article: Chagas disease, caused by Trypanosoma cruzi, affects millions of people in South America and no satisfactory therapy exists, especially for its life threatening chronic phase. We targeted the Proline Racemase of T. cruzi, which is present in all stages of the parasite life cycle, to discover new inhibitors against this disease. The first published crystal structures of the enzyme revealed that the catalytic site is too small to allow any relevant drug design. In previous work, to break through the chemical space afforded to virtual screening and drug design, we generated intermediate models between the open (ligand free) and closed (ligand bound) forms of the enzyme. In the present work, we co-crystallized the enzyme with the selected inhibitors and found that they were covalently bound to the catalytic cysteine residues in the active site, thus explaining why these compounds act as irreversible inhibitors. These results led us to the design of a novel, more potent specific inhibitor, NG-P27. Co-crystallization of this new inhibitor with the enzyme allowed us to confirm the predicted protein functional motions and further characterize the chemical mechanism. Hence, the catalytic Cys300 sulfur atom of the enzyme attacks the C2 carbon of the inhibitor in a coupled, regiospecific—stereospecific Michael reaction with trans-addition of a proton on the C3 carbon. Strikingly, the six different conformations of the catalytic site in the crystal structures reported in this work had key similarities to our intermediate models previously generated by inference of the protein functional motions. These crystal structures span a conformational interval covering roughly the first quarter of the opening mechanism, demonstrating the relevance of modeling approaches to break through chemical space in drug design.
  Chagas disease, with nearly 10 million people infected and 100 million at risk, is the principal cause of lethality from neglected tropical diseases in Central and South America, and a leading one among all infectious diseases [1]. It is often fatal to young children and incurable in its chronic phase, which persists for decades and inflicts 10% annual lethality [2,3]. In addition to its severe socioeconomic burden [1], Chagas disease is becoming a global concern as it extends to northern countries following human migrations. There is currently no effective vaccine, and after substantial restriction in indications for the use of Nifurtimox due to severe side effects [4,5], Benznidazole is the only generally available drug, but still causes serious side effects [6]. Drugs can be efficient in the acute phase, but are of questionable value in the chronic phase of the disease. Hence, it is considered a priority to find more effective treatments [7,8]. Unfortunately, no satisfactory compounds have been identified so far [9] despite the identification of promising therapeutic targets [10]. Proline racemase of Trypanosoma cruzi (TcPRAC) is an enzyme present at all stages of the parasite life cycle, contributing to immune escape and persistence of the parasite in the host [11,12]. Gene over-expression increases virulence, while knockdown appears lethal for T. cruzi [13]. Interestingly, a transition analog inhibitor of TcPRAC, 2-pyrrolecarboxylic acid (PYC), reduces in vitro infection in a dose-dependent manner [14] and decreases the mean number of parasites per cell [15]. These results, despite the poor solubility of PYC, supported TcPRAC as a promising target to fight Chagas disease. Co-crystallization of TcPRAC with PYC showed highly specific and tightly closed catalytic sites of the enzyme (pdb 1W61), which left almost no space for modulation of inhibitor candidates [16]. Accordingly, conventional drug design strategies based on this structure proved unsuccessful. The structure also showed that TcPRAC crystallizes as a homodimer and bears a catalytic site on each subunit. Interestingly, a crystal of a hemi-saturated form (pdb 1W62) showed the free subunit catalytic site in an open form. This suggested that the enzyme function involved an opening/closing mechanism with intermediate forms that could be used to identify and design novel types of inhibitors. To test this hypothesis, we modeled plausible intermediates of the functional opening/closing motions of TcPRAC [17]. This strategy allowed an expansion of the chemical space used in our virtual screening procedure