Synthesis and evaluation of an inhibitor of carboxypeptidase A with a Ki value in the femtomolar range

The importance of binding kinetics and drug-target residence time in pharmacology

A dominant assumption in pharmacology throughout the 20th century has been that in vivo target occupancy-and attendant pharmacodynamics-depends on the systemic concentration of drug relative to the equilibrium dissociation constant for the drug-target complex. In turn, the duration of pharmacodynamics is temporally linked to the systemic pharmacokinetics of the drug. Yet, there are many examples of drugs for which pharmacodynamic effect endures long after the systemic concentration of a drug has waned to (equilibrium) insignificant levels. To reconcile such data, the drug-target residence time model was formulated, positing that it is the lifetime (or residence time) of the binary drug-target complex, and not its equilibrium affinity per se, that determines the extent and duration of drug pharmacodynamics. Here, we review this model, its evolution over time, and its applications to natural ligand-macromolecule biology and synthetic drug-target pharmacology.

Rh-catalyzed asymmetric hydrogenation of α- and β-enamido phosphonates: highly enantioselective access to amino phosphonic acids

Broad substrate scope; high isloated yield and enantioselectivity; novel hybrid bisphosphine ligands; gram-scale reaction with lower catalyst usage.

Identification and characterization of second-generation EZH2 inhibitors with extended residence times and improved biological activity

The histone methyltransferase EZH2 has been the target of numerous small-molecule inhibitor discovery efforts over the last 10+ years. Emerging clinical data have provided early evidence for single agent activity with acceptable safety profiles for first-generation inhibitors. We have developed kinetic methodologies for studying EZH2-inhibitor-binding kinetics that have allowed us to identify a unique structural modification that results in significant increases in the drug-target residence times of all EZH2 inhibitor scaffolds we have studied. The unexpected residence time enhancement bestowed by this modification has enabled us to create a series of second-generation EZH2 inhibitors with sub-pM binding affinities. We provide both biophysical evidence validating this sub-pM potency and biological evidence demonstrating the utility and relevance of such high-affinity interactions with EZH2.

Synthesis and Structural/Functional Characterization of Selective M14 Metallocarboxypeptidase Inhibitors Based on Phosphinic Pseudopeptide Scaffold: Implications on the Design of Specific Optical Probes

Metallocarboxypeptidases (MCPs) of the M14 family are Zn²⁺-dependent exoproteases present in almost every tissue or fluid in mammals. These enzymes perform a large variety of physiological functions and are involved in several pathologies, such as pancreatic diseases, inflammation, fibrinolysis, and cancer. Here, we describe the synthesis and functional/structural characterization of a series of reversible tight-binding phosphinic pseudopeptide inhibitors that show high specificity and potency toward these proteases. Characterization of their inhibitory potential against a large variety of MCPs, combined with high-resolution crystal structures of three selected candidates in complex with human carboxypeptidase A (CPA)1, allowed to decipher the structural determinants governing selectivity for type-A of the M14A MCP family. Further, the phosphinic pseudopeptide framework was exploited to generate an optical probe selectively targeting human CPAs. The phosphinic pseudopeptides presented here constitute the first example of chemical probes useful to selectively report on type-A MCPs activity in complex media.

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.

Synthesis of Chiral Tertiary Boronic Esters: Phosphonate-Directed Catalytic Asymmetric Hydroboration of Trisubstituted Alkenes

Highly enantioselective rhodium-catalyzed hydroboration of allylic phosphonates by pinacolborane affords chiral tertiary boronic esters. The β-borylated phosphonates are readily converted to chiral β- and γ-hydroxyphosphonates and aminophosphonates and to phosphonates bearing a quaternary carbon stereocenter. The utility of the latter is illustrated by the synthesis of (S)-(+)-bakuchiol methyl ether.

