Design, synthesis and antihypertensive evaluation of novel codrugs with combined angiotensin type 1 receptor antagonism and neprilysin inhibition.

The multifactorial etiology of hypertension has promoted the research of blood pressure-lowering agents with multitarget actions to achieve better clinical outcomes. We describe here the discovery of novel dual-acting antihypertensive codrugs combining pharmacophores with angiotensin type 1 (AT1) receptor antagonism and neprilysin (NEP) inhibition. Specifically, the codrugs combine the AT1 antagonists losartan or its carboxylic acid active metabolite (E-3174) with selected monocarboxylic acid NEP inhibitors through a cleavable linker. The resulting codrugs exhibited high rates of in vitro conversion into the active molecules upon incubation with human/rat liver S9 fractions and in vivo conversion after oral administration in rodents. Moreover, the acute effects of one of the designed codrugs (3b) was confirmed at the doses of 10, 30 and 60 mg/kg p.o. in the spontaneous hypertensive rat (SHR) model, showing better antihypertensive response over 24 hours than the administration of an equivalent fixed-dose combination of 15 mg/kg of losartan and 14 mg/kg of the same NEP inhibitor used in 3b. The results demonstrate that the codrug approach is a plausible strategy to develop a single molecular entity with combined AT1 and NEP activities, aiming at achieving improved pharmacokinetics, efficacy and dosage convenience, as well as reduced drug-drug interaction for hypertension patients. In addition, the developability of the codrug should be comparable to the one of marketed AT1 antagonists, most of them prodrugs, but bearing only the AT1 pharmacophore.

Discovery of ACH-000143: A Novel Potent and Peripherally Preferred Melatonin Receptor Agonist that Reduces Liver Triglycerides and Steatosis in Diet-Induced Obese Rats.

The modulation of melatonin signaling in peripheral tissues holds promise for treating metabolic diseases like obesity, diabetes, and nonalcoholic steatohepatitis. Here, several benzimidazole derivatives have been identified as novel agonists of the melatonin receptors MT1 and MT2. The lead compounds 10b, 15a, and 19a demonstrated subnanomolar potency at MT1/MT2 receptors, high oral bioavailability in rodents, peripherally preferred exposure, and excellent selectivity in a broad panel of targets. Two-month oral administration of 10b in high-fat diet rats led to a reduction in body weight gain similar to dapagliflozin with superior results on hepatic steatosis and triglyceride levels. An early toxicological assessment indicated that 10b (also codified as ACH-000143) was devoid of hERG binding, genotoxicity, and behavioral alterations at doses up to 100 mg/kg p.o., supporting further investigation of this compound as a drug candidate.

Brain-wide mapping of c-fos expression in the single prolonged stress model and the effects of pretreatment with ACH-000029 or prazosin.

Post-traumatic stress disorder (PTSD) is a mental health condition that is triggered by a stressful event, with symptoms including exaggerated startle response, intrusive traumatic memories and nightmares. The single prolonged stress (SPS) is a multimodal stress protocol that comprises a sequential exposure to physical restraint, forced swimming, predator scent and ether anesthesia. This procedure generates behavioral and neurobiological alterations that resemble clinical findings of PTSD, and thus it is commonly used to model the disease in rodents. Here, we applied c-fos mapping to produce a comprehensive view of stress-activated brain regions in mice exposed to SPS alone or to SPS after oral pretreatment with the serotonin-noradrenaline receptor dual modulator ACH-000029 or the α1-adrenergic blocker prazosin. The SPS protocol evoked c-fos expression in several brain regions that control the stress-anxiety response, including the central and medial amygdala, the bed nucleus of the stria terminalis, the pallidum, the paraventricular hypothalamus, the intermediodorsal, paraventricular and central medial thalamic nuclei, the periaqueductal gray, the lateral habenula and the cuneiform nucleus. These effects were partially blocked by pretreatment with prazosin but completely prevented by ACH-000029. Collectively, these findings contribute to the brain-wide characterization of neural circuits involved in PTSD-related stress responses. Furthermore, the identification of brain areas regulated by ACH-000029 and prazosin revealed regions in which SPS-induced activation may depend on the combined or isolated action of the noradrenergic and serotonergic systems. Finally, the dual regulation of serotonin and α1 receptors by ACH-000029 might represent a potential pharmacotherapy that can be applied in the peri-trauma or early post-trauma period to mitigate the development of symptoms in PTSD patients.

