Cele Abad-Zapatero

Ligand efficiency indices for effective drug discovery

Successful drug discovery requires the optimization of a large number of variables ranging from strictly physicochemical parameters such as molecular weight to more complex parameters related to toxicity and bioavailability. Presently, structure-based methodologies influence many aspects of the drug discovery process from lead discovery to the final preclinical characterization. However, critical biological issues along the path to the market have diminished the impact and power of this methodology. The physicochemical properties of the novel chemical entities designed and guided by structural methods have become the subject of intense scrutiny from lead discovery to drug candidate. The idea of ligand efficiency (binding energy/non-hydrogen atoms) has recently emerged as a useful guide to optimize fragment and lead selection in the discovery process. More generalized concepts of ligand efficiency, related to efficiency per dalton and per unit of polar surface area, have also been introduced and will be discussed in the broader context. Preliminary results and trends obtained using ligand efficiencies as guides are reviewed and their future application to guide drug discovery will be discussed, as well as their integration into the structure-based drug design methods to make them more effective and numerically robust.

Ligand efficiency indices for an effective mapping of chemico-biological space: the concept of an atlas-like representation.

We propose a numerical framework that permits an effective atlas-like representation of chemico-biological space based on a series of Cartesian planes mapping the ligands with the corresponding targets connected by an affinity parameter (K(i) or related). The numerical framework is derived from the concept of ligand efficiency indices, which provide a natural coordinate system combining the potency toward the target (biological space) with the physicochemical properties of the ligand (chemical space). This framework facilitates navigation in the multidimensional drug discovery space using map-like representations based on pairs of combined variables related to the efficiency of the ligands per Dalton (molecular weight or number of non-hydrogen atoms) and per unit of polar surface area (or number of polar atoms).

Inhibition of MptpB phosphatase from Mycobacterium tuberculosis impairs mycobacterial survival in macrophages

OBJECTIVES The secreted Mycobacterium tuberculosis protein tyrosine phosphatase (MptpB) is a virulence factor for M. tuberculosis and contributes to its survival within host macrophages. The aim of this study was to identify potent selective inhibitors of MptpB and to determine the efficacy of these compounds in mycobacterium-infected macrophages. METHODS The inhibitory effect of a small library of compounds on MptpB was first examined in vitro. The efficacy of these compounds was further examined in mycobacterium-infected macrophages. RESULTS We have identified a new family of double-site isoxazole-based compounds that are potent selective inhibitors of MptpB. Importantly, the inhibitors substantially reduce mycobacterial survival in infected macrophages. In contrast with current anti-tubercular drugs, these MptpB inhibitors do not have bactericidal action but rather, severely impair mycobacterial growth within macrophages. Docking analysis suggests a double-site binding mechanism of inhibition with the isoxazole head in the active site and a salicylate group in a secondary binding pocket that is a unique structural feature of MptpB. CONCLUSIONS These results provide the first evidence that inhibition of phosphatases can be exploited against mycobacterial infections. The cell activity of the inhibitors together with the lack of MptpB human orthologues suggests a strong potential for these compounds to be developed as drug candidates against tuberculosis and promises a new therapeutic strategy to tackle clearance and reduce the persistence of M. tuberculosis infection.

Potent, Selective Inhibitors of Protein Tyrosine Phosphatase 1B

We have previously reported a novel series of oxalyl-aryl-amino benzoic acid-based, catalytic site-directed, competitive, reversible protein tyrosine phosphatase 1B (PTP1B) inhibitors. With readily access to key intermediates, we utilized a solution phase parallel synthesis approach and rapidly identified a highly potent PTP1B inhibitor (19, K(i)=76 nM) with moderate selectivity (5-fold) over T-cell PTPase (TCPTP) through interacting with a second phosphotyrosine binding site (site 2) in the close proximity to the catalytic site.

Discovery and Characterization of Non-ATP Site Inhibitors of the Mitogen Activated Protein (MAP) Kinases