and led us to identify two inhibitors of the enzyme, (E) -4-Oxo-pent-2-enoic acid (OxoPA) [18] and its derivative (E) -5-Bromo-4-oxo-pent-2-enoic acid (BrOxoPA) which were far more potent than PYC [17]. Although conventional strategies in drug design focus on competitive inhibitors, the identification of covalent inhibitors is fortunate considering the growing interest in this type of enzymatic inhibitors [19,20]. Indeed, a number of previously known anti-infectious agents (β-lactames, antivirals) [21,22] or more recently the proton pump inhibitors [23], are irreversible inhibitors that have been successfully used for therapeutic purposes. This strategy was used by Ellmann and colleagues to design cruzipaine inhibitors for T. cruzi [24,25]. Optimization of irreversible inhibitors requires the development of advanced and specific methods taking pre- and post-reaction states into account in the design of chemical chemical analogues aiming at therapeutic use [23]. Resolution of the OxoPA and BrOxoPA co-complexes in this work turned out to be a key step in the design of improved drug candidates, since it showed their detailed atomic interactions in the catalytic site and identified atoms involved in covalent bond formation. This enabled us to model the candidate structures and their interactions with the enzyme both before and after the reaction, allowing the induced changes in chemical connectivity and geometry to be taken into account in the design process. Accordingly, we could probe the determinants for affinity and selectivity by modulation of the electrophilic moieties of design candidates taking into account the position of the nucleophilic catalytic cysteine. The designed candidate displaying the best TcPRAC enzymatic inhibition, NG-P27, exhibited trypanostatic/trypanocydal activity in preliminary in vitro experiments. The crystal structure of NG-P27 in complex with the enzyme revealed the position of the inhibitor after reaction along a regiospecific and stereospecific Michael mechanism. The structure also revealed that the cyclopentane moiety of the inhibitor could adopt multiple conformations, suggesting that space was available for further chemical modulations. Interestingly, the conformation of the active site in the co-crystal structures with our inhibitors was highly similar to that of the transitional intermediate models built to identify the first inhibitors by virtual screening [17]. This could be viewed as a demonstration of the relevance of molecular modeling in enlarging chemical space search in drug design.
  Recombinant Trypanosoma cruzi proline racemase (EC 5. 1. 1. 4) was produced in E. coli BL21 (DE3) (Invitrogen) and purified by immobilized metal affinity chromatography on nickel columns, as previously described [11]. Proline racemization conditions for TcPRAC were determined as previously described [12] and L- to D- proline conversion took place in 1. 0 mL reaction. The concentrations of D-proline were determined by optical rotation of the solution at 365 nm with a 10 cm optical path cell, at 37°C for 103 seconds using a polarimeter (Jasco, P-2000, Bouguenais, France). Assays were performed as follows: 40 mM of L-Proline in 0. 2 M sodium acetate pH 6. 0 and 5 μg/mL of TcPRAC were loaded into tubes with serial dilutions of PYC, OxoPA and BrOxoPA (from 0. 3125 to 5 μM), or similar concentrations of potential optimized inhibitors. Inactivation kinetics were performed at different inhibitor concentrations as described previously [17,26,27]. A program developed in-house was used to fit the data [17,26,27]. As global fitting appeared difficult and was unsuccessful, single exponential models were simply fit to the individual kinetics. Each fit was checked visually. Crystallization screening trials for TcPRAC in complex with the compounds BrOxoPA, OxoPA, and NG-P27 were carried out by the sitting drop vapor-diffusion method with a Mosquito automated nanoliter dispensing system (TTP Labtech, Melbourn, UK). Sitting drops of 400 nL were set up in Greiner plates for 672 commercially available screening solutions with a 1: 1 mixture of protein complex at 10mg/mL equilibrated against 150 μL of reservoir solution. The plates were stored at 18°C in a RockImager (Formulatrix, Bedford, USA) automated imaging system to monitor crystal growth. Best crystals of TcPRAC in complex with the inhibitors in 1mM solutions were obtained with a solution of 0. 