Preclinical characterization of ACH-000029, a novel anxiolytic compound acting on serotonergic and alpha-adrenergic receptors.

Anxiety disorders are serious and common mental diseases, yet there is still a need for the development of more effective anxiolytics with better safety profiles than benzodiazepines and serotonin reuptake inhibitors. The serotonergic and noradrenergic systems have reciprocal interactions and are intricately related to the pathogenesis of anxiety. In this study, the anxiolytic-like effect of the novel compound ACH-000029, 3-(2-(4-(2-methoxyphenyl) piperazine-1-yl) ethyl) quinazoline-4(3H)-one, is reported. This compound acts at selected serotonergic (5-HT1A and 5-HT1D partial agonism and 5-HT2A antagonism) and α-adrenergic (α-1A, 1B and 1D antagonism) receptors, with good selectivity over other G-protein-coupled receptors. ACH-000029 exhibited high blood-brain barrier permeation and acute anxiolytic effects in the marble burying (MB) and light-dark box (LDB) models of anxiety over the dose ranges of 8-32 mg/kg i.p. and 16-30 mg/kg p.o. The anxiolytic activity was comparable to that observed for serotonin reuptake inhibitors (paroxetine and fluoxetine) and benzodiazepines (alprazolam, diazepam and clobazam). The analysis of the whole-brain c-fos expression following oral dosing showed that ACH-000029 regulated regions highly associated with the processing of environmental stimuli and anxiety behavior, such as the amygdala, paraventricular nucleus of the thalamus, retrosplenial dorsal, pallidum, bed nuclei of the stria terminalis, and locus ceruleus. No safety concerns were identified for ACH-000029 in the functional observational battery up to 50 mg/kg i.p. and in the nonprecipitated withdrawal test up to 30 mg/kg p.o. twice daily for 20 days. This work supports the further development of ACH-000029 as a drug candidate for the treatment of anxiety disorders. The analysis of the in vitro pharmacology and brain regions regulated by this compound may also lead to the exploration of other indications within the psychiatry field.

Descoberta de fármacos a partir de produtos naturais e a abordagem Molecular Power House (MPH) / Natural product-based drug discovery and the Molecular Power House (MPH) approach

A descoberta de fármacos a partir de produtos naturais vivencia uma nova era graças ao uso de tecnologias de ponta e abordagens integradas para superar as dificuldades inerentes à pesquisa com produtos naturais. Estes são substâncias químicas altamente complexas e inovadoras produzidas pela biota, em especial organismos sésseis como plantas e micro-organismos, e representam a principal fonte de inspiração de novos fármacos. Resultante do reavivado interesse na descoberta de medicamentos à base de produtos naturais, novas abordagens para a identificação, caracterização, e reabastecimento de produtos naturais estão sendo desenvolvidas, que podem endereçar alguns dos desafios relacionados ao desenvolvimento de fármacos inspirados em moléculas da biodiversidade. Almeja-se a capacidade de detecção e caracterização de novos produtos naturais bioativos, concomitantemente à redução dos custos e tempo para obtenção destas moléculas. Para isto, é necessário inovar nos processos e nas tecnologias aplicadas à descoberta de fármacos a partir de produtos naturais. A abordagem Molecular Power House (MPH) apresentada neste trabalho faz uso de tecnologias integradas como uma forma de superar gargalos clássicos da pesquisa com produtos naturais de plantas, alinhada ao acesso à maior biodiversidade do planeta, posicionando o Brasil no cenário mundial de descoberta de fármacos inovadores.

Investigation of the induced-fit mechanism and catalytic activity of the human cytomegalovirus protease homodimer via molecular dynamics simulations.

