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JB Cooper - One of the best experts on this subject based on the ideXlab platform.
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The structure of Endothiapepsin complexed with a Phe-Tyr reduced-bond inhibitor at 1.35 Å resolution.
Acta Crystallographica Section F Structural Biology Communications, 2013Co-Authors: J Guo, JB Cooper, S P WoodAbstract:Endothiapepsin is a typical member of the aspartic proteinase family. The catalytic mechanism of this family is attributed to two conserved catalytic aspartate residues, which coordinate the hydrolysis of a peptide bond. An oligopeptide inhibitor (IC50 = 0.62 µM) based on a reduced-bond transition-state inhibitor of mucorpepsin was co-crystallized with Endothiapepsin and the crystal structure of the enzyme–inhibitor complex was determined at 1.35 A resolution. A total of 12 hydrogen bonds between the inhibitor and the active-site residues were identified. The resulting structure demonstrates a number of novel subsite interactions in the active-site cleft.
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atomic resolution analysis of the catalytic site of an aspartic proteinase and an unexpected mode of binding by short peptides
Protein Science, 2003Co-Authors: P.t. Erskine, L Coates, S P Wood, S Mall, R. Gill, D A Myles, JB CooperAbstract:The X-ray structures of native Endothiapepsin and a complex with a hydroxyethylene transition state analog inhibitor (H261) have been determined at atomic resolution. Unrestrained refinement of the carboxyl groups of the enzyme by using the atomic resolution data indicates that both catalytic aspartates in the native enzyme share a single negative charge equally; that is, in the crystal, one half of the active sites have Asp 32 ionized and the other half have Asp 215 ionized. The electron density map of the native enzyme refined at 0.9 Å resolution demonstrates that there is a short peptide (probably Ser-Thr) bound noncovalently in the active site cleft. The N-terminal nitrogen of the dipeptide interacts with the aspartate diad of the enzyme by hydrogen bonds involving the carboxyl of Asp 215 and the catalytic water molecule. This is consistent with classical findings that the aspartic proteinases can be inhibited weakly by short peptides and that these enzymes can catalyze transpeptidation reactions. The dipeptide may originate from autolysis of the N-terminal Ser-Thr sequence of the enzyme during crystallization.
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The structure of Endothiapepsin complexed with the gem-diol inhibitor PD-135,040 at 1.37 A.
Acta crystallographica. Section D Biological crystallography, 2003Co-Authors: L Coates, S P Wood, P.t. Erskine, S Mall, P A Williams, R S Gill, JB CooperAbstract:The crystal structure of Endothiapepsin complexed with the gem-diol inhibitor PD-135,040 has been anisotropically refined to a resolution of 1.37 A. The structure of this inhibitor complex is in agreement with previous structures of Endothiapepsin gem-diol inhibitor complexes that have been used to develop proposed catalytic mechanisms. However, the increase in resolution over previous structures confirms the presence of a number of short hydrogen bonds within the active site that are likely to play an important role in the catalytic mechanism. The presence of low-barrier hydrogen bonds was indicated in a previous one-dimensional H NMR spectrum.
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five atomic resolution structures of Endothiapepsin inhibitor complexes implications for the aspartic proteinase mechanism
Journal of Molecular Biology, 2002Co-Authors: L Coates, Matthew P Crump, S P Wood, P.t. Erskine, JB CooperAbstract:Endothiapepsin is derived from the fungus Endothia parasitica and is a member of the aspartic proteinase class of enzymes. This class of enzyme is comprised of two structurally similar lobes, each lobe contributing an aspartic acid residue to form a catalytic dyad that acts to cleave the substrate peptide bond. The three-dimensional structures of Endothiapepsin bound to five transition state analogue inhibitors (H189, H256, CP-80,794, PD-129,541 and PD-130,328) have been solved at atomic resolution allowing full anisotropic modelling of each complex. The active sites of the five structures have been studied with a view to studying the catalytic mechanism of the aspartic proteinases by locating the active site protons by carboxyl bond length differences and electron density analysis. In the CP-80,794 structure there is excellent electron density for the hydrogen on the inhibitory statine hydroxyl group which forms a hydrogen bond with the inner oxygen of Asp32. The location of this proton has implications for the catalytic mechanism of the aspartic proteinases as it is consistent with the proposed mechanism in which Asp32 is the negatively charged aspartate. A number of short hydrogen bonds (∼2.6 A) with ESD values of around 0.01 A that may have a role in catalysis have been identified within the active site of each structure; the lengths of these bonds have been confirmed using NMR techniques. The possibility and implications of low barrier hydrogen bonds in the active site are considered.
