure 7) suggested this functionality as the “warhead.” Further evidence to support this hypothesis was based on several pieces of data. First, we designed, synthesized and evaluated analogs in which the reactivity of the C2 carbonyl was modified. The carbon analog (17) proved inactive, the nitrogen analog (18) modestly active and the oxygen analog (19) was as potent as the thiocarbazate.xxxviii This modulation in potency reflected the changes in the reactivity of the C2 carbonyl. Second, docking studies of 15a (R1=H, R2=o-ethylphenyl) placed the C2 carbonyl in close proximity to the active site cysteine.xxxix The kinetic characterization of 15a revealed a slowly reversible inhibition.xl Additional studies provided further insight into the mode of action of these inhibitors. We conducted experiments in which stoichiometric amounts of enzyme were incubated with 15a, and monitored the reaction by LC/MS for the appearance of products of hydrolysis 20 and 21 (independently synthesized). No products were detected. Furthermore, a similar reaction in the presence of cysteine produced no detectable products either (Scheme 7). Taken together, these results suggested that the active site cysteine reacts with the C2 carbonyl of the thiocarbazate to form a stable tetrahedral intermediate 22 (Scheme 8). Unlike substrates of the enzyme, this intermediate does not collapse further as evidenced by the lack of hydrolysis products detected. In time, however, intermediate 22 may covert back to the thiocarbazate and active enzyme.

Figure 7
Analogs with modified reactivity at C2 carbonyl
Scheme 7
Proposed mechanism of activity of 15a with cathepsin L.
Scheme 8
Reaction of thiocarbazate 15a with cathepsin L or cysteine.

Identification of CID16725315 (15a) as a Probe of Cathepsin L

The potent activity and selectivity of 15a warranted the designation of this compound as a MLSCN Table 1 summarizes its activity, kinetic properties, selectivity and toxicity. As cathepsin inhibitors have been reported to be efficacious in cellular models of Leishmania major and Plasmodium falciparum infection, 15a was evaluated and exhibited IC50’s of 12.5μM and 15.4μM respectively.xl

Table 1
Biological and kinetic data on CID16725315

Docking Studies with Compound 15a

Docking experiments were performed using an x-ray structure of papain bound to a diketo-epoxide inhibitorxli as a model of cathepsin L (Figure 9).xxxix These studies find that thiocarbazate 15a binds to the active site with similar energies as the diketo-epoxide inhibitor, and makes a number of identical interactions. Three sub-sites are fully occupied: the S1’ sub-site is occupied by the 2-ethylphenyl group; the indole group occupies the S2 sub-site, and the tert-butoxy group sits in the S3 sub-site. Table 1 records the types of interactions 15a makes with specific residues in papain/cathepsin L as suggested by the docking studies. This model was useful to rationalize the activity of analogs, as well as to help optimize them.

Figure 9
Structure of cathepsin L probe CID 23631927

Design and Synthesis of Analogs of 15a

A series of analogs in which modifications to the amino acid side chain (A) and sulfur substituent (B) were designed and prepared. For example, the N-Boc tryptophan moiety was replaced with the corresponding phenylalanine, leucine, alanine and glycine units to afford 23, 24, 25 and 26 respectively.xlii All exhibited reduced activity, with decreased potency correlating with decreased size. This result is consistent with the docking model that positions the indole group of 15a in the relatively large S2 site, and predicts that smaller substitutents would be less active. Deletion of the NH-Boc group (27)xxxviii,xxxix reduced potency by nearly 400-fold, presumably due to loss of the H-bond to Asp158/162 and lack of occupancy of the S3 site.

Modification at position B revealed trends that also could be rationalized by the docking studies. Replacement of the anilide with constrained analogs such as tetrahydroquinoline (28) or tetrahydroisoquinoline (29) resulted in comparable or improved potency. However, removal of the carbonyl function through incorporation of an aniline (30) generated an inactive compound.xlii This result provided support for the importance of the hydrogen bond between the anilide carbonyl and Trp177/189. An extensive library of compounds was prepared that incorporated a wide diversity of additional modifications at each of these positions. The compounds were evaluated in cathepsin L, as well as cathepsin B and cathepsin S assays, and SAR trends were delineated.xlii

Identification of CID 23631927 (19) as an Optimized Probe of Cathepsin L

One of the most potent analogs identified was Compound 19 (CID 23631927). We designed this molecule by combining the improved potency of oxacarbazates with ring constraints at the anilide moiety. This compound exhibited an IC50 against cathepsin L at 7nM (0.4nM with a 4 hour pre-incubation) and exhibited exquisite selectivity compared to cathepsin B (>700 fold). Furthermore, in a zebrafish whole organism assay, no toxicity was detected up to 100μM. In cellular models, analog 19 prevented the entry of SARS-CoV and Ebola virus into cells at sub-micromolar This result confirms the role of cathepsin L in viral entry, and suggests compounds such as 19 may find utility as starting points in drug discovery efforts.


Our experience with identification, characterization and triage of hits from screening of the NIH SMR for inhibitors of cysteine proteases enforced several important lessons. First, as demonstrated in our work on cathepsin B, the mechanism of action of hits should be evaluated prior to significant assignment of resources. False positives plague all high throughput screens, and rapid elimination of compounds that act through such mechanisms such as redox cycling assures that poor hits and leads are not pursued. Second, the stability of hits in assay media should always be evaluated to confirm that the integrity of the structure is intact throughout the biological assay. The availability of the public database, PubChem, if correctly annotated, should provide a wealth of information about compounds and substructures with these liabilities. Third, the mechanism of action of hits should be considered and evaluated prior to hit and lead optimization. Finally, careful analysis of library samples for purity and integrity is essential, as is re-synthesis and re-assay of hit samples. This process ensures that the activity is ascribed to the correct structure, and provides high quality data for generating valid structure activity relationships. Through studies such as these, we were able to quickly eliminate false positives and nuisance compounds identified in primary HTS assays for cathepsin B. We were also able to identify potential liabilities, such as instability, to distinguish alternate substrates from inhibitors, and to focus medicinal chemistry efforts accordingly. In the cathepsin L project, analysis of purity and integrity lead to the identification of a novel chemotype, a thiocarbazate, that acted as a potent inhibitor of cathepsins. Optimization of this moiety led to novel, potent and highly selective probes of cathepsin L that have considerable potential in preventing viral entry to cells.

Figure 5
CID 655490
Figure 6
Reported structure of oxadiazole cathepsin L hits 12 and true active species 13.
Figure 8
Compound 15a docked to papain
Table 2
Binding Interactions of 15b docked to papain
Table 3
Analogs of 15a and cathepsin L inhibitory activity


Financial support for this work was provided by the NIH (5U54HG003915-03). The authors would like to thank our PCMD colleagues Scott Diamond, Mary Pat Beavers, Michael Myers, Zhuqing Liu, Phillip Beneditti, Barry Cooperman, Parag Shah, Andrew Napper and Barry Cooperman along with Paul Bates. DMH is grateful to Jay Kostman for editorial assistance.


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