Human cytomegalovirus (HCMV) is a highly species-specific DNA virus infecting up to 80% of the general population. The viral genome contains the open reading frame UL80, which encodes the full-length 80 kDa HCMV serine protease and its substrate. Full-length HCMV protease is composed of an N-terminal 256-amino-acid proteolytic domain, called assemblin, a linker region, and a C-terminal structural domain, the assembly protein precursor. Biochemical studies have shown that dimerization activates assemblin because of an induced stabilization of the oxyanion hole (Arg166). Thus, we performed here molecular dynamics (MD) simulations on HCMV protease models to study the induced-fit mechanism of the enzyme upon the binding of substrates and peptidyl inhibitors, and structural and energetic factors that are responsible for the catalytic activity of the enzyme dimer. Long and stable trajectories were obtained for the models of the monomeric and dimeric states, free in solution and bound to a peptidyl-activated carbonyl inhibitor, with very good agreement between theoretical and experimental results. Our results suggest that HCMV protease is indeed a novel example of serine protease that operates by an induced-fit mechanism. Also, in agreement with mutagenesis studies, our MD simulations suggest that the dimeric form is necessary to activate the enzyme because of an induced stabilization of the oxyanion hole.

Thrombin inhibition by novel benzamidine derivatives: a free-energy perturbation study.

Thrombin is a serine protease responsible for blood coagulation. Since thrombin inhibitors appear to be effective in the treatment and prevention of thrombotic and embolic disorders, considerable attention has been focused on the structure and interactions of this enzyme. In this work, to evaluate the relative free energies of hydration and binding to thrombin for some benzamidine derivatives, we used the finite difference thermodynamic integration (FDTI) algorithm within the Discover program of MSI. By this method, two possible orders of hydration for the candidates were obtained: p-amidinophenylpyruvate > p-(2-oxo-1-propyl)benzamidine > p-methylbenzamidine > p-ethylbenzamidine > p-(1-propyl)benzamidine > benzamidine and p-amidinophenylpyruvate > p-(2-oxo-1-propyl)benzamidine > p-methylbenzamidine > p-ethylbenzamidine > benzamidine > p-(1-propyl)benzamidine. We also obtained the following order for thrombin binding: p-(2-oxo-1-propyl)benzamidine > p-ethylbenzamidine > p-(1-propyl)benzamidine > p-methylbenzamidine > benzamidine > p-amidinophenylpyruvate.

Human Cytomegalovirus Protease: Why is the Dimer Required for Catalytic Activity?

Human cytomegalovirus (HCMV) is a pathogenic agent responsible for morbidity and mortality in immunocompromised and immunosuppressed individuals. HCMV encodes a serine protease that is essential for the production of infectious virions. In this work, we applied molecular dynamics (MD) simulations on HCMV protease models in order to investigate the experimentally observed (i) catalytic activity of the enzyme homodimer and (ii) induced-fit mechanism upon the binding of substrates and peptidyl inhibitors. Long and stable trajectories were obtained for models of the monomeric and dimeric states, free in solution and bound covalently and noncovalently to a peptidyl-activated carbonyl inhibitor, with very good agreement between theoretical and experimental results. The MD results suggest that HCMV protease indeed operates by an induced-fit mechanism. Also, our analysis indicates that the catalytic activity of the dimer is a result of more favorable interactions between the oxyanion in the covalently bound state and the backbone nitrogen of Arg165, resulting in a reaction that is 7.0 kcal/mol more exergonic and a more significant thermodynamic driving force. The incipient oxyanion in the transition state should also benefit from the stronger interactions with Arg165, reducing in this manner the intrinsic activation barrier for the reaction in the dimeric state.

Extension of the PDDG/PM3 Semiempirical Molecular Orbital Method to Sulfur, Silicon, and Phosphorus.

