Semicarbazone-based inhibitors of cathepsin K, are they prodrugs for aldehyde inhibitors?

Adkison, Kim K.; Barrett, David; Deaton, David N.; Gampe, Robert T.; Hassell, Anne M.; Long, Stacey T.; McFadyen, Robert B.; Miller, A. Whitman; Miller, Larry R.; Payne, J. Alan; Shewchuk, Lisa M.; Wells‐Knecht, Kevin J.; Willard, Derril H.; Wright, Laura

doi:10.1016/j.bmcl.2005.10.108

Cited by 14 publications

(11 citation statements)

References 14 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…X-ray structures show that the side chain of the P1 residue is fully exposed to the solvent. 25,[37][38][39] The specificity at the P1′-binding position by cathepsin K was examined by Alves et al, 28 and it was found that larger side chains are preferred with a binding order of Asn > Phe > Leu > Gly at this site. 40,41 In the complex structure of cathepsin K and an inhibitor (called INA), 26 the P1′ amino group of the substrate is oriented toward the carbonyl oxygen of Asn161, and its carbonyl group is hydrogen-bonded to the N ε1 atom of Trp184 side chain.…”

Section: The Construction Of a Model For The Enzyme-substrate (Michaementioning

confidence: 99%

Molecular Dynamics Simulations of the Catalytic Pathway of a Cysteine Protease: A Combined QM/MM Study of Human Cathepsin K

2007

View full text Add to dashboard Cite

Molecular dynamics simulations using a combined QM/MM potential have been performed to study the catalytic mechanism of human cathepsin K, a member of the papain family of cysteine proteases. We have determined the two-dimensional free energy surfaces of both acylation and deacylation steps to characterize the reaction mechanism. These free energy profiles show that the acylation step is rate limiting with a barrier height of 19.8 kcal/mol in human cathepsin K and of 29.3 kcal/mol in aqueous solution. The free energy of activation for deacylation step is 16.7 kcal/mol in cathepsin K and 17.8 kcal/mol in aqueous solution. The reduction of free energy barrier is achieved by stabilization of the oxyanion in the transition state. Interestingly, although the "oxyanion hole" has been formed in the Michaelis complex, the amide units do not donate hydrogen bonds directly to the carbonyl oxygen of the substrate, but they stabilize the thiolate anion nucleophile. Hydrogen bonding interactions are induced as the substrate amide group approaches the nucleophile, moving more than 2 angstroms and placing the oxy-anion in contact with Gln19 and the backbone amide of Cys25. The hydrolysis of peptide substrate shares a common mechanism both for the catalyzed reaction in human cathepsin K and the uncatalyzed reaction in water. Overall, the nucleophilic attack by Cys25 thiolate and the proton transfer reaction from His162 to the amide nitrogen are highly coupled, whereas a tetrahedral intermediate is formed along the nucleophilic reaction pathway.

show abstract

Section: The Construction Of a Model For The Enzyme-substrate (Michaementioning

confidence: 99%

Molecular Dynamics Simulations of the Catalytic Pathway of a Cysteine Protease: A Combined QM/MM Study of Human Cathepsin K

2007

View full text Add to dashboard Cite

show abstract

“…Instead, it interacts with 162 His of the catalytic triad, as well as 161 Asn, while the amide moiety resides in the oxyanion site. Thus, the active site thiol attacks the electrophile carbonyl group from the opposite face to that observed for previously reported aldehyde and ketone cathepsin K co-crystal structures [150,170,169,174].…”

mentioning

confidence: 59%

“…It was surmised that semicarbazones could provide access to S 1' and S 2' subsite binding interactions as well as potentially improve drug properties like aqueous solubility versus aldehydes. Numerous semicarbazones, derived from Boc-Nle-H 2, were synthesized [174]. As shown in Table 5, most of the terminally monosubstituted semicarbazones (74)(75)(76)(77)(78)(79)(80)(81) were slightly less active than the starting aldehyde 2 with IC 50 s ranging from 160-490 nM.…”

Section: Semicarbazonesmentioning

confidence: 99%

“…The ex vivo pharmacodynamic properties of representative analogs from several classes of inhibitors were determined in the rat calvaria bone resorption assay, including aldehydes 1, 46, and 48, semicarbazones 86, 88, and 89, cyanamide 105, and ketoamides 147, 169, 299-302 [182,152,174,153,179,191]. These inhibitors were all less active against the rat ortholog of cathepsin K. For example, ketoamides 300 (rat IC 50 = 1.3 nM) and 302 (rat IC 50 = 1.0 nM) are 20-40-fold less potent inhibitors of the rat enzyme than the human enzyme.…”

