Macrocyclic Inhibitors of Penicillopepsin. 2. X-ray Crystallographic Analyses of Penicillopepsin Complexed with a P3−P1 Macrocyclic Peptidyl Inhibitor and with Its Two Acyclic Analogues

Transition-Metal-Free Addition of Dialkyl Phosphites to Phthalazin-2-ium Bromide: Synthesis of α-Aminophosphonate Analogues

α-Aminophosphonate analogues containing a phthalazine skeleton were efficiently obtained by a new transition-metal-free addition of dialkyl phosphites to phthalazin-2-ium bromide under mild conditions. A mechanistic study using isotope labeling and radical inhibition experiment revealed that the present transformation passes through a nucleophilic addition of dialkyl phosphates, rather than an insertion of P-H to carbenes.

Organocatalytic 1,6-hydrophosphination of para-quinone methides: enantioselective access to chiral 3-phosphoxindoles bearing phosphorus-substituted quaternary carbon stereocenters

An efficient organocatalytic enantioselective 1,6-hydrophosphonylation of para-quinone methides has been achieved for the construction of phosphorus-substituted quaternary carbon stereocenters.

Paired refinement under the control of PAIREF

Crystallographic resolution is a key characteristic of diffraction data and represents one of the first decisions an experimenter has to make in data evaluation. Conservative approaches to the high-resolution cutoff determination are based on a number of criteria applied to the processed X-ray diffraction data only. However, high-resolution data that are weaker than arbitrary cutoffs can still result in the improvement of electron-density maps and refined structure models. Therefore, the impact of reflections from resolution shells higher than those previously used in conservative structure refinement should be analysed by the paired refinement protocol. For this purpose, a tool called PAIREF was developed to provide automation of this protocol. As a new feature, a complete cross-validation procedure has also been implemented. Here, the design, usage and control of the program are described, and its application is demonstrated on six data sets. The results prove that the inclusion of high-resolution data beyond the conventional criteria can lead to more accurate structure models.

An Efficient Implementation of the Nwat-MMGBSA Method to Rescore Docking Results in Medium-Throughput Virtual Screenings

Nwat-MMGBSA is a variant of MM-PB/GBSA based on the inclusion of a number of explicit water molecules that are the closest to the ligand in each frame of a molecular dynamics trajectory. This method demonstrated improved correlations between calculated and experimental binding energies in both protein-protein interactions and ligand-receptor complexes, in comparison to the standard MM-GBSA. A protocol optimization, aimed to maximize efficacy and efficiency, is discussed here considering penicillopepsin, HIV1-protease, and BCL-XL as test cases. Calculations were performed in triplicates on both classic HPC environments and on standard workstations equipped by a GPU card, evidencing no statistical differences in the results. No relevant differences in correlation to experiments were also observed when performing Nwat-MMGBSA calculations on 4 or 1 ns long trajectories. A fully automatic workflow for structure-based virtual screening, performing from library set-up to docking and Nwat-MMGBSA rescoring, has then been developed. The protocol has been tested against no rescoring or standard MM-GBSA rescoring within a retrospective virtual screening of inhibitors of AmpC β-lactamase and of the Rac1-Tiam1 protein-protein interaction. In both cases, Nwat-MMGBSA rescoring provided a statistically significant increase in the ROC AUCs of between 20 and 30%, compared to docking scoring or to standard MM-GBSA rescoring.

Enantioselective access to multi-cyclic α-amino phosphonates via carbene-catalyzed cycloaddition reactions between enals and six-membered cyclic imines

A carbene-catalyzed enantioselective [4 + 2] cycloaddition reaction is developed and quarternary α-amino phosphonates are afforded with encouraging anti-bacterial activities.

Facile access to a heterocyclic, sp3-rich chemical scaffold via a tandem condensation/intramolecular nitrone–alkene [3+2] cycloaddition strategy

A heterocyclic, sp³-rich chemical scaffold was synthesised in just 6 steps via a highly regio- and diastereo-selective tandem nitrone formation/intramolecular nitrone–alkene [3+2] cycloaddition reaction.

Quinine-thiourea catalyzed enantioselective hydrophosphonylation of trifluoromethyl 2(1H)-quinazolinones

An organocatalytic enantioselective addition reaction of cyclic ketoimines with phosphites has been developed for the first time. The process, catalyzed by Soós' quinine thiourea, affords synthetically and medicinally interesting enantioenriched trifluoromethyl dihydroquinazolinones in high yields and with high enantioselectivities.

Explicit Ligand Hydration Shells Improve the Correlation between MM-PB/GBSA Binding Energies and Experimental Activities

Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) and Molecular Mechanics Generalized Born Surface Area (MM-GBSA) methods are widely used for drug design/discovery purposes. However, it is not clear if the correlation between predicted and experimental binding affinities can be improved by explicitly considering selected water molecules in the calculation of binding energies, since different and sometimes diverging opinions are found in the literature. In this work, we evaluated how variably populated hydration shells explicitly considered around the ligands may affect the correlation between MM-PB/GBSA computed binding energy and biological activities (IC50 and ΔGbind, depending on the available experimental data). Four different systems-namely, the DNA-topoisomerase complex, α-thrombin, penicillopepsin, and avidin-were considered and ligand hydration shells populated by 10-70 water molecules were systematically evaluated. We found that the consideration of a hydration shell populated by a number of water residues (Nwat) between 30 and 70 provided, in all of the considered examples, a positive effect on correlation between MM-PB/GBSA calculated binding affinities and experimental activities, with a negligible increment of computational cost.