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a neutron laue diffraction study of Endothiapepsin implications for the aspartic proteinase mechanism
Biochemistry, 2001Co-Authors: L Coates, S P Wood, P.t. Erskine, D A Myles, JB CooperAbstract:Current proposals for the catalytic mechanism of aspartic proteinases are largely based on X-ray structures of bound oligopeptide inhibitors possessing nonhydrolyzable analogues of the scissile peptide bond. However, the positions of protons on the catalytic aspartates and the ligand in these complexes have not been determined with certainty. Thus, our objective was to locate crucial protons at the active site of an inhibitor complex since this will have major implications for a detailed understanding of the mechanism of action. We have demonstrated that high-resolution neutron diffraction data can be collected from crystals of the fungal aspartic proteinase Endothiapepsin bound to a transition state analogue (H261). The neutron structure of the complex has been refined at a resolution of 2.1 A to anR-factor of 23.5% and an Rfree of 27.4%. This work represents the largest protein structure studied to date by neutron crystallography at high resolution. The neutron data demonstrate that 49% of the main chain nitrogens have exchanged their hydrogen atoms with D2O in the mother liquor. The majority of residues resisting exchange are buried within core ‚-sheet regions of the molecule. The neutron maps confirm that the protein has a number of buried ionized carboxylate groups which are likely to give the molecule a net negative charge even at very low pH, thereby accounting for its low pI. The functional groups at the catalytic center have clearly undergone H-D exchange despite being buried by the inhibitor occupying the active site cleft. Most importantly, the data provide convincing evidence that Asp 215 is protonated and that Asp 32 is the negatively charged residue in the transition state complex. This has an important bearing on mechanistic proposals for this class of proteinase.
Anna K. H. Hirsch - One of the best experts on this subject based on the ideXlab platform.
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Design and Synthesis of Bioisosteres of Acylhydrazones as Stable Inhibitors of the Aspartic Protease Endothiapepsin.
ChemMedChem, 2018Co-Authors: Varsha R. Jumde, Milon Mondal, M. Yagiz Unver, Andreas Heine, Gerhard Klebe, Robin M. Gierse, F. Magari, Roos C. W. Van Lier, Anna K. H. HirschAbstract:Acylhydrazone-based dynamic combinatorial chemistry (DCC) is a powerful strategy for the rapid identification of novel hits. Even though acylhydrazones are important structural motifs in medicinal chemistry, their further progression in development may be hampered by major instability and potential toxicity under physiological conditions. It is therefore of paramount importance to identify stable replacements for acylhydrazone linkers. Herein, we present the first report on the design and synthesis of stable bioisosteres of acylhydrazone-based inhibitors of the aspartic protease Endothiapepsin as a follow-up to a DCC study. The most successful bioisostere is equipotent, bears an amide linker, and we confirmed its binding mode by X-ray crystallography. Having some validated bioisosteres of acylhydrazones readily available might accelerate hit-to-lead optimization in future acylhydrazone-based DCC projects.
