The bioisosteric concept applied to cannabinoid ligands.

Bioisosterism is widely used in medicinal chemistry as an approach aimed at either rationally modifying a hit compound into a more potent and/or selective molecule or a lead compound into a more drug-like one. Two different cannabinoid receptors have been cloned from mammalian tissues, the CB1 receptor, mostly expressed in brain, and the CB2 receptor, mostly expressed in the immune system, both regulating a variety of physiological functions. Synthetic cannabinoids have been developed that act as highly selective agonists or antagonists/inverse agonists at one or other of these receptor types with the ultimate goal of modulating the endocannabinoid system. This review takes into account the use of the bioisosteric substitution in the field of cannabinoid ligands as a tool for improving both their pharmacodynamic and pharmacokinetic properties.

Computational studies of competitive inhibitors of nitric oxide synthase (NOS) enzymes: towards the development of powerful and isoform-selective inhibitors.

Crystallographic structures of wild-type and mutant NOS isoforms complexed with substrate, intermediate, inhibitor, cofactor, and cofactor analogs are currently available. However, because of the high level of amino-acid conservation and the consequent similarity in dimeric quaternary structure as well as in the active site of NOS isoforms, structure-based isoform-selective inhibitor design is still a very challenging task. Nevertheless, the comprehension of the structural determinants for selectivity among the isoforms is fundamental for the design of further potent and more selective inhibitors. Computational techniques, based on the knowledge of the tridimensional structure of the isozymes, have been already applied to understand the significant isoform selectivity shown by some compounds. Collectively these structure-based approaches, in combination with SAR studies, have been able to explain the structural reasons of this selectivity.

The role of substance P in cerebral ischemia.

Tackykinins are involved in the inflammatory process of a large number of diseases. The role of the tachykinins in ischemic brain injury was evaluated by the serum levels of Substance P (SP), one of the most known tachykinins and detected by a competitive enzyme immunoassay. The study was performed in 15 human females and 3 human males with typical manifestation of complete stroke (12 cases) or transient ischemic attack (6 cases). The mean SP level in the serum of patients with transient ischemic attack (0.53+/-0.25 ng/ml) and of patients with complete stroke (0.31+/-0.14 ng/ml), showed significantly higher values than in controls (0.10+/-0.02 ng/ml). Moreover, in transient ischemic attack, the SP values were significantly higher than in cerebral complete stroke. But SP levels, based on the timings of classification of patients (i.e. before 12 hours: 0.34+/-0.15 ng/ml vs. 12 to 24 hours: 0.26+/-0.11 ng/ml) with brain injury, did not show any significant difference. Both values anyway were significantly higher than in controls. Our original results demonstrate the SP increase during cerebral ischemia. Further studies are necessary to verify if SP has an effective physiopathological role in the neurological ischemic damage, or if it is only a concomitant phenomenon. Our data, if confirmed, will be particularly important, not only to improve the knowledge of cerebral ischemic injury, but also for diagnosis and therapeutic approaches.

Arylpiperazines with affinity toward alpha(1)-adrenergic receptors.

In the last years, alpha(1) adrenoceptors (alpha(1)-AR) have been the subject of intense research, in part because receptor-binding studies and molecular biology have opened up new aspects of understanding but also because of the potential to find new drugs possibly acting toward pathophysiological processes where alpha(1)-AR are involved, such as benign prostatic hyperplasia (BPH) or hypertension. At present, arylpiperazines represent one of the most studied classes of molecules with affinity at alpha(1)-AR. In fact, a large amount of work has been done and reported, describing synthetic procedures, biological evaluation at both alpha(1)-AR and the corresponding subtypes, and structure-activity relationships (SARs). In this paper, a review based on a literature survey aimed at focusing on the structural properties that a compound should possess to show affinity toward alpha(1)-AR is presented. Moreover, the identification and optimization of the structural features of a hit compound derived from a pharmacophore-based database search, leading to a new class of arylpiperazinylalkyl pyridazinone derivatives with alpha(1)-AR affinity is reported.