Section: Pharmacodynamic Studiesmentioning

confidence: 99%

See 1 more Smart Citation

Design of Cathepsin K Inhibitors for Osteoporosis

Deaton

Tavares²

2005

CTMC

View full text Add to dashboard Cite

Osteoporosis is a progressive, debilitating bone disease resulting in increased cost and morbidity to the elderly. This review summarizes the therapeutic approaches taken in the treatment of osteoporosis with particular emphasis on cathepsin K inhibitors. Cathepsin K, a cysteine protease predominantly expressed in osteoclasts, is a key player involved in bone matrix degradation. Both genetic ablation and small molecule inhibitor strategies versus cathepsin K have validated the importance of this enzyme in bone resorption. Starting from aldehyde-based leads, this review synopsizes the design of improved small molecule inhibitors by GlaxoWellcome researchers. These efforts involved the evaluation of various warheads, including cyanamides, ketoheterocycles, and ketoamides. Initial structure/activity relationships of aldehyde-based inhibitors proved useful in the design of ketoamide-based cathepsin K inhibitors. Further exploration of S(3), S(2), S(1), and S(1') subsites with P(3), P(2), P(1), and P(1') probes have resulted in the identification of potent, selective, orally bioavailable ketoamide-based inhibitors of cathepsin K with demonstrated in vivo efficacy.

show abstract

“…In a previous study, semicarbazones derived from aldehyde-based Cathepsin K inhibitors were shown to have poor CN bond stability, which, along with other evidence, led researchers to conclude that the semicarbazones were functioning as prodrugs delivering a bioactive aldehyde. 5 On the other hand, structurally distinct peptide-semicarbazones were shown to be stable in acidic media, requiring reflux to induce decomposition. 6 In our case, incubating RAW 264.7 macrophages with the semicarbazide (6) and the benzaldehyde component of 1 (both individually and in combination) prior to addition of LT did not prevent toxin-induced cell death, which indicates that the complete semicarbazone structure is required for bioactivity (Supporting Information, Figure 1).…”

mentioning

confidence: 99%

Structure–Activity Relationship of Semicarbazone EGA Furnishes Photoaffinity Inhibitors of Anthrax Toxin Cellular Entry

Jung

Chamberlain

et al. 2014

ACS Med. Chem. Lett.

View full text Add to dashboard Cite

EGA, 1, prevents the entry of multiple viruses and bacterial toxins into mammalian cells by inhibiting vesicular trafficking. The cellular target of 1 is unknown, and a structure− activity relationship study was conducted in order to develop a strategy for target identification. A compound with midnanomolar potency was identified (2), and three photoaffinity labels were synthesized (3−5). For this series, the expected photochemistry of the phenyl azide moiety is a more important factor than the IC 50 of the photoprobe in obtaining a successful photolabeling event. While 3 was the most effective reversible inhibitor of the series, it provided no protection to cells against anthrax lethal toxin (LT) following UV irradiation. Conversely, 5, which possessed weak bioactivity in the standard assay, conferred robust irreversible protection vs LT to cells upon UV photolysis. KEYWORDS: Photoaffinity labeling, semicarbazone, aryl azide, anthrax lethal toxin, endosomal trafficking A common mechanism by which viruses and bacterial toxins enter host cells involves trafficking from an early to a late endosome followed by release into the cytoplasm as triggered by endosomal acidification. 1−3 Inhibition of this process represents a host-targeted strategy for the development of broad-spectrum antiviral and antibacterial drugs. Recently, EGA, N 1 -(4-bromobenzylidene)-N 4 -(2,6-dimethylphenyl)-semicarbazone, 1, was identified from a high-throughput phenotypic screen to protect cells from anthrax lethal toxin (LT). 4 Further investigations showed that 1 protected cells from multiple viruses and bacterial toxins that rely on pHdependent endosomal trafficking to enter cells. Although the details of the biochemical mechanism have been studied, the cellular target(s) remain unknown. We have conducted a structure−activity relationship (SAR) study with the goal of improving the potency of 1 and developing a strategy for photoaffinity labeling and identification of the involved proteins.A series of derivatives of 1 were synthesized and tested, revealing precise requirements for activity in a tight and relatively flat structure−activity landscape. The 2,6-dimethyl substitution in the N 4 -ring as well as an unaltered semicarbazone core were shown to be optimal for activity while certain modifications to the N 1 -phenyl ring were tolerated. From the SAR, a compound more potent than the original hit was generated, namely the N 1 -2-fluoro-4-bromophenyl analogue (IC 50 = 0.4 μM), 2. In addition, three photoaffinity probes, 3−5, two of which possess low micromolar activity, were designed and synthesized. Our key finding is that the expected photochemistry of the phenyl azide moiety is a more important factor than the IC 50 of the photoprobe in achieving successful photolabeling. While 3 was the most potent inhibitor of intoxication by LT in the standard assay, it did not provide protection to the cells upon UV photolysis. Conversely 5, which possesses two fluorine atoms ortho to the azido function, was a poor inhibitor in the stand...

show abstract

Semicarbazone-based inhibitors of cathepsin K, are they prodrugs for aldehyde inhibitors?

Cited by 14 publications

References 14 publications

Molecular Dynamics Simulations of the Catalytic Pathway of a Cysteine Protease: A Combined QM/MM Study of Human Cathepsin K

Molecular Dynamics Simulations of the Catalytic Pathway of a Cysteine Protease: A Combined QM/MM Study of Human Cathepsin K

Design of Cathepsin K Inhibitors for Osteoporosis

Structure–Activity Relationship of Semicarbazone EGA Furnishes Photoaffinity Inhibitors of Anthrax Toxin Cellular Entry

Contact Info

Product

Resources

About