Synthesis, modelling and kinetic assays of potent inhibitors of purple acid phosphatase

Mohd-Pahmi, Siti Hajar; Hussein, Waleed M.; Schenk, Gerhard; McGeary, Ross P.

doi:10.1016/j.bmcl.2011.03.024

Cited by 22 publications

(30 citation statements)

References 49 publications

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“…The three compounds also inhibit rkbPAP in a similar manner (Table 2; Figure S1), an observation that suggests that despite some structural variations between the two enzymes (discussed in detail later), the overall interactions between inhibitor and enzyme are largely conserved. This interpretation is also in agreement with previous studies using phosphonate derivatives as inhibitors for pig and rkbPAP -in each case, the observed modes and magnitudes of inhibition were similar in the two enzymes (32,33).…”

Section: Resultssupporting

confidence: 93%

“…These molecules have IC 50 values in the mid-micromolar range (31). More recently, a-alkoxynaphthylmethylphosphonic acids and acyl derivatives of a-aminonaphthylmethyl phosphonic acid have also been shown to be PAP inhibitors with K i and IC 50 values in the low micromolar range (32,33). These molecules were designed as the derivatives of 1-naphthylmethylphosphonic acid, a PAP inhibitor previously reported by Schwender et al (34).…”

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confidence: 96%

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Identification of Purple Acid Phosphatase Inhibitors by Fragment‐Based Screening: Promising New Leads for Osteoporosis Therapeutics

et al. 2012

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Purple acid phosphatases are metalloenzymes found in animals, plants and fungi. They possess a binuclear metal centre to catalyse the hydrolysis of phosphate esters and anhydrides under acidic conditions. In humans, elevated purple acid phosphatases levels in sera are correlated with the progression of osteoporosis and metabolic bone malignancies, making this enzyme a target for the development of new chemotherapeutics to treat bone-related illnesses. To date, little progress has been achieved towards the design of specific and potent inhibitors of this enzyme that have drug-like properties. Here, we have undertaken a fragment-based screening approach using a 500-compound library identifying three inhibitors of purple acid phosphatases with K i values in the 30-60 lM range. Ligand efficiency values are 0.39-0.44 kcal ⁄ mol per heavy atom. X-ray crystal structures of these compounds in complex with a plant purple acid phosphatases (2.3-2.7 Å resolution) have been determined and show that all bind in the active site within contact of the binuclear centre. For one of these compounds, the phenyl ring is positioned within 3.5 Å of the binuclear centre. Docking simulations indicate that the three compounds fit into the active site of human purple acid phosphatases. These studies open the way to the design of more potent and selective inhibitors of purple acid phosphatases that can be tested as anti-osteoporotic drug leads.Key words: X-ray, crystallography, drug design, fragment screening, purple acid phosphatase, osteoporosis Purple acid phosphatases (PAP) are metalloenzymes that hydrolyse phosphate esters and anhydrides, generally at low pH values (1). The distinctive purple colour of these enzymes is due to a metal to ligand charge transfer from a tyrosine phenolate to a chromophoric Fe(III) (2,3). The cornerstone of the active site of PAP is the presence of two metal ions; Fe(III) is always present in the chromophoric site, while the second site can be occupied by a redox active Fe(II ⁄ III) in mammals (4,5) or a Zn(II) or Mn(II) in plants (6,7). Mammalian PAP is a 35 kDa monomeric protein also known as tartrate-resistant acid phosphatase (TRAP or TRAcP). In contrast, plant PAP is a 110 kDa homodimer, with each subunit consisting of two domains, an N-terminal one whose function is unknown and a catalytic C-terminal domain that strongly resembles the overall structure of the mammalian enzyme (1). Crystal structures of human (8), pig (9), rat (10,11) and plant PAPs (12,13) have been determined and show that the amino acid ligands of the metal ions are completely conserved across plant and animal PAPs, but there are some differences in the identities of the residues that line the active site.A number of biological roles for PAP have been proposed. These include (i) the transport of iron from the mother to the developing foetus during gestation (14); (ii) bone resorption in osteoclasts (evidence for this activity is derived from the effect of PAP on osteoclasts that were cultured on cortical bone slices (15) and from t...