2 M potassium phosphate dibasic and 21% (w/v) PEG-3350. Crystals with dimensions of up to 0. 1 mm x 0. 1 mm x 0. 05 mm appeared within one week. For data collection, the crystals were flash-cooled in liquid nitrogen using a paratone-paraffin oil mixture (50%/50%) as cryoprotectant. X-ray diffraction data were collected on beamline PROXIMA-1 at synchrotron SOLEIL (St Aubin, France). Diffraction images were integrated with the program XDS [28–32] and crystallographic calculations were carried out with programs from the CCP4 program suite [28–32]. The structures were solved by molecular replacement using Phaser [28–32] with TcPRAC in complex with PYC (pdb 1W61) [16] as a template. Refinement was done using Refmac5 [28–32] with alternating manual rebuilding in Coot [28–32]. Crystallographic data and refinement statistics are shown in Table 1. The refined models and structure factors have been deposited in the Research Collaboratory for Structural Biology Protein Data Bank (hyperlink" http: //www. rcsb. org/" ) under the following accession numbers: TcPRAC-BrOxoPA (6HJF), TcPRAC-OxoPA (6HJG), TcPRAC-NG-P27 (6HJE). Description of the synthesis of TcPRAC inhibitors is given in" General Information on Chemical Synthesis" (S1 Text)," Synthetic procedures" (S2 Text) and Refs. [33–35]. The spectral characterization of the compounds is given in the" 1H and 13C spectra" (S1 Spectra). For conformational analysis, the atomic coordinates of the TcPRAC structures were limited to residues 45–394 for which the electron density could be traced in all structures. Amino acids (K152, E178, R210, P280, E281, Y294), whose side chains were not visible in all the structures, were replaced by alanine. Symmetric structures were generated by swapping the chain names (e. g. A to B and B to A) before alignment. The crystal structures, the 49 models [17], and their symmetric forms were structurally aligned by rotation and translation minimizing the root mean square distances for each set of atoms subjected to Principal Component Analysis (PCA). These sets were, respectively, the dimers, the protomers, and the amino-acids (E56, F102, L127, N128, M129, C130, G131, H132, G217, N218, F220, D269, C270, V288, F290, G291, D296, S298, C300, G301, T302, G303) defining the pocket used for virtual screening in the previous study [17]. In the description of the analysis, the protomers from the crystal structures are named according to the following scheme: Code-C, or Lig-C, with Code, the PDB code, and Lig, OxoPA or NG-P27, the ligand present in the structure, and C the chain, A or B of the protein. The protomers from the transitional models are designated: confNC, with N, the index of the model intermediate in the transitional series, and C, the chain name as indicated above. We used an in-house program to calculate cavity volumes in the pockets on a grid of voxels [36,37]. Settings and parameters were similar to those previously reported [17], but further refinements were incorporated to delineate cavities opened to the bulk solvent. The latter was scooped out with a large rolling probe sphere of 10 Å radius with an extra erosion shell of 3. 3 Å to remove the exposed part of the cavity. To discriminate the volume of the channel induced by opening from the volume delineated by the binding pocket, only cavity voxels that had one of the residues of the pocket as closest neighbor were counted. Epimastigote forms of CL Brener (clone F11-F5) and Y strains of Trypanosoma cruzi [38] constitutively expressing luciferase were maintained by weekly passage in Liver Infusion Tryptose (LIT) medium. Stock solutions (1M) of Benznidazole and NG-P27 were prepared in DMSO and subsequently diluted in LIT medium. Trypanosomal growth inhibition was determined by the evaluation of parasite number after 72h in triplicates. 105 epimastigotes cultured in white microtiter plates in absence or presence of 5–1000 μM of NG-P27 were compared to results obtained with the same concentrations of Benznidazole (added once, or every day for three days) in a final volume of 200 μL. Luminescence signals emitted by live parasites in the microplate wells were quantified by the addition of 0. 3 mg/mL D-luciferin (122799, Perkin Elmer, Villebon-sur-Yvette, France) in a TECAN luminometer (Infinity F200 Pro, Lyon, France). IC 50 was determined by using a non-linear fitting of the percentage of inhibition calculated after comparison to untreated controls.