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fragment based drug design facilitated by protein templated click chemistry fragment linking and optimization of inhibitors of the aspartic protease Endothiapepsin
Chemistry: A European Journal, 2016Co-Authors: Milon Mondal, Asish Pal, Matthijs Bakker, Stephan P. Berrier, Yagiz M Unver, Anna K. H. HirschAbstract:There is an urgent need for the development of efficient methodologies that accelerate drug discovery. We demonstrate that the strategic combination of fragment linking/optimization and protein-templated click chemistry is an efficient and powerful method that accelerates the hit-identification process for the aspartic protease Endothiapepsin. The best binder, which inhibits Endothiapepsin with an IC50 value of 43 μm, represents the first example of triazole-based inhibitors of Endothiapepsin. Our strategy could find application on a whole range of drug targets.
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www.mdpi.com/journal/ijms Article Structure-Based Optimization of Inhibitors of the Aspartic
2016Co-Authors: Protease Endothiapepsin, Milon Mondal, Gerhard Klebe, Alwin M. Hartman, Nedyalka Radeva, Anna K. H. HirschAbstract:Abstract: Aspartic proteases are a class of enzymes that play a causative role in numerous diseases such as malaria (plasmepsins), Alzheimer’s disease (β-secretase), fungal infections (secreted aspartic proteases), and hypertension (renin). We have chosen Endothiapepsin as a model enzyme of this class of enzymes, for the design, preparation and biochemical evaluation of a new series of inhibitors of Endothiapepsin. Here, we have optimized a hit, identified by de novo structure-based drug design (SBDD) and DCC, by using structure-based design approaches focusing on the optimization of an amide–π interaction. Biochemical results are in agreement with SBDD. These results will provide useful insights for future structure-based optimization of inhibitors for the real drug targets as well as insights into molecular recognition
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fragment linking and optimization of inhibitors of the aspartic protease Endothiapepsin fragment based drug design facilitated by dynamic combinatorial chemistry
Angewandte Chemie, 2016Co-Authors: Milon Mondal, Gerhard Klebe, Nedyalka Radeva, Hugo Fanlovirgos, Sijbren Otto, Anna K. H. HirschAbstract:Fragment-based drug design (FBDD) affords active compounds for biological targets. While there are numerous reports on FBDD by fragment growing/optimization, fragment linking has rarely been reported. Dynamic combinatorial chemistry (DCC) has become a powerful hit-identification strategy for biological targets. We report the synergistic combination of fragment linking and DCC to identify inhibitors of the aspartic protease Endothiapepsin. Based on X-ray crystal structures of Endothiapepsin in complex with fragments, we designed a library of bis-acylhydrazones and used DCC to identify potent inhibitors. The most potent inhibitor exhibits an IC50 value of 54 nm, which represents a 240-fold improvement in potency compared to the parent hits. Subsequent X-ray crystallography validated the predicted binding mode, thus demonstrating the efficiency of the combination of fragment linking and DCC as a hit-identification strategy. This approach could be applied to a range of biological targets, and holds the potential to facilitate hit-to-lead optimization.
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fragmentverknupfung und optimierung von hemmstoffen der aspartylprotease Endothiapepsin fragmentbasiertes wirkstoffdesign beschleunigt durch dynamische kombinatorische chemie
Angewandte Chemie, 2016Co-Authors: Milon Mondal, Gerhard Klebe, Nedyalka Radeva, Hugo Fanlovirgos, Sijbren Otto, Anna K. H. HirschAbstract:Fragmentbasiertes Wirkstoffdesign (FBWD) fuhrt zu pharmakologisch aktiven Substanzen fur biologische Targets. Obschon es zahlreiche Beispiele fur FBWD anhand von Fragmentwachstum und -optimierung gibt, wird die Verknupfung von Fragmenten nur selten verwendet. Dynamische kombinatorische Chemie (DKC) ist zu einer erfolgreichen Strategie fur die Identifizierung von Hits fur biologische Targets herangewachsen. Wir berichten hier uber die synergistische Kombination von Fragmentverknupfung und DKC, um Inhibitoren der Aspartylprotease Endothiapepsin zu identifizieren. Aufbauend auf Rontgenkristallstrukturen von Endothiapepsin im Komplex mit Fragmenten haben wir eine Bibliothek von Bisacylhydrazonen entworfen und DKC benutzt, um potente Hemmstoffe des Enzyms zu identifizieren: Der starkste Hemmstoff besitzt einen IC50-Wert von 54 nm, was eine 240-fache Steigerung der Affinitat im Vergleich zu den Ausgangstreffern darstellt. Anschliesend hat die Rontgenkristallographie den vorhergesagten Bindungsmodus bestatigt und somit die Effizienz der Kombination aus Fragmentverknupfung und DKC als Strategie fur die Identifizierung von Hits unterstrichen. Die Methode kann fur eine Reihe biologischer Targets Anwendung finden und sollte das Potenzial haben, die Optimierung eines Hits zu einer Leitstruktur zu vereinfachen.