A Bacterial Cell Shape-Determining Inhibitor

Helicobacter pylori and Campylobacter jejuni are human pathogens and causative agents of gastric ulcers/cancer and gastroenteritis, respectively. Recent studies have uncovered a series of proteases that are responsible for maintaining the helical shape of these organisms. The H. pylori metalloprotease Csd4 and its C. jejuni homologue Pgp1 cleave the amide bond between meso-diaminopimelate and iso-d-glutamic acid in truncated peptidoglycan side chains. Deletion of either csd4 or pgp1 results in bacteria with a straight rod phenotype, a reduced ability to move in viscous media, and reduced pathogenicity. In this work, a phosphinic acid-based pseudodipeptide inhibitor was designed to act as a tetrahedral intermediate analog against the Csd4 enzyme. The phosphinic acid was shown to inhibit the cleavage of the alternate substrate, Ac-l-Ala-iso-d-Glu-meso-Dap, with a Ki value of 1.5 μM. Structural analysis of the Csd4-inhibitor complex shows that the phosphinic acid displaces the zinc-bound water and chelates the metal in a bidentate fashion. The phosphinate oxygens also interact with the key acid/base residue, Glu222, and the oxyanion-stabilizing residue, Arg86. The results are consistent with the "promoted-water pathway" mechanism for carboxypeptidase A catalysis. Studies on cultured bacteria showed that the inhibitor causes significant cell straightening when incubated with H. pylori at millimolar concentrations. A diminished, yet observable, effect on the morphology of C. jejuni was also apparent. Cell straightening was more pronounced with an acapsular C. jejuni mutant strain compared to the wild type, suggesting that the capsule impaired inhibitor accessibility. These studies demonstrate that a highly polar compound is capable of crossing the outer membrane and altering cell shape, presumably by inhibiting cell shape determinant proteases. Peptidoglycan proteases acting as cell shape determinants represent novel targets for the development of antimicrobials against these human pathogens.

Rhodium-catalyzed asymmetric hydrogenation of unprotected β-enamine phosphonates

We have successfully developed a strategy for the first time for the enantioselective Rh-TaniaPhos catalyzed asymmetric hydrogenation of unprotected β-enamine phosphonates to free β-amino phosphonates directly with good enantioselectivities (80%–86% ee) and high conversions (>99% conversion).

Affinity enhancement of antibodies: how low-affinity antibodies produced early in immune responses are followed by high-affinity antibodies later and in memory B-cell responses

The antibodies produced initially in response to most antigens are high molecular weight (MW) immunoglobulins (IgM) with low affinity for the antigen, while the antibodies produced later are lower MW classes (e.g., IgG and IgA) with, on average, orders of magnitude higher affinity for that antigen. These changes, often termed affinity maturation, take place largely in small B-cell clusters (germinal center; GC) in lymphoid tissues in which proliferating antigen-stimulated B cells express the highly mutagenic cytidine deaminase that mediates immunoglobulin class-switching and sequence diversification of the immunoglobulin variable domains of antigen-binding receptors on B cells (BCR). Of the large library of BCR-mutated B cells thus rapidly generated, a small minority with affinity-enhancing mutations are selected to survive and differentiate into long-lived antibody-secreting plasma cells and memory B cells. BCRs are also endocytic receptors; they internalize and cleave BCR-bound antigen, yielding peptide-MHC complexes that are recognized by follicular helper T cells. Imperfect correlation between BCR affinity for antigen and cognate T-cell engagement may account for the increasing affinity heterogeneity that accompanies the increasing average affinity of antibodies. Conservation of mechanisms underlying mutation and selection of high-affinity antibodies over the ≈200 million years of evolution separating bird and mammal lineages points to the crucial role of antibody affinity enhancement in adaptive immunity.

New β-phospholactam as a carbapenem transition state analog: Synthesis of a broad-spectrum inhibitor of metallo-β-lactamases

In an effort to test whether a transition state analog is an inhibitor of the metallo-β-lactamases, a phospholactam analog of carbapenem has been synthesized and characterized. The phospholactam 1 proved to be a weak, time-dependent inhibitor of IMP-1 (70%), CcrA (70%), L1 (70%), NDM-1 (53%), and Bla2 (94%) at an inhibitor concentration of 100μM. The phospholactam 1 activated ImiS and BcII at the same concentration. Docking studies were used to explain binding and to offer suggestions for modifications to the phospholactam scaffold to improve binding affinities.

Synthesis and modifications of phosphinic dipeptide analogues

Pseudopeptides containing the phosphinate moiety (-P(O)(OH)CH₂-) have been studied extensively, mainly as transition state analogue inhibitors of metalloproteases. The key synthetic aspect of their chemistry is construction of phosphinic dipeptide derivatives bearing appropriate side-chain substituents. Typically, this synthesis involves a multistep preparation of two individual building blocks, which are combined in the final step. As this methodology does not allow simple variation of the side-chain structure, many efforts have been dedicated to the development of alternative approaches. Recent achievements in this field are summarized in this review. Improved methods for the formation of the phosphinic peptide backbone, including stereoselective and multicomponent reactions, are presented. Parallel modifications leading to the structurally diversified substituents are also described. Finally, selected examples of the biomedical applications of the title compounds are given.