Synthesis, biological evaluation, and pharmacophore generation of uracil, 4(3H)-pyrimidinone, and uridine derivatives as potent and selective inhibitors of parainfluenza 1 (Sendai) virus.

Several new 6-oxiranyl-, 6-oxiranylmethyluracils, and pyrimidinone derivatives, synthesized by lithiation-alkylation sequence of 1,3,6-trimethyluracil, 1,3-dimethyl-6-chloromethyluracil, and 2-alkoxy-6-methyl-4(3H)-pyrimidinones, showed a potent and selective antiviral activity against Sendai virus (SV) replication. To gain insight into the structural features required for SV inhibition activity, the new compounds were submitted to a pharmacophore generation procedure using the program Catalyst. The resulting pharmacophore model showed high correlation and predictive power. It also rationalized the relationships between structural properties and biological data of these inhibitors of SV replication.

Novel hypotensive agents from Verbesina caracasana. 8. Synthesis and pharmacology of (3,4-dimethoxycinnamoyl)-N(1)-agmatine and synthetic analogues.

The more polar metabolites from the Venezuelan plant Verbesina caracasana, i.e., N(3)-prenylagmatine, (3,4-dimethoxycinnamoyl)-N(1)-agmatine, agmatine, and galegine (prenylguanidine), previously reported (Delle Monache, G.; et al. BioMed. Chem. Lett. 1999, 9, 3249-3254), have been synthesized following a biosynthetic strategy. The pharmacologic profiles of various synthetic analogues of (3,4-dimethoxycinnamoyl)-N(1)-agmatine (G5) were also analyzed, to shed some light on the structure-activity relationship of these compounds. Derivatives with the (E)-configuration and/or with a p-methoxybenzoyl moiety were found to be responsible for higher hypotensive effects, which were associated with a slight and, in some cases, not dose-related increase of cardiac inotropism, with variable and not significant chronotopic responses, and, only at higher doses, with effects of respiratory depression. Either an increase (to six) or a decrease (to two) of the number of methylene groups in the alkyl chain of (E)-G5 did not change blood pressure responses, while slightly increasing the positive inotropic ones. At pharmacological doses, all the studied compounds showed hypotensive and slight positive inotropic effects without relevant chronotropic and respiratory actions.

Synthesis, biological evaluation, and pharmacophore generation of new pyridazinone derivatives with affinity toward alpha(1)- and alpha(2)-adrenoceptors.

A series of new pyridazin-3(2H)-one derivatives (3 and 4) were evaluated for their in vitro affinity toward both alpha(1)- and alpha(2)-adrenoceptors by radioligand receptor binding assays. All target compounds showed good affinities for the alpha(1)-adrenoceptor, with K(i) values in the low nanomolar range. The polymethylene chain constituting the spacer between the furoylpiperazinyl pyridazinone and the arylpiperazine moiety was shown to influence the affinity and selectivity of these compounds. Particularly, a gradual increase in affinity was observed by lengthening the polymethylene chain up to a maximum of seven carbon atoms. In addition, compound 3k, characterized by a very interesting alpha(1)-AR affinity (1.9 nM), was also shown to be a highly selective alpha(1)-AR antagonist, the affinity ratio for alpha(2)- and alpha(1)-adrenoceptors being 274. To gain insight into the structural features required for alpha(1) antagonist activity, the pyridazinone derivatives were submitted to a pharmacophore generation procedure using the program Catalyst. The resulting pharmacophore model showed high correlation and predictive power. It also rationalized the relationships between structural properties and biological data of, and external to, the pyridazinone class.

Fibroblast growth factors and their inhibitors.