Nedyalka Radeva - One of the best experts on this subject based on the ideXlab platform.
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A False-Positive Screening Hit in Fragment-Based Lead Discovery: Watch out for the Red Herring.
Angewandte Chemie (International ed. in English), 2017Co-Authors: J. Cramer, Johannes Schiebel, Nedyalka Radeva, F R Ehrmann, Tobias Wulsdorf, Kristof Grohe, Eszter E. Najbauer, Nina Zitzer, Uwe Linne, Rasmus LinserAbstract:With the rising popularity of fragment-based approaches in drug development, more and more attention has to be devoted to the detection of false-positive screening results. In particular, the small size and low affinity of fragments drives screening techniques to their limit. The pursuit of a false-positive hit can cause significant loss of time and resources. Here, we present an instructive and intriguing investigation into the origin of misleading assay results for a fragment that emerged as the most potent binder for the aspartic protease Endothiapepsin (EP) across multiple screening assays. This molecule shows its biological effect mainly after conversion into another entity through a reaction cascade that involves major rearrangements of its heterocyclic scaffold. The formed ligand binds EP through an induced-fit mechanism involving remarkable electrostatic interactions. Structural information in the initial screening proved to be crucial for the identification of this false-positive hit.
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active site mapping of an aspartic protease by multiple fragment crystal structures versatile warheads to address a catalytic dyad
Journal of Medicinal Chemistry, 2016Co-Authors: Nedyalka Radeva, Xiaojie Wang, Johannes Schiebel, S G Krimmer, Martin Stieler, F R Ehrmann, A Metz, Thomas Rickmeyer, Michael Betz, Johan WinquistAbstract:Crystallography is frequently used as follow-up method to validate hits identified by biophysical screening cascades. The capacity of crystallography to directly screen fragment libraries is often underestimated, due to its supposed low-throughput and need for high-quality crystals. We applied crystallographic fragment screening to map the protein-binding site of the aspartic protease Endothiapepsin by individual soaking experiments. Here, we report on 41 fragments binding to the catalytic dyad and adjacent specificity pockets. The analysis identifies already known warheads but also reveals hydrazide, pyrazole, or carboxylic acid fragments as novel functional groups binding to the dyad. A remarkable swapping of the S1 and S1′ pocket between structurally related fragments is explained by either steric demand, required displacement of a well-bound water molecule, or changes of trigonal-planar to tetrahedral geometry of an oxygen functional group in a side chain. Some warheads simultaneously occupying both S...