The PDDG/PM3 semiempirical molecular orbital method has been parameterized for molecules, ions, and complexes containing sulfur; the mean absolute error (MAE) for heats of formation, DeltaH(f), of 6.4 kcal/mol is 35 - 40 % smaller than for PM3, AM1, and MNDO/d. For completeness, parameterization was also carried out for silicon and phosphorous. For 144 silicon-containing molecules, the DeltaH(f) MAE for PDDG/PM3, PM3, and AM1 is 11 - 12 kcal/mol, while MNDO/d yields 9.4 kcal/mol. For the limited set of 43 phosphorus-containing molecules, MNDO/d also yields the best results followed by PDDG/PM3, AM1, and PM3. The benefits of the d-orbitals in MNDO/d for hypervalent compounds are apparent for silicon and phosphorous, while they are masked in the larger dataset for sulfur by large errors for branched compounds. Overall, for 1480 molecules, ions, and complexes containing the elements H, C, N, O, F, Si, P, S, Cl, Br, and I, the MAEs in kcal/mol for DeltaH(f) are 6.5 (PDDG/PM3), 8.7 (PM3), 10.3 (MNDO/d), 10.8 (AM1), and 19.8 (MNDO).

Effects of Arg90 Neutralization on the Enzyme-Catalyzed Rearrangement of Chorismate to Prephenate.

Chorismate mutase (CM) is an enzyme that catalyzes the Claisen rearrangement of chorismate to prephenate. In a recent effort to understand the basis for catalysis by CM, Kienhöfer and co-workers (J. Am. Chem. Soc. 2003, 125, 3206-3207) reported results on the mutation of Arg90 in Bacillus subtilis CM (BsCM) to citrulline (Cit), an isosteric but neutral arginine analogue. An ca. 10(4)-fold decrease in kcat or 5.9 kcal/mol increase in the free-energy barrier (ΔG(‡)) for the overall catalysis was observed upon mutation. In this work, attention is turned to determining the key factors that contribute to the reduced catalytic efficiency of Arg90Cit BsCM. Using a combined QM/MM Monte Carlo/Free-Energy Perturbation method, a ΔΔG(‡) value of 3.3 kcal/mol is obtained. The higher free-energy barrier for the mutant is exclusively related to inferior stabilization of the TS, particularly one of its carboxylate groups, by neutral Cit. In addition, the reaction becomes 2.0 kcal/mol more exergonic. As BsCM is limited by product release, this step contributes to the remainder of the 10(4)-fold decrease in the rate constant in going from Arg90 to Cit.

Elucidation of fatty acid amide hydrolase inhibition by potent alpha-ketoheterocycle derivatives from Monte Carlo simulations.

Fatty acid amide hydrolase (FAAH) is a serine hydrolase responsible for the degradation of anandamide, an endogenous cannabinoid agonist, and oleamide, a sleep-inducing lipid. Recently, Boger and co-workers reported a potent, selective, and efficacious class of reversible alpha-ketoheterocycle inhibitors of FAAH that produce analgesia in animal models (J. Med. Chem. 2005, 48, 1849-1856; Bioorg. Med. Chem. Lett. 2005, 15, 1423-1428). Key aspects of the structure-activity data are addressed here through computational analysis of FAAH inhibition using Monte Carlo (MC) simulations in conjunction with free energy perturbation (FEP) calculations. The MC/FEP simulations demonstrate that incorporation of pyridine at the C5 position of the 2-keto-oxazole and 2-keto-1,3,4-oxadiazole derivatives significantly enhances binding affinity by formation of a hydrogen-bonded array between the pyridyl nitrogen and Lys142 and Thr236. The results also attribute the activity boost upon substitution of oxazole by oxadiazole to reduced steric interactions in the active site and a lower torsional energy penalty upon binding.

Macrophomate synthase: QM/MM simulations address the Diels-Alder versus Michael-Aldol reaction mechanism.

Macrophomate synthase (MPS) of the phytopathogenic fungus Macrophoma commelinae catalyzes the transformation of 2-pyrone derivatives to the corresponding benzoate analogues. The transformation proceeds through three separate chemical reactions, including decarboxylation of oxalacetate to produce pyruvate enolate, two C-C bond formations between 2-pyrone and pyruvate enolate that form a bicyclic intermediate, and final decarboxylation with concomitant dehydration. Although some evidence suggests that the second step of the reaction catalyzed by MPS is a Diels-Alder reaction, definite proof that the C-C bond formations occur via a concerted mechanism is still required. An alternative route for formation of the C-C bonds is a stepwise Michael-aldol reaction. In this work, mixed quantum and molecular mechanics (QM/MM) combined with Monte Carlo simulations and free-energy perturbation (FEP) calculations were performed to investigate the relative stabilities of the transition states (TS) for both reaction mechanisms. The key results are that the Diels-Alder TS model is 17.7 and 12.1 kcal/mol less stable than the Michael and aldol TSs in the stepwise route, respectively. Therefore, this work indicates that the Michael-aldol mechanism is the route used by MPS to catalyze the second step of the overall transformation, and that the enzyme is not a natural Diels-Alderase, as claimed by Ose and co-workers (Nature 2003, 422, 185-189; Acta Crystallogr. 2004, D60, 1187-1197). A modified link-atom treatment for the bonds at the QM/MM interface is also presented.