Catalytic asymmetric synthesis of α,β-disubstituted α,γ-diaminophosphonic acid precursors by Michael addition of α-substituted nitrophosphonates to nitroolefins

Michael additions of α-substituted nitrophosphonates to various nitroolefins are shown to proceed with high diastereo- and enantioselectivity when catalyzed by a quinine-derived thiourea-tertiary amine bifunctional catalyst and generate α,γ-diaminophosphonic acid precursors with contiguous quaternary and tertiary stereocenters.

Enantioselective synthesis of quaternary α-aminophosphonates via conjugate addition of α-nitrophosphonates to enones

Enantioselective Michael addition of α-nitrophosphonates to enones for the synthesis of α-aminophosphonates is reported for the first time. The reaction proceeds in good to high yields and moderate to high selectivity in the presence of a new quinine thiourea catalyst. The quaternary nitrophosphonates were conveniently transformed to cyclic quaternary α-aminophosphonates via in situ reduction-intramolecular cyclization or Baeyer-Villiger oxidation followed by in situ reduction-intramolecular cyclization.

Progress in metallocarboxypeptidases and their small molecular weight inhibitors

In what corresponds to a life span, metallocarboxypeptidases (MCPs) have jumped from being mere contaminants in animal pancreas powders (in depression year 1929) to be key players in cellular and molecular processes (in yet-another-depression years 2009-2010). MCPs are unique zinc-dependent enzymes that catalyze the breakdown of the amide bond at the C-terminus of peptide and protein substrates and participate in the recovery of dietary amino acids, tissue organogenesis, neurohormone and cytokine maturation and other important physiological processes. More than 26 genes code for MCPs in the human genome, many of them still waiting to be fully understood in terms of physiological function. A variety of MCPs have been linked to diseases in man: acute pancreatitis and pancreas cancer, type 2 diabetes, Alzheimer's Disease, various types of cancer, and fibrinolysis and inflammation. Many of these discoveries have been made possible thanks to recent advances, as exemplified by plasma carboxypeptidases N and B, known for fifty and twenty years, respectively, which have had their structures released only very recently. Plasma carboxypeptidase B is a biological target for therapy because of its involvement in the coagulation/fibrinolysis processes. Besides, the widespread use of carboxypeptidase A as a benchmark metalloprotease since the early days of Biochemistry has allowed the identification and design of an increasingly vast repertory of small molecular weight inhibitors. With these two examples we wish to emphasize that MCPs have become part of the drug discovery portfolio of pharmaceutical companies and academic research laboratories. This paper will review key developments in the discovery and design of MCP small molecular weight inhibitors, with an emphasis on the discovery of chemically diverse entities. Although encouraging advances have been achieved in the last few years, the specificity and oral bioavailability of the new chemotherapeutic agents seem to pose a challenge to medicinal chemists.

Computational chemistry approaches to drug discovery in signal transduction

The advent of therapeutic strategies aimed at targeting specific macromolecular components of deregulated signaling pathways associated with particular disease states has given rise to the idea that it should be possible to design ligands as drug candidates to these targets from first principles. This concept has been beckoning for a long time but structure-based ligand design only became feasible once it was possible to determine the 3-D structures of molecular targets at atomic resolution. However, structure-based design turned out to be difficult, chiefly because under physiological conditions both receptors and ligands are not static but they behave dynamically. While it is possible to design ligands with high steric and electronic complementarity to a receptor site, it is always uncertain how biologically relevant the assumed conformations of both ligand and receptor actually are. The fact that it remains beyond our current abilities to predict with sufficient accuracy the affinity between hypothetical ligand and receptor poses is in part connected with this problem and continues to confound the reliable prediction of drug-like ligands for therapeutic targets. Nevertheless, significant progress has been made and so-called virtual screening methods that use computational methods to dock candidate ligands into receptor sites and to score the resulting complexes are now used routinely as one of the components in drug discovery screening campaigns. Here an overview is given of the underlying principles, implementations, and applications of structure-guided computational design technologies. Although the emphasis is on receptor-based strategies, mention will also be made of some of the more established ligand-based approaches, such as similarity analyses and quantitative structure-activity relationship methods.

Study on [(4-substituted benzoylamino)phenylmethyl]phosphonic acid diisopropyl esters under electrospray ionization tandem mass spectrometric conditions

Phosphonate esters were synthesized and investigated by positive ion electrospray ionization mass spectrometry (ESI-MS) in conjunction with tandem mass spectrometry (MS/MS). It was found that for the sodiated adduct there were two novel rearrangement reactions, in which the phosphoryl oxygen atom migrated to the carbonyl carbon and a cleavage occurred at the amide bond, or a benzylamine fragment was lost and the phosphorus was reduced. However, when the methyl group substituted for the isopropyl group, these migrations were inhibited. A possible mechanism was proposed, and high-resolution mass spectrometry was applied to identify the formula of these novel ions. These results showed that ESI-MS is a useful tool for the structural determination of phosphonate esters.