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www.mdpi.com/journal/ijms Article Structure-Based Optimization of Inhibitors of the Aspartic
2016Co-Authors: Protease Endothiapepsin, Milon Mondal, Gerhard Klebe, Alwin M. Hartman, Nedyalka Radeva, Anna K. H. HirschAbstract:Abstract: Aspartic proteases are a class of enzymes that play a causative role in numerous diseases such as malaria (plasmepsins), Alzheimer’s disease (β-secretase), fungal infections (secreted aspartic proteases), and hypertension (renin). We have chosen Endothiapepsin as a model enzyme of this class of enzymes, for the design, preparation and biochemical evaluation of a new series of inhibitors of Endothiapepsin. Here, we have optimized a hit, identified by de novo structure-based drug design (SBDD) and DCC, by using structure-based design approaches focusing on the optimization of an amide–π interaction. Biochemical results are in agreement with SBDD. These results will provide useful insights for future structure-based optimization of inhibitors for the real drug targets as well as insights into molecular recognition
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Experimental Active-Site Mapping by Fragments: Hot Spots Remote from the Catalytic Center of Endothiapepsin
Journal of medicinal chemistry, 2016Co-Authors: Nedyalka Radeva, F.u. Huschmann, Xiaojie Wang, Alexander Metz, Manfred S. Weiss, S G Krimmer, Martin Stieler, F R Ehrmann, Uwe MuellerAbstract:Successful optimization of a given lead scaffold requires thorough binding-site mapping of the target protein particular in regions remote from the catalytic center where high conservation across protein families is given. We screened a 361-entry fragment library for binding to the aspartic protease Endothiapepsin by crystallography. This enzyme is frequently used as a surrogate for the design of renin and β-secretase inhibitors. A hit rate of 20% was achieved, providing 71 crystal structures. Here, we discuss 45 binding poses of fragments accommodated in pockets remote from the catalytic dyad. Three major hot spots are discovered in remote binding areas: Asp81, Asp119, and Phe291. Compared to the dyad binders, bulkier fragments occupy these regions. Many of the discovered fragments suggest an optimization concept on how to grow them into larger ligands occupying adjacent binding pockets that will possibly endow them with the desired selectivity for one given member of a protein family.
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fragment linking and optimization of inhibitors of the aspartic protease Endothiapepsin fragment based drug design facilitated by dynamic combinatorial chemistry
Angewandte Chemie, 2016Co-Authors: Milon Mondal, Gerhard Klebe, Nedyalka Radeva, Hugo Fanlovirgos, Sijbren Otto, Anna K. H. HirschAbstract:Fragment-based drug design (FBDD) affords active compounds for biological targets. While there are numerous reports on FBDD by fragment growing/optimization, fragment linking has rarely been reported. Dynamic combinatorial chemistry (DCC) has become a powerful hit-identification strategy for biological targets. We report the synergistic combination of fragment linking and DCC to identify inhibitors of the aspartic protease Endothiapepsin. Based on X-ray crystal structures of Endothiapepsin in complex with fragments, we designed a library of bis-acylhydrazones and used DCC to identify potent inhibitors. The most potent inhibitor exhibits an IC50 value of 54 nm, which represents a 240-fold improvement in potency compared to the parent hits. Subsequent X-ray crystallography validated the predicted binding mode, thus demonstrating the efficiency of the combination of fragment linking and DCC as a hit-identification strategy. This approach could be applied to a range of biological targets, and holds the potential to facilitate hit-to-lead optimization.
L Coates - One of the best experts on this subject based on the ideXlab platform.
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Preliminary neutron and ultrahigh-resolution X-ray diffraction studies of the aspartic proteinase Endothiapepsin cocrystallized with a gem-diol inhibitor.
Acta Crystallogr Sect F Struct Biol Cryst Commun, 2007Co-Authors: L CoatesAbstract:Endothiapepsin has been cocrystallized with the gem-diol inhibitor PD-135,040 in a low solvent-content (39%) unit cell, which is unprecedented for this enzyme-inhibitor complex and enables ultrahigh-resolution (1.0 A) X-ray diffraction data to be collected. This atomic resolution X-ray data set will be used to deduce the protonation states of the catalytic aspartate residues. A room-temperature neutron data set has also been collected for joint refinement with a room-temperature X-ray data set in order to locate the H/D atoms at the active site.