  BrOxoPA and OxoPA were co-crystallized with the enzyme. The crystallographic data and refinement statistics are shown in Table 1. The complexes crystallized in the same space group and with similar unit cell dimensions as the TcPRAC/PYC complex structure reported previously (pdb 1W61) [16]. The crystallographic asymmetric unit contains two independent polypeptide chains (A, B) forming a homodimer. In the TcPRAC-OxoPA complex, continuous electron density was seen for residues 40–394 in chain A and 45 to 398 in chain B. The overall structure closely resembles that of the enzyme in complex with PYC (1W61; Fig 1A), with an overall RMS deviation in alpha carbon positions of 0. 227 Å. The position and orientation of the side chains of residues in the active site region are similar in both structures (Fig 1B). Significant electron density for the inhibitor was observed in the active site of both chains (Fig 1C). Atoms C2 and C5 of BrOxoPA are covalently bound to the sulfur atoms of Cys300 and Cys130, respectively (Fig 1C, S1 Table). These covalent interactions can explain the irreversible inhibition of TcPRAC by BrOxoPA. The carboxylate moiety of the inhibitor also forms a hydrogen-bonding network with the main polypeptide chain or side chains of Gly131, His132, Gly301, and Thr302 in the active site region (Fig 1C, S1 Table). These residues are also involved in the non-covalent binding of the PYC inhibitor as previously described [16]. No electron density was observed for the bromine atom of the BrOxoPA inhibitor in difference Fourier maps, and X-ray fluorescence scans indicate the absence of bromine in crystals of the complex, suggesting that the bromine atom of the inhibitor was cleaved during the binding reaction of BrOxoPA with the enzyme. The TcPRAC-OxoPA structure presented similar global characteristics. However, comparison with the other structures is less straightforward due to greater dissymmetry between the two monomers. The impact of ligand binding on TcPRAC conformation is described below and a more comprehensive analysis is provided in S3 Text. In both monomers, well defined electron density is seen for the carboxylic moieties as for BrOxoPA and PYC, but the absence of well-defined density for the ketone moiety in the OxoPA complex suggests that this part of the ligand had more relaxation freedom, and covalent interaction was not observed. These observations were confirmed by pharmacomodulations performed to optimize chemically OxoPA and BrOxoPA (see below). Analysis of X-ray crystallographic data of the TcPRAC/BrOxoPA complex revealed two covalent bonds with the catalytic cysteine residues of TcPRAC. This confirmed the high potential of the ligand and prompted us to probe the available chemical space to design a more specific covalent inhibitor. Hence, the nature of the Michael acceptor was modified and substituents were introduced at different positions of the skeleton (Fig 2). About 60 compounds were synthesized following these principles and their ability to inhibit TcPRAC was evaluated by polarimetric assay. Compounds 1 to 6 are key examples of the pharmacomodulations (Fig 2A). Their respective activities on TcPRAC (Fig 2B) are compared with those of OxoPA and BrOxoPA (Fig 2C). Replacement of the ketone group with the highly electroattractive sulfoxide (1) or a sulfone (2), commonly used to design Michael acceptors [39], abolished inhibition. Differences in spatial arrangement and geometry of the tetrahedral sp3 sulfoxide/sulfone as compared to the trigonal sp2 ketone could explain this unforeseen result. Introduction of a triple bond (3) instead of the classical double bond Michael acceptor also abolished inhibition. Further modulations were performed on the skeleton to probe possible extension/modulation sites. Addition on the electrophilic site, C-2, (4) close to the Cys300 attack position, prevented inhibition. By contrast, additions at positions C-3 (5,6), C3 and C5 (7) or C-5 only (8,9) moderately affected