Fernando Mazza

Insights into the mechanism of partial agonism: crystal structures of the peroxisome proliferator-activated receptor gamma ligand-binding domain in the complex with two enantiomeric ligands.

The peroxisome proliferator-activated receptors (PPARs) are transcriptional regulators of glucose and lipid metabolism. They are activated by natural ligands, such as fatty acids, and are also targets of synthetic antidiabetic and hypolipidemic drugs. By using cell-based reporter assays, we studied the transactivation activity of two enantiomeric ureidofibrate-like derivatives. In particular, we show that the R-enantiomer, (R)-1, is a full agonist of PPARγ, whereas the S-enantiomer, (S)-1, is a less potent partial agonist. Most importantly, we report the x-ray crystal structures of the PPARγ ligand binding domain complexed with the R- and the S-enantiomer, respectively. The analysis of the two crystal structures shows that the different degree of stabilization of the helix 12 induced by the ligand determines its behavior as full or partial agonist. Another crystal structure of the PPARγ·(S)-1 complex, only differing in the soaking time of the ligand, is also presented. The comparison of the two structures of the complexes with the partial agonist reveals significant differences and is suggestive of the possible coexistence in solution of transcriptionally active and inactive forms of helix 12 in the presence of a partial agonist. Mutation analysis confirms the importance of Leu465, Leu469, and Ile472 in the activation by (R)-1 and underscores the key role of Gln286 in the PPARγ activity.

Crystal Structure of the Peroxisome Proliferator-Activated Receptor γ (PPARγ) Ligand Binding Domain Complexed with a Novel Partial Agonist: A New Region of the Hydrophobic Pocket Could Be Exploited for Drug Design

The peroxisome proliferator-activated receptors (PPARs) are ligand-dependent transcription factors regulating glucose and lipid metabolism. The search for new PPAR ligands with reduced adverse effects with respect to the marketed antidiabetic agents thiazolidinediones (TZDs) and the dual-agonists glitazars is highly desired. We report the crystal structure and activity of the two enantiomeric forms of a clofibric acid analogue, respectively complexed with the ligand-binding domain (LBD) of PPARgamma, and provide an explanation on a molecular basis for their different potency and efficacy against PPARgamma. The more potent S-enantiomer is a dual PPARalpha/PPARgamma agonist which presents a partial agonism profile against PPARgamma. Docking of the S-enantiomer in the PPARalpha-LBD has been performed to explain its different subtype pharmacological profile. The hypothesis that partial agonists show differential stabilization of helix 3, when compared to full agonists, is also discussed. Moreover, the structure of the complex with the S-enantiomer reveals a new region of the PPARgamma-LBD never sampled before by other ligands.

γ-Turn conformation induced by α,α-disubstituted amino acids with a cyclic six-membered side chain

Abstract 4-Aminotetrahydrothiopyran-4-carboxylic acid (Thp) is an unusual achiral cyclic α,α-disubstituted amino acid mimicking the natural Met residue. The conformational energy map computed for Ac-Thp-NHMe shows that the γ-turn is the lowest minimum. 1 H-NMR and IR studies performed on For-Thp-Leu-OMe ( 2a ), a short peptide unable to give a 4…>1 H-bond, indicate that the γ-turn is adopted in CDCl 3 solution, whereas is not retained in (CD 3 ) 2 SO. An analogous conformational behaviour in solution has been observed for the strictly related For-Ac 6 c-Leu-OMe ( 2b ), containing 1-aminocyclohexane carboxylic acid (Ac 6 c).

New 2-Aryloxy-3-phenyl-propanoic Acids As Peroxisome Proliferator-Activated Receptors alpha/gamma Dual Agonists with Improved Potency and Reduced Adverse Effects on Skeletal Muscle Function

The preparation of a new series of 2-aryloxy-3-phenyl-propanoic acids, resulting from the introduction of a linker into the diphenyl system of the previously reported PPARalpha/gamma dual agonist 1, allowed the identification of new ligands with improved potency on PPARalpha and unchanged activity on PPARgamma. For the most interesting stereoisomers S-2 and S-4, X-ray studies in PPARgamma and docking experiments in PPARalpha provided a molecular explanation for their different behavior as full and partial agonists of PPARalpha and PPARgamma, respectively. Due to the adverse effects provoked by hypolipidemic drugs on skeletal muscle function, we also investigated the blocking activity of S-2 and S-4 on skeletal muscle membrane chloride channel conductance and found that these ligands have a pharmacological profile more beneficial compared to fibrates currently used in therapy.

Cation–π interactions between ammonium ion and aromatic rings: an energy decomposition study

Abstract The nature of the cation–π interaction between ammonium ion and a series of aromatic groups has been revisited through standard supermolecular energy decomposition schemes such as the Kitaura–Morokuma and the reduced variational space self-consistent field approaches. The emerged picture describes the ammonium–aromatics interaction as basically governed by electrostatics with significant contributions from the polarization, dispersion, and at a minor extent from, even from the aromatic–ammonium charge transfer. The role of molecular properties of the aromatic partners such as their mutipole moments, first and second order polarizability as well as the electronic properties of the frontier orbitals have been investigated in the light of the decomposed components. A final comment on the implications of our results on the reliability of the force fields currently employed for classical simulations and drug design investigations, has also been addressed.