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atomic resolution analysis of the catalytic site of an aspartic proteinase and an unexpected mode of binding by short peptides
Protein Science, 2003Co-Authors: P.t. Erskine, L Coates, S P Wood, S Mall, R. Gill, D A Myles, JB CooperAbstract:The X-ray structures of native Endothiapepsin and a complex with a hydroxyethylene transition state analog inhibitor (H261) have been determined at atomic resolution. Unrestrained refinement of the carboxyl groups of the enzyme by using the atomic resolution data indicates that both catalytic aspartates in the native enzyme share a single negative charge equally; that is, in the crystal, one half of the active sites have Asp 32 ionized and the other half have Asp 215 ionized. The electron density map of the native enzyme refined at 0.9 Å resolution demonstrates that there is a short peptide (probably Ser-Thr) bound noncovalently in the active site cleft. The N-terminal nitrogen of the dipeptide interacts with the aspartate diad of the enzyme by hydrogen bonds involving the carboxyl of Asp 215 and the catalytic water molecule. This is consistent with classical findings that the aspartic proteinases can be inhibited weakly by short peptides and that these enzymes can catalyze transpeptidation reactions. The dipeptide may originate from autolysis of the N-terminal Ser-Thr sequence of the enzyme during crystallization.
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The structure of Endothiapepsin complexed with the gem-diol inhibitor PD-135,040 at 1.37 A.
Acta crystallographica. Section D Biological crystallography, 2003Co-Authors: L Coates, S P Wood, P.t. Erskine, S Mall, P A Williams, R S Gill, JB CooperAbstract:The crystal structure of Endothiapepsin complexed with the gem-diol inhibitor PD-135,040 has been anisotropically refined to a resolution of 1.37 A. The structure of this inhibitor complex is in agreement with previous structures of Endothiapepsin gem-diol inhibitor complexes that have been used to develop proposed catalytic mechanisms. However, the increase in resolution over previous structures confirms the presence of a number of short hydrogen bonds within the active site that are likely to play an important role in the catalytic mechanism. The presence of low-barrier hydrogen bonds was indicated in a previous one-dimensional H NMR spectrum.
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five atomic resolution structures of Endothiapepsin inhibitor complexes implications for the aspartic proteinase mechanism
Journal of Molecular Biology, 2002Co-Authors: L Coates, Matthew P Crump, S P Wood, P.t. Erskine, JB CooperAbstract:Endothiapepsin is derived from the fungus Endothia parasitica and is a member of the aspartic proteinase class of enzymes. This class of enzyme is comprised of two structurally similar lobes, each lobe contributing an aspartic acid residue to form a catalytic dyad that acts to cleave the substrate peptide bond. The three-dimensional structures of Endothiapepsin bound to five transition state analogue inhibitors (H189, H256, CP-80,794, PD-129,541 and PD-130,328) have been solved at atomic resolution allowing full anisotropic modelling of each complex. The active sites of the five structures have been studied with a view to studying the catalytic mechanism of the aspartic proteinases by locating the active site protons by carboxyl bond length differences and electron density analysis. In the CP-80,794 structure there is excellent electron density for the hydrogen on the inhibitory statine hydroxyl group which forms a hydrogen bond with the inner oxygen of Asp32. The location of this proton has implications for the catalytic mechanism of the aspartic proteinases as it is consistent with the proposed mechanism in which Asp32 is the negatively charged aspartate. A number of short hydrogen bonds (∼2.6 A) with ESD values of around 0.01 A that may have a role in catalysis have been identified within the active site of each structure; the lengths of these bonds have been confirmed using NMR techniques. The possibility and implications of low barrier hydrogen bonds in the active site are considered.