Fibroblast growth factors (FGFs) are members of a family of polypeptides synthesized by a variety of cell types during the processes of embryonic development and in adult tissues. FGFs have been detected in normal and malignant cells and show a biological profile that includes mitogenic and angiogenic activity with a consequent crucial role in cell differentiation and development. To activate signal transduction pathways, FGFs use a dual receptor system based on tyrosine kinases and heparan sulfate (HS) proteoglycans. Based on these considerations, a variety of inhibitors able to block the interactions between FGFs and their receptors have been designed and investigated for their biological properties related to antiangiogenesis and antitumor activity. In this paper, in addition to an extensive description of the FGF family members, we report several compounds acting as FGF inhibitors by direct interaction with the growth factors. Suramin and other diverse polyanionic polysulfated and polysulfonated compounds are described, with a particular focus on suradistas. For this class of molecules, by means of molecular modeling procedures, a binding model to FGF-2 has been proposed and the structure-activity relationships of suradistas have been analyzed on the basis of the computational model described.

Design and realization of a tailor-made enzyme to modify the molecular recognition of 2-arylpropionic esters by Candida rugosa lipase.

Within a research project aimed at probing the substrate specificity and the enantioselectivity of Candida rugosa lipase (CRL), computer modeling studies of the interactions between CRL and methyl (+/-)-2-(3-benzoylphenyl)propionate (Ketoprofen methyl ester) have been carried out in order to identify which amino acids are essential to the enzyme/substrate interaction. Different binding models of the substrate enantiomers to the active site of CRL were investigated by applying a computational protocol based on molecular docking, conformational analysis, and energy minimization procedures. The structural models of the computer generated complexes between CRL and the substrates enabled us to propose that Phe344 and Phe345, in addition to the residues constituting the catalytic triad and the oxyanion hole, are the amino acids mainly involved in the enzyme-ligand interactions. To test the importance of these residues for the enzymatic activity, site-directed mutagenesis of the selected amino acids has been performed, and the mutated enzymes have been evaluated for their conversion and selectivity capabilities toward different substrates. The experimental results obtained in these biotransformation reactions indicate that Phe344 and especially Phe345 influence CRL activity, supporting the findings of our theoretical simulations.

Computer simulations of enantioselective ester hydrolyses catalyzed by Pseudomonas cepacia lipase.

On the basis of the X-ray crystal structure of the lipase from Pseudomonas cepacia (PcL)-an enzyme representative for a whole family of Pseudomonas lipases (lipase PS, SAM-2, AK 10, and others with a high degree of homology with PcL)-a computational study was performed to rationalize both the enantioselectivity and substrate specificity (tolerance) displayed by this lipase in the enantioselective hydrolysis of racemic esters 1a-12a from various secondary aromatic alcohols. The major goal of this project was the development of a binding model for PcL which is able to rationalize the experimental findings to predict "a priori the enantioselective behavior of PcL toward a wider range of substrates. A two-step modeling procedure, namely, docking experiments followed by construction of tetrahedral intermediates, was used for the simulation of the involved enzyme-substrate recognition/hydrolysis processes. The study of the recognition process (docking experiments) led to unambiguous identification of the binding geometry for the two enantiomeric series of substrates, but did not suggest a definitive interpretation of the behavior of PcL. Taking into consideration the stereoelectronic requirements of the enzymatic hydrolysis reaction, both the enantioselectivity and tolerance of the enzyme were then explained through the study of the tetrahedral intermediates, in turn constructed from the calculated docking geometries of 1a-12a.

Research on anti-HIV-1 agents. Investigation on the CD4-Suradista binding mode through docking experiments.

Sulfonated distamycin (Suradista) derivatives exhibit anti-HIV-1 activity by inhibiting the binding of the viral envelope glycoprotein gp120 to its receptor (CD4). With the aim to propose a possible binding mode between Suradistas and the CD4 macromolecule, molecular docking experiments, followed by energy minimization of the complexes thus obtained, were performed. Computational results show that ligand binding at the CD4 surface involves two or three positively charged regions of the macromolecule, in agreement with the results of X-ray crystallographic analysis of a ternary complex (CD4/gp120/neutralizing antibody) recently reported in the literature. Our findings account well for the structure-activity relationship found for Suradista compounds.

Building a pharmacophore model for a novel class of antitubercular compounds.

Starting from a set of 32 antitubercular compounds, for the first time a three-dimensional pharmacophore model has been derived through a computational approach based on CATALYST software. The model proved to be able to identify compounds belonging to classes of molecules already reported as antitubercular agents.