A facile and highly efficient route to α-amino phosphonates via three-component reactions catalyzed by Mg(ClO4)2or molecular iodine

Three-component reactions of aldehydes, amines, and diethyl phosphite catalyzed by Mg(ClO4)2 or molecular iodine afforded the corresponding alpha-amino phosphonates in excellent yields under mild reaction conditions.

Catalytic asymmetric synthesis of α- and β-amino phosphonic acid derivatives

Catalytic asymmetric reactions provide one of the most powerful and economical synthetic approaches to a variety of enantiomerically enriched compounds. As being analogues of the corresponding alpha- and beta-amino acids, optically active alpha- and beta-amino phosphonic acid derivatives have found widespread use in medicinal chemistry and the pharmaceutical sciences. Using catalytic amounts of chiral materials, asymmetric synthesis of enantiomerically enriched alpha- and beta-amino phosphonates has been a subject of growing interest. This tutorial review contains a compilation of the catalytic asymmetric synthetic methods developed to date and highlights their utility for obtaining these target compounds.

Phosphinate, sulfonate, and sulfonamidate dipeptides as potential inhibitors of Escherichia coli aminopeptidase N

In an effort to prepare novel inhibitors of bacterial aminopeptidase N (PepN), the phosphinate, propenylphosphinate, decylphosphinate, sulfonate, and sulfonamidate analogs of Ala-Ala were synthesized and tested as inhibitors. Phosphinate 1 was shown to inhibit PepN with a K(i) of 10microM, and propenylphosphinate 2 and decylphosphinate 3 inhibited PepN with a K(i) of ca. 1microM. Sulfonate and sulfonamidate analogs did not inhibit PepN.

Configurational biomimesis in drug delivery: molecular imprinting of biologically significant molecules

This review focuses on trends in the macromolecular recognition of biologically significant molecules (e.g., drugs, amino acids, steroids, nucleotide bases, carbohydrates, etc.) via molecular imprinting methods. An extensive list of prior art including type of functional monomers and crosslinkers for each biomolecule imprinted polymer is presented. Representative samples of receptor-ligand dissociation constants and polymer capacities are presented as well as typical values that occur in classes of biological recognition systems. Imprinting technology has direct impact in enhanced drug loading of controlled-release carriers for the sustained release of therapeutic agents as well as robust biosensors for novel therapeutic and diagnostic devices. This review also discusses the future of designed recognition, configurational biomimesis within polymeric gels, and highlights recent efforts toward integrating imprinted polymers in controlled drug delivery systems and sensing devices. In particular, the application of imprinted polymers for sustained release, enhanced loading capacity, and enantioselective loading or release are discussed. This article also highlights the most important problems to be solved in the design of synthetic recognition-based networks for biological molecules.

Preorganization and protein dynamics in enzyme catalysis

Recently, an alternative has been offered to the concept of transition state (TS) stabilization as an explanation for rate enhancements in enzyme-catalyzed reactions. Instead, most of the rate increase has been ascribed to preorganization of the enzyme active site to bind substrates in a geometry close to that of the TS, which then transit the activation barrier impelled by motions along the reaction coordinate. The question as to how an enzyme achieves such preorganization and concomitant TS stabilization as well as potential coupled motions along the reaction coordinate leads directly to the role of protein dynamic motion. Dihydrofolate reductase (DHFR) is a paradigm in which the role of dynamics in catalysis continues to be unraveled by a wealth of kinetic, structural, and computational studies. DHFR has flexible loop regions adjacent to the active site whose motions modulate passage through the kinetically preferred pathway. The participation of residues distant from the DHFR active site in enhancing the rate of hydride transfer, however, is unanticipated and may signify the importance of long range protein motions. The general significance of protein dynamics in understanding other biological processes is briefly discussed.

An intramolecular benzyl rearrangement of 1-(N-benzyloxycarbonylamino)alkylphosphonate diesters under electrospray ionization conditions

The mass spectrometric behavior of eleven 1-(N-benzyloxycarbonyl(Cbz)amino)alkylphosphonate diesters was studied under positive ion electrospray ionization (ESI) conditions. Their fragmentation pathways are depicted and supported by tandem mass spectrometry. Besides the common eliminations of ether, benzyl alcohol, phosphite and an ether plus benzyl alcohol from molecular ions, the title compounds show a tendency to undergo an interesting intramolecular benzyl rearrangement to yield benzylphosphonate ions. The fragmentation patterns do not depend on the substituent attached to the alpha-carbon atom.