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a neutron laue diffraction study of Endothiapepsin implications for the aspartic proteinase mechanism
Biochemistry, 2001Co-Authors: L Coates, S P Wood, P.t. Erskine, D A Myles, JB CooperAbstract:Current proposals for the catalytic mechanism of aspartic proteinases are largely based on X-ray structures of bound oligopeptide inhibitors possessing nonhydrolyzable analogues of the scissile peptide bond. However, the positions of protons on the catalytic aspartates and the ligand in these complexes have not been determined with certainty. Thus, our objective was to locate crucial protons at the active site of an inhibitor complex since this will have major implications for a detailed understanding of the mechanism of action. We have demonstrated that high-resolution neutron diffraction data can be collected from crystals of the fungal aspartic proteinase Endothiapepsin bound to a transition state analogue (H261). The neutron structure of the complex has been refined at a resolution of 2.1 A to anR-factor of 23.5% and an Rfree of 27.4%. This work represents the largest protein structure studied to date by neutron crystallography at high resolution. The neutron data demonstrate that 49% of the main chain nitrogens have exchanged their hydrogen atoms with D2O in the mother liquor. The majority of residues resisting exchange are buried within core ‚-sheet regions of the molecule. The neutron maps confirm that the protein has a number of buried ionized carboxylate groups which are likely to give the molecule a net negative charge even at very low pH, thereby accounting for its low pI. The functional groups at the catalytic center have clearly undergone H-D exchange despite being buried by the inhibitor occupying the active site cleft. Most importantly, the data provide convincing evidence that Asp 215 is protonated and that Asp 32 is the negatively charged residue in the transition state complex. This has an important bearing on mechanistic proposals for this class of proteinase.
Milon Mondal - One of the best experts on this subject based on the ideXlab platform.
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Design and Synthesis of Bioisosteres of Acylhydrazones as Stable Inhibitors of the Aspartic Protease Endothiapepsin.
ChemMedChem, 2018Co-Authors: Varsha R. Jumde, Milon Mondal, M. Yagiz Unver, Andreas Heine, Gerhard Klebe, Robin M. Gierse, F. Magari, Roos C. W. Van Lier, Anna K. H. HirschAbstract:Acylhydrazone-based dynamic combinatorial chemistry (DCC) is a powerful strategy for the rapid identification of novel hits. Even though acylhydrazones are important structural motifs in medicinal chemistry, their further progression in development may be hampered by major instability and potential toxicity under physiological conditions. It is therefore of paramount importance to identify stable replacements for acylhydrazone linkers. Herein, we present the first report on the design and synthesis of stable bioisosteres of acylhydrazone-based inhibitors of the aspartic protease Endothiapepsin as a follow-up to a DCC study. The most successful bioisostere is equipotent, bears an amide linker, and we confirmed its binding mode by X-ray crystallography. Having some validated bioisosteres of acylhydrazones readily available might accelerate hit-to-lead optimization in future acylhydrazone-based DCC projects.
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fragment based drug design facilitated by protein templated click chemistry fragment linking and optimization of inhibitors of the aspartic protease Endothiapepsin
Chemistry: A European Journal, 2016Co-Authors: Milon Mondal, Asish Pal, Matthijs Bakker, Stephan P. Berrier, Yagiz M Unver, Anna K. H. HirschAbstract:There is an urgent need for the development of efficient methodologies that accelerate drug discovery. We demonstrate that the strategic combination of fragment linking/optimization and protein-templated click chemistry is an efficient and powerful method that accelerates the hit-identification process for the aspartic protease Endothiapepsin. The best binder, which inhibits Endothiapepsin with an IC50 value of 43 μm, represents the first example of triazole-based inhibitors of Endothiapepsin. Our strategy could find application on a whole range of drug targets.