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Section: Resultssupporting

confidence: 93%

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confidence: 96%

Identification of Purple Acid Phosphatase Inhibitors by Fragment‐Based Screening: Promising New Leads for Osteoporosis Therapeutics

et al. 2012

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“…A number of thiol and phosphonate compounds with IC 50 values 80-3000 µM have been developed [30]; similar IC 50 values were reported for a series of phosphotyrosine-containing tripeptides [28]. Our group reported a series of αalkoxynaphthylmethylphosphonic acids [31], acyl derivatives of α-aminonaphthylmethyl phosphonic acid [32] and acyl derivatives of 6-aminopenicillanic acid [33] as inhibitors of PAP with K i and IC 50 values in the low micromolar range. We also employed a fragmentbased screening approach to identify three potential inhibitor leads; crystal structures provided insight about the mode of their binding in the active site of rkbPAP [27].…”

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confidence: 59%

Purple acid phosphatase inhibitors as leads for osteoporosis chemotherapeutics

Hussein

Feder

Schenk

et al. 2018

European Journal of Medicinal Chemistry

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“…Additionally, bone pit formation activity of osteoclasts was inhibited when treated with polyphosphates, associated with a potent inhibition of TRAP activity . Several efforts have been funnelled also into the design and optimization of substrate mimics of TRAP, such as phosphotyrosyl peptides, and phosphonates, such as α‐alkoxy‐naphthylmethyl phosphonic acids and α‐aminonaphthylmethyl phosphonic acids …”

Section: Introductionmentioning

confidence: 99%

Identification of inhibitors of Tartrate‐resistant acid phosphatase (TRAP/ACP5) activity by small‐molecule screening

et al. 2018

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Tartrate-resistant acid phosphatase (TRAP/ACP5) occurs as two isoforms-TRAP 5a with low enzymatic activity due to a loop interacting with the active site and the more active TRAP isoform 5b generated upon proteolytic cleavage of this loop. TRAP has been implicated in several diseases, including cancer. Thus, this study set out to identify small-molecule inhibitors of TRAP activity. A microplate-based enzymatic assay for TRAP 5b was applied in a screen of 30,315 compounds, resulting in the identification of 90 primary hits. After removal of promiscuous compounds, unwanted groups, and false positives by orthogonal assays and three-concentration validation, the properties of 52 compounds were further investigated to better understand their mechanism of action. Full-concentration-response curves for these compounds were established under different enzyme concentrations and (pre)incubation times to remove compounds with inconsistent results and low potencies. Full-concentration-response curves were also performed for both isoforms, to examine isoform prevalence. Filtering led to six prioritized compounds, representing different clusters. One of these, CBK289001 or (6S)-6-[3-(2H-1,3-benzodioxol-5-yl)-1,2,4-oxadiazol-5-yl]-N-(propan-2-yl)-1H,4H,5H,6H,7H-imidazo[4,5-c]pyridine-5-carboxamide, demonstrated efficacy in a migration assay and IC values from 4 to 125 μm. Molecular docking studies and analog testing were performed around CBK289001 to provide openings for further improvement toward more potent blockers of TRAP activity.

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Synthesis, modelling and kinetic assays of potent inhibitors of purple acid phosphatase

Cited by 22 publications

References 49 publications

Identification of Purple Acid Phosphatase Inhibitors by Fragment‐Based Screening: Promising New Leads for Osteoporosis Therapeutics

Identification of Purple Acid Phosphatase Inhibitors by Fragment‐Based Screening: Promising New Leads for Osteoporosis Therapeutics

Purple acid phosphatase inhibitors as leads for osteoporosis chemotherapeutics

Identification of inhibitors of Tartrate‐resistant acid phosphatase (TRAP/ACP5) activity by small‐molecule screening

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