1,3-Dialkyl-8-(hetero)aryl-9-OH-9-deazaxanthines as potent A2B adenosine receptor antagonists: Design, synthesis, structure-affinity and structure-selectivity relationships

A number of 1,3-dialkyl-8-(hetero)aryl-9-OH-9-deazaxanthines were prepared and evaluated as ligands of recombinant human adenosine receptors (hARs). Several 1,3-dipropyl derivatives endowed with nanomolar binding affinity at hA(2B) receptors, but poor selectivity over hA(2A), hA(1) and hA(3) AR subtypes were identified. A comparison with the corresponding 7-OH- and 7,9-unsubstituted-deazaxanthines revealed that 9-OH-9-deazaxanthines are more potent hA(2B) ligands with lower partition coefficients and higher water solubility compared to the other two congeneric classes of deazaxanthines. An optimization of the para-substituent of the 8-phenyl ring of 9-OH-9-deazaxanthines led to the discovery of compound 38, which exhibited outstanding hA(2B) affinity (Ki=1.0 nM), good selectivity over hA(2A), hA(1) and hA(3) (selectivity indices=100, 79 and 1290, respectively) and excellent antagonist potency in a functional assay on rat A(2B) (pA(2B)=9.33).

Exploring the interest of 1,2-dithiolane ring system in peptide chemistry. Synthesis of a chemotactic tripeptide and X-ray crystal structure of a 4-amino-1,2-dithiolane-4-carboxylic acid derivative

Due to their relevant biological functions and specific chemical reactivity 1,2-dithiolanes (five-membered cyclic disulfides) represent an emerging class of heterocyclic compounds. However, despite the extensive research centered on lipoic acid and its analogues, only very few data are at the present available on peptides containing this ring system. We report here synthesis, conformation and bioactivity of a fMLF-OMe analogue, namely For-Met-Adt-Phe-OMe (7), in which the residue of the 4-amino-1,2-dithiolane-4-carboxylic acid (Adt) (4) replaces the central L-leucine. The crystal conformation of the synthetic intermediate Boc-Adt-OMe (5) is also described and compared to that of lipoic acid (R-1,2-dithiolane-3-pentanoic acid) (3) and asparagusic acid (1,2-dithiolane-4-carboxylic acid) (2).

Structural Insight into Peroxisome Proliferator-Activated Receptor γ Binding of Two Ureidofibrate-Like Enantiomers by Molecular Dynamics, Cofactor Interaction Analysis, and Site-Directed Mutagenesis

Molecular dynamics simulations were performed on two ureidofibrate-like enantiomers to gain insight into their different potency and efficacy against PPARgamma. The partial agonism of the S enantiomer seems to be due to its capability to stabilize different regions of the receptor allowing the interaction with both coactivators and corepressors as shown by fluorescence resonance energy transfer (FRET) assays. The recruitment of the corepressor N-CoR1 by the S enantiomer on two different responsive elements of PPARgamma regulated promoters was confirmed by chromatin immunoprecipitation assays. Cell-based transcription assays show that PPARgamma coactivator 1alpha (PGC-1alpha) and cAMP response element binding protein-binding protein (CBP) enhance the basal and ligand-stimulated receptor activity acting as coactivators of PPARgamma, whereas the receptor interacting protein 140 (RIP140) and the nuclear corepressor 1 (N-CoR1) repress the transcriptional activity of PPARgamma. We also tested the importance of the residue Q286 on the transcriptional activity of the receptor by site-directed mutagenesis and confirmed its key role in the stabilization of helix 12. Molecular modeling studies were performed to provide a molecular explanation for the different behavior of the mutants.

Retrosulfonamido peptide analogues. Synthesis and crystal conformation of Boc-Pro-Leu-Ψ(NH-SO2)-Gly-NH2

Abstract Boc-Pro-Leu-Ψ(NH-SO 2 )-Gly-NH 2 ( 3 ) has been synthesized as the first example of a pseudopeptide incorporating the NH-SO 2 junction. The crystal structure of 3 indicates that the Ψ(NH-SO 2 ) induces a cisoidal (gauche − ) conformation which induces a backbone folding and prevents the H-bonded β-turn found in the parent peptide.

Synthesis, conformation, and biological activity of two fMLP‐OMe analogues containing the new 2‐[2′‐(methylthio) ethyl] methionine residue

The new Cα‐tetrasubstituted α‐amino acid residue 2‐[2′‐(methylthio) ethyl]methionine (Dmt) has been introduced into the reference chemotactic tripeptide HCO‐Met‐Leu‐Phe‐OMe (fMLP‐OMe) in place of the leucine or methionine, respectively. The biological activity of the new analogues [Dmt2] fMLP‐OMe (2) and [Dmt1] fMLP‐OMe (3) has been determined; whereas 2 is active toward human neutrophils, stimulating directed migration, superoxide anion generation, and lysozyme release, 3 results practically inactive in all tested assays. A conformational analysis on 2 and 3 has been performed in solution by using ir absorption and 1H‐nmr. The conformation of 2 was also examined in the crystal by x‐ray diffraction methods. Both 2 and 3 adopt fully extended conformation in correspondence with the Dmt residue. Biological and conformational results are discussed and compared with related previously studied models.