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www.mdpi.com/journal/ijms Article Structure-Based Optimization of Inhibitors of the Aspartic
2016Co-Authors: Protease Endothiapepsin, Milon Mondal, Gerhard Klebe, Alwin M. Hartman, Nedyalka Radeva, Anna K. H. HirschAbstract:Abstract: Aspartic proteases are a class of enzymes that play a causative role in numerous diseases such as malaria (plasmepsins), Alzheimer’s disease (β-secretase), fungal infections (secreted aspartic proteases), and hypertension (renin). We have chosen Endothiapepsin as a model enzyme of this class of enzymes, for the design, preparation and biochemical evaluation of a new series of inhibitors of Endothiapepsin. Here, we have optimized a hit, identified by de novo structure-based drug design (SBDD) and DCC, by using structure-based design approaches focusing on the optimization of an amide–π interaction. Biochemical results are in agreement with SBDD. These results will provide useful insights for future structure-based optimization of inhibitors for the real drug targets as well as insights into molecular recognition
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fragment linking and optimization of inhibitors of the aspartic protease Endothiapepsin fragment based drug design facilitated by dynamic combinatorial chemistry
Angewandte Chemie, 2016Co-Authors: Milon Mondal, Gerhard Klebe, Nedyalka Radeva, Hugo Fanlovirgos, Sijbren Otto, Anna K. H. HirschAbstract:Fragment-based drug design (FBDD) affords active compounds for biological targets. While there are numerous reports on FBDD by fragment growing/optimization, fragment linking has rarely been reported. Dynamic combinatorial chemistry (DCC) has become a powerful hit-identification strategy for biological targets. We report the synergistic combination of fragment linking and DCC to identify inhibitors of the aspartic protease Endothiapepsin. Based on X-ray crystal structures of Endothiapepsin in complex with fragments, we designed a library of bis-acylhydrazones and used DCC to identify potent inhibitors. The most potent inhibitor exhibits an IC50 value of 54 nm, which represents a 240-fold improvement in potency compared to the parent hits. Subsequent X-ray crystallography validated the predicted binding mode, thus demonstrating the efficiency of the combination of fragment linking and DCC as a hit-identification strategy. This approach could be applied to a range of biological targets, and holds the potential to facilitate hit-to-lead optimization.
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fragmentverknupfung und optimierung von hemmstoffen der aspartylprotease Endothiapepsin fragmentbasiertes wirkstoffdesign beschleunigt durch dynamische kombinatorische chemie
Angewandte Chemie, 2016Co-Authors: Milon Mondal, Gerhard Klebe, Nedyalka Radeva, Hugo Fanlovirgos, Sijbren Otto, Anna K. H. HirschAbstract:Fragmentbasiertes Wirkstoffdesign (FBWD) fuhrt zu pharmakologisch aktiven Substanzen fur biologische Targets. Obschon es zahlreiche Beispiele fur FBWD anhand von Fragmentwachstum und -optimierung gibt, wird die Verknupfung von Fragmenten nur selten verwendet. Dynamische kombinatorische Chemie (DKC) ist zu einer erfolgreichen Strategie fur die Identifizierung von Hits fur biologische Targets herangewachsen. Wir berichten hier uber die synergistische Kombination von Fragmentverknupfung und DKC, um Inhibitoren der Aspartylprotease Endothiapepsin zu identifizieren. Aufbauend auf Rontgenkristallstrukturen von Endothiapepsin im Komplex mit Fragmenten haben wir eine Bibliothek von Bisacylhydrazonen entworfen und DKC benutzt, um potente Hemmstoffe des Enzyms zu identifizieren: Der starkste Hemmstoff besitzt einen IC50-Wert von 54 nm, was eine 240-fache Steigerung der Affinitat im Vergleich zu den Ausgangstreffern darstellt. Anschliesend hat die Rontgenkristallographie den vorhergesagten Bindungsmodus bestatigt und somit die Effizienz der Kombination aus Fragmentverknupfung und DKC als Strategie fur die Identifizierung von Hits unterstrichen. Die Methode kann fur eine Reihe biologischer Targets Anwendung finden und sollte das Potenzial haben, die Optimierung eines Hits zu einer Leitstruktur zu vereinfachen.