Development of Inhibitors of Plasmodium falciparum Apical Membrane Antigen 1 Based on Fragment Screening

Lim, San Sui; Debono, Cael; MacRaild, Christopher A.; Chandrashekaran, Indu R.; Dolezal, Olan; Anders, Robin F.; Simpson, Jamie S.; Scanlon, M.J.; Devine, Shane M.; Scammells, Peter J.; Norton, Raymond S.

doi:10.1071/ch13266

Cited by 20 publications

(45 citation statements)

References 33 publications

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“…The selected compounds represent five different scaffolds among the 57 www.chemmedchem.org hits that were positive in both saturationt ransfer difference (STD) and Carr-Purcell-Meiboom-Gill (CPMG) experimentsa nd whose bindingw as competed by R1, ap otent peptidei nhibitor of PfAMA1 discovered by phage display of random peptide libraries. [18,44] We also tested ar epresentative of the pyrrolopyrimidine scaffold (6)f or which the binding site on AMA1 is unknown. [45] We observed PRE conferred by the spin label on the spectra of these compounds, which are in fast exchange between the free andb ound states, effectively at ransferred PRE.…”

Section: Pre-based Screening Of Compoundsmentioning

confidence: 99%

“…[17] Previously,afragment screen identified ar ange of smallmolecule ligandsf or the conserved hydrophobic clefto f PfAMA1. [18] Some of those AMA1h itsw eret ested in chemical shift perturbation assays and severals ub-sites on AMA1 were Apical membrane antigen 1(AMA1) is essential for the invasion of host cells by malaria parasites. Several small-molecule ligands have been shown to bind to ac onserved hydrophobic cleft in Plasmodiumf alciparum AMA1.…”

Section: Introductionmentioning

confidence: 99%

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Identification of the Binding Site of Apical Membrane Antigen 1 (AMA1) Inhibitors Using a Paramagnetic Probe

et al. 2019

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Apical membrane antigen 1 (AMA1) is essential for the invasion of host cells by malaria parasites. Several small‐molecule ligands have been shown to bind to a conserved hydrophobic cleft in Plasmodium falciparum AMA1. However, a lack of detailed structural information on the binding pose of these molecules has hindered their further optimisation as inhibitors. We have developed a spin‐labelled peptide based on RON2, the native binding partner of AMA1, to probe the binding sites of compounds on PfAMA1. The crystal structure of this peptide bound to PfAMA1 shows that it binds at one end of the hydrophobic groove, leaving much of the binding site unoccupied and allowing fragment hits to bind without interference. In paramagnetic relaxation enhancement (PRE)‐based NMR screening, the 1H relaxation rates of compounds binding close to the probe were enhanced. Compounds experienced different degrees of PRE as a result of their different orientations relative to the spin label while bound to AMA1. Thus, PRE‐derived distance constraints can be used to identify binding sites and guide further hit optimisation.

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Section: Pre-based Screening Of Compoundsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Identification of the Binding Site of Apical Membrane Antigen 1 (AMA1) Inhibitors Using a Paramagnetic Probe

et al. 2019

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“…To investigate whether the lysine analog TXA alone could bind to Plm, both saturation-transfer differences NMR (STD-NMR) and CarPurcell-Meiboom-Gill NMR (CPMG-NMR) 17 were used. TXA showed positive STD signals at 2.60 and 2.58 ppm in the presence of mPlm but not in its absence (Figure 2A), which suggests that mPlm binds to TXA.…”

Section: Resultsmentioning

confidence: 99%

X-ray crystal structure of plasmin with tranexamic acid–derived active site inhibitors

Law

Leung

et al. 2017

Blood Advances

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Key Points• Plasmin YO inhibitors form extensive interactions with the prime sites, thus anchoring the TXA moiety inside the catalytic pocket.• Structural alignment analysis with urokinase and kallikrein gives insights into the molecular basis of the YO inhibitor specificity.The zymogen protease plasminogen and its active form plasmin perform key roles in blood clot dissolution, tissue remodeling, cell migration, and bacterial pathogenesis. Dysregulation of the plasminogen/plasmin system results in life-threatening hemorrhagic disorders or thrombotic vascular occlusion. Accordingly, inhibitors of this system are clinically important.Currently, tranexamic acid (TXA), a molecule that prevents plasminogen activation through blocking recruitment to target substrates, is the most widely used inhibitor for the plasminogen/plasmin system in therapeutics. However, TXA lacks efficacy on the active form of plasmin. Thus, there is a need to develop specific inhibitors that target the protease active site. Here we report the crystal structures of plasmin in complex with the novel YO (trans-4-aminomethylcyclohexanecarbonyl-L-tyrosine-n-octylamide) class of small molecule inhibitors. We found that these inhibitors form key interactions with the S1 and S39 subsites of the catalytic cleft. Here, the TXA moiety of the YO compounds inserts into the primary (S1) specificity pocket, suggesting that TXA itself may function as a weak plasmin inhibitor, a hypothesis supported by subsequent biochemical and biophysical analyses. Mutational studies reveal that F587 of the S9 subsite plays a key role in mediating the inhibitor interaction. Taken together, these data provide a foundation for the future development of small molecule inhibitors to specifically regulate plasmin function in a range of diseases and disorders.

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“…To identify drug-like inhibitors of AMA1, we have recently screened our in-house fragment library using ligand-detected 1 H-NMR and SPR [51]. From this screen we have identified and further developed a number of fragment series that bind the hydrophobic cleft, competing with the peptide ligand R1.…”

Section: Ligand Binding To Apical Membrane Antigen 1 (Ama1)mentioning

confidence: 99%

Applications of 19F-NMR in Fragment-Based Drug Discovery

et al. 2016

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19 F-NMR has proved to be a valuable tool in fragment-based drug discovery. Its applications include screening libraries of fluorinated fragments, assessing competition among elaborated fragments and identifying the binding poses of promising hits. By observing fluorine in both the ligand and the target protein, useful information can be obtained on not only the binding pose but also the dynamics of ligand-protein interactions. These applications of 19 F-NMR will be illustrated in this review with studies from our fragment-based drug discovery campaigns against protein targets in parasitic and infectious diseases.

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Development of Inhibitors of Plasmodium falciparum Apical Membrane Antigen 1 Based on Fragment Screening

Cited by 20 publications

References 33 publications

Identification of the Binding Site of Apical Membrane Antigen 1 (AMA1) Inhibitors Using a Paramagnetic Probe

Identification of the Binding Site of Apical Membrane Antigen 1 (AMA1) Inhibitors Using a Paramagnetic Probe

X-ray crystal structure of plasmin with tranexamic acid–derived active site inhibitors

Applications of 19F-NMR in Fragment-Based Drug Discovery

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