Potential of mean force calculations on an L-type calcium channel model.

To understand the mechanisms of Na(+)/Li(+) permeation at submicromolar Ca(2+) concentrations, Na(+)/Li(+) blocking at higher Ca(2+) concentrations (10(-6)-10(-4) M) and Ca(2+) permeation at millimolar Ca(2+) concentrations, we used our recently described L-type calcium channel model. For this purpose, we obtained potential of mean force (pmf) curves for the position change of one Na(+) and one Ca(2+) ion inside the channel and for the position change of a second Ca(2+) ion when the EEEE locus is coordinated to Ca(2+). The pmf curves suggest that (i) at submicromolar Ca(2+) concentrations, because of the low velocity of Ca(2+) entry in the channel, monovalent ion flux occurs; (ii) at Ca(2+) concentrations between 10(-6) and 10(-4) M, thermodynamic equilibrium between the channel and Ca(2+) is achieved; as the coordination of Ca(2+) with the locus is more favorable than the coordination of Na(+), the monovalent ion flux is blocked; and (iii) to put a second Ca(2+) ion inside the channel at an appropriate rate, the Ca(2+) concentration should reach millimolar levels. Nevertheless, the entry of a second Ca(2+) is thermodynamically unfavorable, indicating that the competition of two Ca(2+) ions for the locus leads to Ca(2+) permeation.

Extension of the PDDG/PM3 and PDDG/MNDO semiempirical molecular orbital methods to the halogens.

The new semiempirical methods, PDDG/PM3 and PDDG/MNDO, have been parameterized for halogens. For comparison, the original MNDO and PM3 were also reoptimized for the halogens using the same training set; these modified methods are referred to as MNDO' and PM3'. For 442 halogen-containing molecules, the smallest mean absolute error (MAE) in heats of formation is obtained with PDDG/PM3 (5.6 kcal/mol), followed by PM3' (6.1 kcal/mol), PDDG/MNDO (6.6 kcal/mol), PM3 (8.1 kcal/mol), MNDO' (8.5 kcal/mol), AM1 (11.1 kcal/mol), and MNDO (14.0 kcal/mol). For normal-valent halogen-containing molecules, the PDDG methods also provide improved heats of formation over MNDO/d. Hypervalent compounds were not included in the training set and improvements over the standard NDDO methods with sp basis sets were not obtained. For small haloalkanes, the PDDG methods yield more accurate heats of formation than are obtained from density functional theory (DFT) with the B3LYP and B3PW91 functionals using large basis sets. PDDG/PM3 and PM3' also give improved binding energies over the standard NDDO methods for complexes involving halide anions, and they are competitive with B3LYP/6-311++G(d,p) results including thermal corrections. Among the semiempirical methods studied, PDDG/PM3 also generates the best agreement with high-level ab initio G2 and CCSD(T) intrinsic activation energies for S(N)2 reactions involving methyl halides and halide anions. Finally, the MAEs in ionization potentials, dipole moments, and molecular geometries show that the parameter sets for the PDDG and reoptimized NDDO methods reduce the MAEs in heats of formation without compromising the other important QM observables.

A molecular dynamics study of an L-type calcium channel model.