Inhibition of protein kinases has validated therapeutic utility for cancer, with at least seven kinase inhibitor drugs on the market. Protein kinase inhibition also has significant potential for a variety of other diseases, including diabetes, pain, cognition, and chronic inflammatory and immunologic diseases. However, as the vast majority of current approaches to kinase inhibition target the highly conserved ATP-binding site, the use of kinase inhibitors in treating nononcology diseases may require great selectivity for the target kinase. As protein kinases are signal transducers that are involved in binding to a variety of other proteins, targeting alternative, less conserved sites on the protein may provide an avenue for greater selectivity. Here we report an affinity-based, high-throughput screening technique that allows nonbiased interrogation of small molecule libraries for binding to all exposed sites on a protein surface. This approach was used to screen both the c-Jun N-terminal protein kinase Jnk-1 (involved in insulin signaling) and p38α (involved in the formation of TNFα and other cytokines). In addition to canonical ATP-site ligands, compounds were identified that bind to novel allosteric sites. The nature, biological relevance, and mode of binding of these ligands were extensively characterized using two-dimensional (1)H/(13)C NMR spectroscopy, protein X-ray crystallography, surface plasmon resonance, and direct enzymatic activity and activation cascade assays. Jnk-1 and p38α both belong to the MAP kinase family, and the allosteric ligands for both targets bind similarly on a ledge of the protein surface exposed by the MAP insertion present in the CMGC family of protein kinases and distant from the active site. Medicinal chemistry studies resulted in an improved Jnk-1 ligand able to increase adiponectin secretion in human adipocytes and increase insulin-induced protein kinase PKB phosphorylation in human hepatocytes, in similar fashion to Jnk-1 siRNA and to rosiglitazone treatment. Together, the data suggest that these new ligand series bind to a novel, allosteric, and physiologically relevant site and therefore represent a unique approach to identify kinase inhibitors.

Discovery of potent and selective thienopyrimidine inhibitors of Aurora kinases.

In an effort to discover Aurora kinase inhibitors, an HTS hit revealed an amide containing pyrrolopyrimidine compound. Replacement of the pyrrolopyrimidine residue with a thienopyrimidine moiety led to a series of potent and selective Aurora inhibitors.

Discovery and SAR of novel, potent and selective protein tyrosine phosphatase 1B inhibitors.

A salicylate second site binder was linked to three classes of phosphotyrosine mimetics to produce potent protein tyrosine phosphatase 1B (PTP1B) inhibitors which exhibit significant selectivity against other phosphatases including the most homologous member, TCPTP.

Scaffold oriented synthesis. Part 2: Design, synthesis and biological evaluation of pyrimido-diazepines as receptor tyrosine kinase inhibitors

We report the discovery of the pyrimido-diazepine scaffolds as novel adenine mimics. Structure-based design led to the discovery of analogs with potent inhibitory activity against receptor tyrosine kinases, such as KDR, Flt3 and c-Kit. Compound 14 exhibited low nanomolar KDR enzymatic and cellular potencies (IC(50)=9 and 52 nM, respectively).

Ligand Efficiency Indices (LEIs): More than a Simple Efficiency Yardstick

The concept of ligand efficiency and the usage of ligand efficiency values to assess the quality of fragments and compounds is becoming more accepted in the practice of medicinal chemistry. This is particularly true as it refers to the efficiency of ligands per unit size (i.e., binding affinity/number of non‐hydrogen atoms or binding affinity/MW). The use of the Ligand Efficiency Indices (LEIs) as variables for a Cartesian mapping of chemico‐biological space, the concept of AtlasCBS, has been presented in a recent publication with some initial drug‐discovery applications. In this communication, we present additional applications of the concept in three domains of drug discovery: i) analyze and compare the content of databases: inhibitors vs. drugs; ii) polypharmacology; and iii) applications to Fragment‐Based strategies. We suggest that the combined use of LEIs in a Cartesian representation of Chemico‐Biological Space (AtlasCBS) could be a useful tool in various aspects of drug‐discovery in the future.

Structure of Secreted Aspartic Proteinases from Candida

Pathogens of the genus Candida can cause life threatening infections in immunocompromised patients. The three–dimensional structures of two closely related secreted aspartic proteinases from C. albicans complexed with a potent (Ki=0.17 nM) inhibitor, and an analogous enzyme from C. tropicalis reveal variations on the classical aspartic proteinase theme that dramatically alter the specificity of this class of enzymes. The novel fungal proteases present: i) an 8 residue insertion near the first disulfide (Cys45–Cys50, pepsin numbering) that results in a broad flap extending towards the active site; ii) a seven residue deletion replacing helix hN2 (Serll0–Tyrll4), which enlarges the S3 pocket; iii) a short polar connection between the two rigid body domains that alters their relative orientation and provides certain specificity; and iv) an ordered 12 residue addition at the car–boxy terminus. The same inhibitor (A–70450) binds in an extended conformation in the two variants of C albicans protease, and presents a branched structure at the P3 position. However, the conformation of the terminal methylpiperazine ring is different in the two crystals structures. The implications of these findings for the design of potent antifungal agents are discussed.