Direct Access to Enantiomerically Enriched α-Amino Phosphonic Acid Derivatives by Organocatalytic Asymmetric Hydrophosphonylation of Imines

A simple and efficient organocatalytic enantioselective hydrophosphonylation of imines to enantiomerically enriched alpha-amino phosphonates is reported. By using 10 mol % of quinine as the catalyst in the enantioselective addition of diethyl phosphite to N-Boc protected imines, alpha-amino phosphonates are obtained in moderate to good yields and with up to 94% ee.

Asymmetric synthesis of cyclic alpha-amino phosphonates using masked oxo sulfinimines (N-sulfinyl imines)

Five-, six-, and seven-membered cyclic alpha-amino phosphonates, amino acid surrogates, are prepared in enantiomerically pure form via the highly diastereomeric addition of metal phosphonates to masked oxo sulfinimines. Hydrolysis of the resulting masked oxo alpha-amino phosphonates followed by reduction of the intermediate cyclic imino phosphonates affords the title compounds in good yield.

Identification of Novel Macrocyclic Peptidase Substrates via On-Bead Enzymatic Cyclization

Peptidase-catalyzed formation of macrocyclic lactams on solid phase identifies ring systems that are favorably bound in the enzyme active site. We evaluated several cyclic peptide motifs linked by ester bonds between the P2 and P1' or the P1 and P2' side chains. The depsipeptide represented by structure 5 was readily generated by a variety of peptidases from precursor omega-amino acids or omega-amino esters. This strategy for identifying ring systems for potential macrocyclic transition state analogues was demonstrated with the serine peptidases trypsin and chymotrypsin, with the aspartic peptidase pepsin, and with the zinc peptidase thermolysin.

Synthesis and evaluation of keto-glutamine analogues as inhibitors of hepatitis A virus 3C proteinase

Hepatitis A virus (HAV) 3C enzyme is a picornaviral cysteine proteinase involved in the processing of the initially synthesized viral polyprotein and is therefore important for viral maturation and infectivity. Although it is a cysteine proteinase, this enzyme has a topology similar to those of the chymotrypsin-like serine proteinases. Since the enzyme recognizes peptide substrates with a glutamine residue at the P(1) site, a number of ketone-containing glutamine compounds analogous to nanomolar inhibitors of cathepsin K were synthesized and tested for inhibition against HAV 3C proteinase. In addition, a 3-azetidinone scaffold was incorporated into the glutamine fragment but gave only modest inhibition. However, introduction of a phthalhydrazido group alpha to the ketone moiety gave significantly better inhibitors with IC(50) values ranging from 13 to 164 microM, presumably due to the effect of intramolecular hydrogen bonding to the ketone. In addition, the tetrapeptide phthalhydrazide 24 was found to be a competitive reversible inhibitor (K(i) = 9 x 10(-6) M) and also showed no loss of inhibitory potency in the presence of dithiothreitol.

Analysis of crystal structures of aspartic proteinases: on the role of amino acid residues adjacent to the catalytic site of pepsin-like enzymes

To elucidate the role of amino acid residues adjacent to the catalytic site of pepsin-like enzymes, we analyzed and compared the crystal structures of these enzymes, their complexes with inhibitors, and zymogens in the active site area (a total of 82 structures). In addition to the water molecule (W1) located between the active carboxyls and playing a role of the nucleophile during catalytic reaction, another water molecule (W2) at the vicinity of the active groups was found to be completely conserved. This water molecule plays an essential role in formation of a chain of hydrogen-bonded residues between the active site flap and the active carboxyls on ligand binding. These data suggest a new approach to understanding the role of residues around the catalytic site, which can assist the development of the catalytic reaction. The influence of groups adjacent to the active carboxyls is manifested by pepsin activity at pH 1.0. Some features of pepsin-like enzymes and their mutants are discussed in the framework of the approach.

Asymmetric synthesis of quaternary alpha-amino phosphonates using sulfinimines

The addition of lithium diethylphosphonate to enantiopure ketosulfinimines is highly diastereoselective (>95%), affording the first examples of quaternary alpha-alkyl alpha-amino (arylmethyl)phosphonates.

Lowering the entropic barrier for binding conformationally flexible inhibitors to enzymes

The design of inhibitors with enhanced potency against proteolytic enzymes has many applications for the treatment of human diseases. In addition to the optimization of chemical interactions between the enzyme and inhibitor, the binding affinity can be increased by constraining the inhibitor to the conformation that is recognized by the enzyme, thus lowering the entropic barrier to complex formation. We have structurally characterized the complexes of a macrocyclic pentapeptide inhibitor and its acyclic analogue with penicillopepsin, an aspartic proteinase, to study the effect of conformational constraint on the binding affinity. The phosphonate-based macrocycle PPi4 (Ki = 0.10 nM) is covalently linked at the P2-Asn and P1'-Phe side chains [nomenclature of Schechter and Berger, Biochim. Biophys. Res. Commun. (1967) 27, 157-162] via an amide bond, relative to the acyclic compound PPi3 (Ki = 42 nM). Comparisons of the high-resolution crystal structures of PPi4-penicillopepsin (0.95 A) and PPi3-penicillopepsin (1.45 A) reveal that the conformations of the inhibitors and their interactions with the enzyme are similar. The 420-fold increase in the binding affinity of PPi4 is attributed to a reduction in its conformational flexibility, thus providing the first rigorous measure of the entropic contribution to the binding energy in a protein-ligand complex and stressing the advantages of the design strategy.