Further hypotensive metabolites from Verbesina caracasana.

After the isolation of caracasanamide and caracasandiamide, further hypotensive components of Verbesina caracasana were shown to be N3-prenylagmatine, N1-3',4'-dimethoxycinnamoylagmatine, agmatine and galegin (prenylguanidine). The structures were assigned on the basis of the spectral data of both metabolites and products from their alkaline hydrolyses. A pharmacological analysis of these products is also presented.

Novel hypotensive agents from Verbesina caracasana. 6. Synthesis and pharmacology of caracasandiamide.

Caracasandiamide, a second hypotensive agent isolated from Verbesina caracasana, is the cyclobutane dimer (truxinic type) of the previously reported 1-[(3, 4-dimethoxycinnamoyl)amino]-4-[(3-methyl-2-butenyl)guanidino]butane (caracasanamide) (Delle Monache, G.; et al. BioMed. Chem. Lett. 1992, 25, 415-418). The structure was confirmed by synthesis starting from beta-truxinic acid obtained by photoaddition of 3, 4-dimethoxycinnamic acid. The dimer was coupled with 2 mol of prenylagmatine to give caracasandiamide in satisfactory yield. By contrast, the direct photodimerization of caracasanamide was unsuccessful. Caracasandiamide, assayed by the iv route in anesthetized rats at doses ranging from 50 to 3200 microgram/kg of body weight, was found to have no appreciable effect on heart rate. At lower doses, the drug stimulates breathing and increases cardiac inotropism, stroke volume, and cardiac output, thus augmenting blood pressure and aortic flow. At higher doses, caracasandiamide depresses breathing likely through central neurogenic mechanisms (not involved in the cardiovascular effects), continues to stimulate cardiac inotropism, and induces, by reducing peripheral vascular resistance, arterial hypotension with reduction of both aortic flow and stroke volume. These cardiovascular effects appear to involve complex interactions at the level of the peripheral beta(1)-, beta(2)-, and alpha(2)-adrenoreceptor-dependent as well as M(2)- and M(4)-cholinergic receptor-dependent transductional pathways both in cardiovascular myocells and at the level of the postganglionic sympathetic endings (with reserpine- and guanethidine-like mechanisms). The cardiovascular effects of caracasandiamide, different from those of caracasanamide, do not depend on significant actions on the central nervous system and on baroreflex pathways. In a similar manner and more effective than caracasanamide, caracasandiamide may be considered a hypotensive and antihypertensive drug. It is devoid of some of the negative side effects, e.g., reflex tachycardia and decreased cardiac inotropism, which are shown by the majority of the most common antihypertensive and vasodilator drugs.

Synthesis and binding mode of heterocyclic analogues of suramin inhibiting the human basic fibroblast growth factor.

The design, synthesis, and biological evaluation of a series of pyrrole and pyrazole congeners 2 of suramin, directed toward the development and identification of new ligands that complex the human fibroblast growth factor (bFGF), thereby inhibiting tumor-promoted angiogenesis, is reported. Compounds 2 were evaluated for their ability to inhibit binding of bFGF to its receptor, in vivo bFGF-induced angiogenesis, and neovascularization of the chorioallantoic membrane in comparison with suramin. These assays showed that ligands 2 exhibit moderate to good activity, comparable to that of suramin, and are less toxic than suramin itself. In this study, affinity data of ligands in combination with the crystal structure of bFGF were used to explain structure-affinity relationships and to gain an insight into the possible mode of ligand-protein interaction. Due to the lack of experimental structural data on the ligand-bFGF complexes, molecular mechanics techniques were used to obtain putative bioactive conformations and to generate docked complexes with the three-dimensional structure of bFGF. These experiments led to suggest that compounds 2 give rise to 1:1 complexes with bFGF through an unprecedented, bidentate attachment of their naphthylsulfonate groups to two main domains, commonly referred to as the heparin binding site and the receptor binding site, on bFGF, thus preventing the interaction of the growth factor with its receptor.

