Marta Murcia

Benzimidazole derivatives. Part 1: Synthesis and structure–activity relationships of new benzimidazole-4-carboxamides and carboxylates as potent and selective 5-HT4 receptor antagonists

New benzimidazole-4-carboxamides 1-16 and -carboxylates 17-26 were synthesized and evaluated for binding affinity at serotonergic 5-HT4 and 5-HT3 receptors in the CNS. Most of the synthesized compounds exhibited moderate-to-very high affinity (in many cases subnanomolar) for the 5-HT4 binding site and no significant affinity for the 5-HT3 receptor. SAR observations and structural analyses (molecular modeling, INSIGHT II) indicated that the presence of a voluminous substituent in the basic nitrogen atom of the amino moiety and a distance of ca. 8.0 A from this nitrogen to the aromatic ring are of great importance for high affinity and selectivity for 5-HT4 receptors. These results confirm our recently proposed model for recognition by the 5-HT4 binding site. Amides 12-15 and esters 24 and 25 bound at central 5-HT4 sites with very high affinity (Ki = 0.11-2.9 nM) and excellent selectivity over serotonin 5-HT3, 5-HT2A, and 5-HT1A receptors (Ki > 1000-10,000 nM). Analogues 12 (Ki(5-HT4) = 0.32 nM), 13 (Ki(5-HT4) = 0.11 nM), 14 (Ki(5-HT4) = 0.29 nM) and 15 (Ki(5-HT4) = 0.54 nM) were pharmacologically characterized as selective 5-HT4 antagonists in the isolated guinea pig ileum (pA2 = 7.6, 7.9, 8.2 and 7.9, respectively), with a potency comparable to the 5-HT4 receptor antagonist RS 39604 (pA2 = 8.2). The benzimidazole-4-carboxylic acid derivatives described in this paper represent a novel class of potent and selective 5-HT4 receptor antagonists. In particular, compounds 12-15 could be interesting pharmacological tools for the understanding of the role of 5-HT4 receptors.

Computational Approaches to Model Ligand Selectivity in Drug Design

To be effective, a designed drug must discriminate successfully the macromolecular target from alternative structures present in the organism. The last few years have witnessed the emergence of different computational tools aimed to the understanding and modeling of this process at molecular level. Although still rudimentary, these methods are shaping a coherent approach to help in the design of molecules with high affinity and specificity, both in lead discovery and in lead optimization. It is the purpose of this review to illustrate the array of computational tools available to consider selectivity in the design process, to summarize the most relevant applications, and to sketch the challenges ahead.

3-D-QSAR/CoMFA and recognition models of benzimidazole derivatives at the 5-HT4 receptor

3-D-QSAR/CoMFA methodology and computational simulation of ligand recognition have been successfully applied to explain the binding affinities of a series of benzimidazole derivatives 1-24 acting at serotonin 5-HT(4)Rs. Both derived computational models have facilitated the identification of the structural elements of the ligands that are key to high 5-HT(4)R affinity. The results provide the tools for predicting the affinity of related compounds, and for guiding the design and synthesis of new ligands with predetermined affinities and selectivity.

Pd(0) Amination of Benzimidazoles as an Efficient Method towards New (Benzimidazolyl)piperazines with High Affinity for the 5-HT1A Receptor

Abstract New (benzimidazolyl)amines have been synthesized from 4- and 6-bromobenzimidazole derivatives via palladium-mediated amination reactions. Among them, (benzimidazol-4(7)-yl)piperazine derivatives have been shown to be a new family of high affinity 5-HT1A receptor ligands.

Effects of Limiting Extension at the αIIb Genu on Ligand Binding to Integrin αIIbβ3

Structural data of integrin αIIbβ3 have been interpreted as supporting a model in which: 1) the receptor exists primarily in a “bent,” low affinity conformation on unactivated platelets and 2) activation induces an extended, high affinity conformation prior to, or following, ligand binding. Previous studies found that “clasping” the αIIb head domain to the β3 tail decreased fibrinogen binding. To study the role of αIIb extension about the genu, we introduced a disulfide “clamp” between the αIIb thigh and calf-1 domains. Clamped αIIbβ3 had markedly reduced ability to bind the large soluble ligands fibrinogen and PAC-1 when activated with monoclonal antibody (mAb) PT25-2 but not when activated by Mn2+ or by coexpressing the clamped αIIb with a β3 subunit containing the activating mutation N339S. The clamp had little effect on the binding of the snake venom kistrin (Mr 7,500) or αIIbβ3-mediated adhesion to immobilized fibrinogen, but it did diminish the enhanced binding of mAb AP5 in the presence of kistrin. Collectively, our studies support a role for αIIb extension about the genu in the binding of ligands of 340,000 and 900,000 Mr with mAb-induced activation but indicate that it is not an absolute requirement. Our data are consistent with αIIb extension resulting in increased access to the ligand-binding site and/or facilitating the conformational change(s) in β3 that affect the intrinsic affinity of the binding pocket for ligand.