or maintained inhibition (Fig 2D et 2E). Compound 6 (NG-P27), bearing a five-membered ring (reminiscent of proline) was the most active derivative. Inhibition kinetics were recorded at various concentrations of PYC, OxoPA and NG-P27 (Fig 3). The kinetic curves in the absence of inhibitor were linear, validating the initial velocity approximation. Except for PYC, the asymptotes of the single exponential fit model depended on the inhibitor concentration and differed from the zero rotatory power line. Hence, the enzyme appeared to reach full inactivation during the reaction. This is typical of an irreversible inhibition mechanism and rules out a reversible competitive inhibition mechanism. The apparent exponential kinetics constant (kobs) varied linearly with the concentration of OxoPA and NG-P27 as expected for an irreversible inhibition mechanism (Fig 3, inset). These results indicate that NG-P27 is a significantly more potent inhibitor than OxoPA. By contrast, the kobs values were nearly zero for PYC, a reversible competitive inhibitor. The NG-P27 compound was co-crystallized with TcPRAC in the same conditions as the BrOxoPA complex (Table 1). The overall structure of the TcPRAC/NG-P27 complex and the conformation of residues in the active site displayed some deviation to the TcPRAC/BrOxoPA, TcPRAC/OxoPA and TcPRAC/PYC complexes, but remained globally similar. Continuous electron density was observed from residues 38–394 in chain A and 43 to 398 in chain B. Difference Fourier electron density maps indicate the presence of the inhibitor NG-P27 covalently bound to Cys300 in the active site of both polypeptide chains in the dimer. Electron density maps suggested possible multiple conformations of the cyclopentanone moiety of the inhibitor, but no attempt was made to refine alternative conformers and we describe here a single conformation of the ligand that best fits the electron density (Fig 4). The C2 atom of NG-P27 is covalently linked to the sulfur Sγ atom of the catalytic Cys300 (Fig 4, S2 Table). In both monomers the inhibitor is very tightly packed, making numerous van der Waals contacts in the active site, and a hydrogen-bonding network stabilizes the carboxylate moiety of NG-P27 as observed for the TcPRAC/BrOxoPA complex (Fig 4B and S2 Table). Ligand binding strongly affects the conformation of the protomers. For example, the two protomers of the hemi-saturated PYC-TcPRAC complex (pdb: 1W62) deviate by 2. 25 Å RMS on Cα positions after alignment. To gain a more comprehensive understanding of the relative motions in all the structures (5 crystal dimers, and 49 intermediate dimer models) we used Principal Component Analysis (see S3 Text for details). The dimers and their symmetric forms (chains A and B swapped) roughly projected as a triangle on their first two Principal Components (Fig 5A). The saturated closed forms (1W61 and BrOxoPA) marked the top vertex. The hemisaturated 1W62 and its symmetric form constituted the base of the triangle, approximately followed by the transition models. Interestingly, OxoPA and NG-P27 displayed structures roughly midway between 1W61 and 1W62 in their direct and symmetrized forms, respectively. One concern with Michael acceptors is their general reactivity, especially towards enzymes with reactive cysteines [40] and thus their lack of specificity. Hence, we tested the reactivity of our inhibitors towards cysteine proteases. As shown in Fig 7, the compounds did not inhibit papain or bromelain. Unlike OxoPA and BrOxoPA, NG-P27 displayed effects on parasite cultures. These effects were determined after 72h on cultures for two parasite populations and compared with the effect of Benznidazole (Fig 8). Both compounds exhibited dose-dependent trypanocydal activity for the CL and Y parasite strains. However, while multiple additions (three times) of Beznidazole increased parasite growth inhibition, no particular cumulative effect was observed after single or multiple treatments with NG-P27.