Probing the substrate specificity for lipases. II. Kinetic and modeling studies on the molecular recognition of 2-arylpropionic esters by Candida rugosa and Rhizomucor miehei lipases.

Racemic arylpropionic esters 1-3, precursors of therapeutically important non-steroidal antiinflammatory drugs, were subjected to hydrolyses in the presence of either Candida rugosa or Rhizomucor miehei crude lipases. The hydrolyses of 1 and 2 proved to be highly enantioselective, whereas 3 was not transformed at all. Both the substrate specificity and the enantioselectivity of these lipases were explained through a molecular modeling study involving docking experiments between 1-3 and the amino acids forming the enzymes active-sites, whose three dimensional structures were obtained from X-ray crystallographic data, followed by extensive conformational analysis on their computer-generated complexes. The results of this study also account for the high enantioselective and good yielding hydrolysis of 3 (as the corresponding 2-chloroethyl ester) catalyzed by CRL pretreated with 2-propanol, recently reported in the literature, and lead to admit that such a treatment may operate very deep conformational changes on the amino acids of the enzyme active-site.

Diltiazem-like calcium entry blockers: a hypothesis of the receptor-binding site based on a comparative molecular field analysis model.

A series of 26 pyrrolo[2,1-c][1,4]benzothiazines, which have been already synthesized and reported to show calcium antagonist activity in both radioligand-binding assays and functional studies, were investigated using the comparative molecular field analysis (CoMFA) paradigm. Due to the lack of experimental structural data on these derivatives, the minimum energy conformers obtained by molecular mechanics calculations were used in the subsequent study. Structures were aligned following an alignment criterion based on the pharmacophoric groups of the studied compounds. The predictive ability of the CoMFA model was evaluated using a test set consisting of three representative compounds. The best 3D-quantitative structure-activity relationship model found yields significant cross-validated, conventional, and predictive r2 values equal to 0.703, 0.970, and 0.865, respectively, the average absolute error of predictions being 0.26 log unit. The predictive capability of this model was also tested on a further test set of molecules consisting of diltiazem and nine pyrrolo[2,1-d][1,5]benzothiazepines endowed with calcium antagonist activity. The accurate results obtained also in this case revealed the robustness of the model. On the basis of the same alignment, the structural moieties of the studied calcium entry blockers which are thought to contribute to the biological activity were identified, and a possible receptor-binding site for all these compounds is presented taking into account the information derived from the analysis of the steric and electrostatic CoMFA contour maps.

Investigation on QSAR and binding mode of a new class of human rhinovirus-14 inhibitors by CoMFA and docking experiments.

A 3-D QSAR study has been carried out on a new class of potent and selective human rhinovirus-14 (HRV-14) inhibitors. In particular, the CoMFA (comparative molecular field analysis) technique has been applied to develop a model able to explain and predict the anti-HRV-14 activity of a class of compounds 4 and potentially helpful to design new and more potent antirhinovirus agents. Docking experiments have also been performed with the aim of elucidating the possible binding mode of these inhibitors. These two approaches are combined to highlight a single, highly favoured mode of interaction of the compounds with the viral capsid proteins.

Probing the substrate specificity for lipases. A CoMFA approach for predicting the hydrolysis rates of 2-arylpropionic esters catalyzed by Candida rugosa lipase.

The enzyme catalyzed hydrolysis of esters 1-3, precursors of therapeutically important non-steroidal antiinflammatory drugs, in the presence of the lipase from Candida rugosa was studied and the relative rates of the enzymatic hydrolysis were determined. With the exception of 3, which was not transformed under the reaction conditions, all transformations proved to be highly enantiospecific. Usually the mechanism of enantiorecognition is probed by substrate mapping. Although more theoretical approaches are existing, these all require knowledge of the three-dimensional structure of the enzyme. A model capable of correlating the extent of substrate hydrolysis as well as the initial reaction rates with their stereoelectronic properties has been developed by a Comparative Molecular Field Analysis (CoMFA) approach. This model does not require detailed knowledge of the three-dimensional structure of the enzyme and proved to be highly predictive. It is possible that this kind of approach holds promise for future work on enzyme-substrate interactions.