Stability of macromolecular complexes

Macromolecular interactions are crucial in numerous biologic processes, yet few general principles are available that establish firm expectations for the strength of these interactions or the expected contribution of specific forces. The simplest principle would be a monotonic increase in interactions as the size of the interface grows. The exact relationship might be linear or nonlinear depending on the nature of the forces involved. Simple "linear-free energy" relationships based on atomic properties have been well documented, for example, additivity for the interaction of small molecules with solvent, and, recently, have been explored for ligand-receptor interactions. Horton and Lewis propose such additivity based on buried surface area for protein-protein complexes. We investigated macromolecular interactions and found that the highest-affinity complexes do not fulfill this simple expectation. Instead, binding free energies of the tightest macromolecular complexes are roughly constant, independent of interface size, with the notable exception of DNA duplexes. By comparing these results to an earlier study of protein-ligand interactions we find that: (1) The maximum affinity is approximately 1.5 kcal/mol per nonhydrogen atom or 120 cal/mol A(2) of buried surface area, comparable to results of our earlier work; (2) the lack of an increase in affinity with interface size is likely due to nonthermodynamic factors, such as functional and evolutionary constraints rather than some fundamental physical limitation. The implication of these results have some importance for molecular design because they suggest that: (1) The stability of any given complex can be increased significantly if desired; (2) small molecule inhibitors of macromolecular interactions are feasible; and (3) different functional classes of protein-protein complexes exhibit differences in maximal stability, perhaps in response to differing evolutionary pressures. These results are consistent with the widespread observation that proteins have not evolved to maximize thermodynamic stability, but are only marginally stable.

Changes in zinc ligation promote remodeling of the active site in the zinc hydrolase superfamily

The zinc hydrolase superfamily is a group of divergently related proteins that are predominantly enzymes with a zinc-based catalytic mechanism. The common structural scaffold of the superfamily consists of an eight-stranded beta-sheet flanked by six alpha-helices. Previous analyses, while acknowledging the likely divergent origins of leucine aminopeptidase, carboxypeptidase A and the co-catalytic enzymes of the metallopeptidase H clan based on their structural scaffolds, have failed to find any homology between the active sites in leucine aminopeptidase and the metallopeptidase H clan enzymes. Here we show that these two groups of co-catalytic enzymes have overlapping dizinc centers where one of the two zinc atoms is conserved in each group. Carboxypeptidase A and leucine aminopeptidase, on the other hand, no longer share any homologous zinc-binding sites. At least three catalytic zinc-binding sites have existed in the structural scaffold over the period of history defined by available structures. Comparison of enzyme-inhibitor complexes show that major remodeling of the substrate-binding site has occurred in association with each change in zinc ligation in the binding site. These changes involve re-registration and re-orientation of the substrate. Some residues important to the catalytic mechanism are not conserved amongst members. We discuss how molecules acting in trans may have facilitated the mutation of catalytically important residues in the active site in this group.

The role of ecotin dimerization in protease inhibition

Ecotin is a homodimeric protein from Escherichia coli that inhibits many serine proteases of the chymotrypsin fold, often with little effect from the character or extent of enzyme substrate specificity. This pan-specificity of inhibition is believed to derive from formation of a heterotetrameric complex with target proteases involving three types of interface: the dimerization interface, a primary substrate-like interaction, and a smaller secondary interaction between the partner ecotin subunit and the protease. A monomeric ecotin variant (mEcotin) and a single-chain ecotin dimer (scEcotin) were constructed to study the effect of a network of protein interactions on binding affinity and the role of dimerization in broad inhibitor specificity. mEcotin was produced by inserting a beta-turn into the C-terminal arm, which normally exchanges with the other subunit. While the dimerization constant (K(dim)) of wild-type (WT) ecotin was found to be picomolar by subunit exchange experiments using FRET and by association kinetics, mEcotin was monomeric up to 1 mM as judged by gel filtration and analytical centrifugation. A crystal structure of uncomplexed mEcotin to 2.0 A resolution verifies the design, showing a monomeric protein in which the C-terminal arm folds back onto itself to form a beta-barrel structure nearly identical to its dimeric counterpart. The kinetic rate constants and equilibrium dissociation constants for monomeric and dimeric ecotin variants were determined with both trypsin and chymotrypsin. The effect of the secondary binding site on affinity was found to vary inversely with the strength of the interaction at the primary site. This compensatory effect yields a nonadditivity of up to 5 kcal/mol and can be explained in terms of the optimization of binding orientation. Such a mechanism of adaptability allows femtomolar affinities for two proteases with very different specificities.