  The effects of ligand binding on enzyme conformation range from the displacement of a few key residues [51] to global conformational changes [52]. The crystal structures show here a series of stable complexes in intermediate conformations representing a significant portion of the molecular mechanism (projections of protomer conformations ranging from 12 to 49% of the change on the axis between chains A and B of 1W62). This observation highlights the plasticity of the protein and its binding site. Interestingly, this flexibility does not preclude asymmetry, visible in the hemi-saturated form (1W62) and in forms bearing the same ligand in both sites (the OxoPA and NG-P27 complexes, see Fig 5A). The protomer conformations appear to follow a mostly linear opening motion (Fig 5B). Nonetheless, projections of the dimers do not align (Fig 5A) indicating that within dimers, the protomer motions are not coupled in a linear fashion. This asymmetry can be related to the described binding anti-cooperativity of the dimers [16]. Interestingly, our transitional model [17] incorporated asymmetry compatible with the simulation force field. In the active site, significant local reorganization such as refolding of the 130–132 loop is observed (Fig 5C). This refolding process is essential to establish interactions with the carboxylate moiety of the inhibitor and to position Cys130 for catalysis. Interestingly, in conf1A to conf10A of our transition model (Figs 5C and 6A), the 130–132 loop of chain A is folded as observed in the OxoPA and NG-P27 co-crystal structures (Fig 6B). The model for chain B was different and could represent a type of relaxations in the absence of ligand. The binding site conformation and the hydrogen bond network oriented our choice to use chain A of our transition model in our early design strategy [17]. The OxoPA and NG-P27 complex structures show that partial opening of the binding site was an appropriate assumption in our design approach. The conformation of monomer B in the OxoPA and NG-P27 complexes suggests that even larger ligands could be accommodated in the binding site (Table 2), possibly exploiting more open structures of our transitional model. There is an urgent need to develop innovative drugs addressing neglected diseases, multi-drug resistance, and more broadly unmet therapeutic needs. As a new strategy for drug design, we exploit protein functional motions to model plausible structural intermediates of a therapeutic target. We show here that the TcPRAC protein target adopted conformations strikingly close to those of the modeled intermediates, allowing us to design inhibitors that may lead to innovative treatments for Chagas disease. These results demonstrate how modeling protein functional motions can be exploited in a rational approach to create opportunities in drug design. This method should also be useful to complement information provided by static experimental structures for other targets involving functional molecular motions, such as GPCR, neuronal receptors, kinase involving allostery [53].
  Using functional intermediate models to design inhibitors proved successful with the identification of OxoPA, BrOxoPA, and finally NG-P27, a possible starting scaffold in the search for effective therapies against Chagas disease. The similarity between the binding site conformation in our models and in the crystallographic structures reported here demonstrates that computational approaches can make valuable hypotheses to exploit protein functional motions. As a perspective, this approach could also be useful to identify cryptic pockets which are now experimentally recognized as important in drug design [54].
summary: There is an urgent need to develop innovative medicines addressing neglected diseases, multi-drug resistance and other unmet therapeutic needs. To create new drug design opportunities, we attempted to exploit protein functional motions by using a rational approach to model structural intermediates of a therapeutic target. After successfully designing inhibitors based on modeled intermediates of T. Cruzi proline racemase, the determination of crystal structures of the target protein in complex with the inhibitors revealed conformations that were strikingly close to the predicted models. Thus, beyond the discovery of compounds establishing a novel mode of action that can lead to innovative treatments of Chagas disease, we illustrate how modeling protein functional motions can be exploited in a rational approach to create opportunities in drug design.
keywords: medicine and health sciences
  crystal structure
  chemical compounds
  enzymes
  condensed matter physics
  enzymology
  parasitic protozoans
  organic compounds
  protozoans
  drug design
  amino acids
  pharmacology
  crystallography
  enzyme inhibitors
  solid state physics
  proteins
  chemistry
  cyclic amino acids
  proline
  physics
  biochemistry
  enzyme structure
  trypanosoma cruzi
  trypanosoma
  eukaryota
  drug research and development
  organic chemistry
  electron density
  biology and life sciences
  physical sciences
  organisms
title: Designed mono- and di-covalent inhibitors trap modeled functional motions for Trypanosoma cruzi proline racemase in crystallography