Effects of limiting extension at the αIIb genu on ligand binding to αIIbβ3

Structural data of integrin αIIbβ3 have been interpreted as supporting a model in which: 1) the receptor exists primarily in a “bent,” low affinity conformation on unactivated platelets and 2) activation induces an extended, high affinity conformation prior to, or following, ligand binding. Previous studies found that “clasping” the αIIb head domain to the β3 tail decreased fibrinogen binding. To study the role of αIIb extension about the genu, we introduced a disulfide “clamp” between the αIIb thigh and calf-1 domains. Clamped αIIbβ3 had markedly reduced ability to bind the large soluble ligands fibrinogen and PAC-1 when activated with monoclonal antibody (mAb) PT25-2 but not when activated by Mn2+ or by coexpressing the clamped αIIb with a β3 subunit containing the activating mutation N339S. The clamp had little effect on the binding of the snake venom kistrin (Mr 7,500) or αIIbβ3-mediated adhesion to immobilized fibrinogen, but it did diminish the enhanced binding of mAb AP5 in the presence of kistrin. Collectively, our studies support a role for αIIb extension about the genu in the binding of ligands of 340,000 and 900,000 Mr with mAb-induced activation but indicate that it is not an absolute requirement. Our data are consistent with αIIb extension resulting in increased access to the ligand-binding site and/or facilitating the conformational change(s) in β3 that affect the intrinsic affinity of the binding pocket for ligand.

Study of the bioactive conformation of novel 5-HT4 receptor ligands: influence of an intramolecular hydrogen bond

Abstract By using NMR and IR techniques and theoretical methods, we have studied the prototropic equilibrium present in the benzimidazole ring of a series of derivatives acting at serotonin 5-HT 4 receptors. The structural study has allowed us to get insight into the bioactive conformation of the novel 5-HT 4 receptor ligands which has been supported by biological data. This will help the docking of the ligands into a 3-D model of the receptor binding site in order to guide the design and synthesis of new compounds with predetermined pharmacological activities.

Computational model of the complex between GR113808 and the 5-HT4 receptor guided by site-directed mutagenesis and the crystal structure of rhodopsin

A computational model of the transmembrane domain of the human 5-HT4 receptor complexed with the GR113808 antagonist was constructed from the crystal structure of rhodopsin and the putative residues of the ligand-binding site, experimentally determined by site-directed mutagenesis. The recognition mode of GR113808 consist of: (i) the ionic interaction between the protonated amine and Asp3.32; (ii) the hydrogen bond between the carbonylic oxygen and Ser5.43; (iii) the hydrogen bond between the ether oxygen and Asn6.55; (iv) the hydrogen bond between the C-H groups adjacent to the protonated piperidine nitrogen and the π electrons of Phe6.51; and (v) the π-σ aromatic-aromatic interaction between the indole ring and Phe6.52.This computational model offers structural indications about the role of Asp3.32, Ser5.43, Phe6.51, Phe6.52, and Asn6.55 in the experimental binding affinities. Asp3.32Asn mutation does not affect the binding of GR113808 because the loss of binding affinity from an ion pair to a charged hydrogen bond is compensated by the larger energetical penalty of Asp to disrupt its side chain environment in the ligand-free form, and the larger interaction between Phe6.51 and the piperidine ring of the ligand in the mutant receptor. In the Phe6.52Val mutant the indole ring of the ligand replaces the interaction with Phe6.52 by a similarly intense interaction with Tyr5.38, with no significant effect in the binding of GR113808. The mutation of Asn6.55 to Leu replaces the hydrogen bond of the ether oxygen of the ligand from Asn6.55 to Cys5.42, with a decrease of binding affinity that approximately equals the free energy difference between the SH⋯O and NH⋯O hydrogen bonds.Because these residues are also present in the other members of the neurotransmitter family of G protein-coupled receptors, these findings will also serve for our understanding of the binding of related ligands to their cognate receptors.

Synthesis of new (benzimidazolyl)piperazines with affinity for the 5-HT1A receptor via Pd(0) amination of bromobenzimidazoles

The synthesis of a new family of (benzimidazolyl)piperazines has been developed through Pd(0) mediated amination of 4- and 6-bromobenzimidazole derivatives. Preliminary studies showed that some of these compounds are potent 5-HT1A receptor ligands.

Targeted molecular dynamics reveals overall common conformational changes upon hybrid domain swing‐out in β3 integrins

The β3 integrin family members αIIβ3 and αVβ3 signal bidirectionally through long‐range allosteric changes, including a transition from a bent unliganded‐closed low‐affinity state to an extended liganded‐open high‐affinity state. To obtain an atomic‐level description of this transition in an explicit solvent, we carried out targeted molecular dynamics simulations of the headpieces of αIIβ3 and αVβ3 integrins. Although minor differences were observed between these receptors, our results suggest a common transition pathway in which the hybrid domain swing‐out is accompanied by conformational changes within the β3 βA (I‐like) domain that propagate through the α7 helix C‐terminus, and are followed by the α7 helix downward motion and the opening of the β6‐α7 loop. Breaking of contact interactions between the β6‐α7 loop and the α1 helix N‐terminus results in helix straightening, internal rearrangements of the specificity determining loop (SDL), movement of the β1‐α1 loop toward the metal ion dependent adhesion site (MIDAS), and final changes at the interfaces between the β3 βA (I‐like) domain and either the hybrid or the α β‐propeller domains. Taken together, our results suggest novel testable hypotheses of intradomain and interdomain interactions responsible for β3 integrin activation. Proteins 2009.