In this work, we propose a molecular model of the L-type calcium channel pore from the human cardiac alpha1 subunit. Four glutamic acid residues, the EEEE locus, located at highly conserved P loops (also called SS1-SS2 segments) of the alpha1 subunit, molecularly express the calcium channel selectivity. The proposed alpha-helix structure for the SS1 segment, analyzed through molecular dynamics simulations in aqueous-phase, was validated by the plotting of Ramachandran diagrams for the averaged structures and by the analysis of i and i + 4 helical hydrogen bonding between the amino acid residues. The results of the simulation of the calcium channel model with one and two Ca2+ ions at the binding site are in accordance with mutation studies which suggest that the EEEE locus in the L-type calcium channel must form a single high-affinity binding site. These results suggest that the Ca2+ permeation through the channel would be derived from competition between two ions for the only high-affinity binding site. Furthermore, the experimentally observed blocking of the Na+ flux at micromolar Ca2+ concentrations, probably due to the occupancy of the single high-affinity binding site for one Ca2+, was also reproduced by our model.

Investigation of solvent effects for the Claisen rearrangement of chorismate to prephenate: mechanistic interpretation via near attack conformations.

Solvent effects on the rate of the Claisen rearrangement of chorismate to prephenate have been examined in water and methanol. The preequilibrium free-energy differences between diaxial and diequatorial conformers of chorismate, which had previously been implicated as the sole basis for the observed 100-fold rate increase in water over methanol, have been reframed using the near attack conformation (NAC) concept of Bruice and co-workers. Using a combined QM/MM Monte Carlo/free-energy perturbation (MC/FEP) method, 82%, 57%, and 1% of chorismate conformers were found to be NAC structures (NACs) in water, methanol, and the gas phase, respectively. As a consequence, the conversion of non-NACs to NACs provides no free-energy contributions to the overall relative reaction rates in water versus methanol. Free-energy perturbation calculations yielded differences in free energies of activation for the two polar protic solvents and the gas phase. The rate enhancement in water over the gas phase arises from preferential hydration of the transition state (TS) relative to the reactants via increased hydrogen bonding and long-range electrostatic interactions, which accompany bringing the two negatively charged carboxylates into closer proximity. More specifically, there is an increase of 1.3 and 0.6 hydrogen bonds to the carboxylate groups and the ether oxygen, respectively, in going from the reactant to the TS in water. In methanol, the corresponding changes in hydrogen bonding with first shell solvent molecules are small; the rate enhancement arises primarily from the enhanced long-range interactions with solvent molecules. Thus, the reaction occurs faster in water than in methanol due to greater stabilization of the TS in water by specific interactions with first shell solvent molecules.

Contributions of conformational compression and preferential transition state stabilization to the rate enhancement by chorismate mutase.

The rate enhancement provided by the chorismate mutase (CM) enzyme for the Claisen rearrangement of chorismate to prephenate has been investigated by application of the concept of near attack conformations (NACs). Using a combined QM/MM Monte Carlo/free-energy perturbation (MC/FEP) method, 82% and 100% of chorismate conformers were found to be NAC structures in water and in the CM active site, respectively. Consequently, the conversion of non-NACs to NACs does not contribute to the free energy of activation from preorganization of the substrate into NACs. The FEP calculations yielded differences in free energies of activation that well reproduce the experimental data. Additional calculations indicate that the rate enhancement by CM over the aqueous phase results primarily from conformational compression of NACs by the enzyme and that this process is enthalpically controlled. This suggests that preferential stabilization of the transition state in the enzyme environment relative to water plays a secondary role in the catalysis by CM.

Synthetic and theoretical studies on the reduction of electron withdrawing group conjugated olefins using the Hantzsch 1,4-dihydropyridine ester.

The Hantzsch 1,4-dihydropyridine ester (1) has been observed to be a useful selective reducing agent for the reduction of electron-withdrawing conjugated double bonds. The rate of this reaction was observed to be dependent upon the nature of the conjugated substituents and, consequently, the electronic nature of the unsaturated double bond. Theoretical calculations confirmed the importance of the HOMO-LUMO gap for this reaction and implicated a hydride transfer, agreeing with the experimentally observed reaction rate order. The calculations also revealed the importance of a boatlike structure of the 1,4-dihydropyridine nucleus as well as a trans arrangement of the ester groups to facilitate the hydride transfer.