Pharmacophore-based discovery of 3,4-disubstituted pyrrolidines as a novel class of monoamine transporter inhibitors

Synthesis of a pyrrolidine derivative of a carvotacetone and monoterpenes for anti-methicillin-resistant Staphylococcus aureus and anti-cryptococcal properties

Monoterpene derivatives are of great biological relevance in the pharmaceutical industry. In the present study, pyrrolidine derivative of a carvotacetone, 3-O-benzylcarvotacetone (1), and selected monoterpenes (3-hydroxy-2-isopropyl-5-methyl-p-benzoquinone (3) and cis-piperitol (5)) were prepared to provide (R)-1-(4-(benzyloxy)-5-isopropyl-2-methylcyclohexa-1,3-dien-1-yl)-pyrrolidine (2), 2-isopropyl-5-methyl-3,6-dioxocyclohexa-1,4-dien-1-yl acetate (4), cis-3-hydroxypiperitone (6) and carvacrol (7). Structure of 2 was determined based on NMR and HRMS spectral data. Compound 4 exhibited activity against fungi Cryptococcus neoformans with an IC₅₀ value of < 0.8 µg/mL. In addition, this compound 4 had an IC₅₀ value of 14.97 µg/mL against methicillin resistant Staphylococcus aureus bacteria. Previous to the current study, both compound 6 and 7 had been reported to have anti-microbial and anti-fungal activities.

Regio- and stereoselective synthesis of spiropyrrolidine-oxindole and bis-spiropyrrolizidine-oxindole grafted macrocycles through [3 + 2] cycloaddition of azomethine ylides

A convenient and efficient method for the regioselective macrocyclization of triazole bridged spiropyrrolidine-oxindole, and bis-spiropyrrolizidine-oxindole derivatives was accomplished through intra and self-intermolecular [3 + 2] cycloaddition of azomethine ylides. The chalcone isatin precursors 9a-i required for the click reaction were obtained from the reaction of N-alkylazidoisatin 4 and propargyloxy chalcone 8a-i which in turn were obtained by the aldol condensation of propargyloxy salicylaldehyde 6 and substituted methyl ketones 7a-i. The regio- and stereochemical outcome of the cycloadducts were assigned based on 2D NMR and confirmed by single crystal XRD analysis. High efficiency, mild reaction conditions, high regio- and stereoselectivity, atom economy and operational simplicity are the exemplary advantages of the employed macrocyclization procedure.

Identification of novel serotonin transporter compounds by virtual screening

The serotonin (5-hydroxytryptamine, 5-HT) transporter (SERT) plays an essential role in the termination of serotonergic neurotransmission by removing 5-HT from the synaptic cleft into the presynaptic neuron. It is also of pharmacological importance being targeted by antidepressants and psychostimulant drugs. Here, five commercial databases containing approximately 3.24 million drug-like compounds have been screened using a combination of two-dimensional (2D) fingerprint-based and three-dimensional (3D) pharmacophore-based screening and flexible docking into multiple conformations of the binding pocket detected in an outward-open SERT homology model. Following virtual screening (VS), selected compounds were evaluated using in vitro screening and full binding assays and an in silico hit-to-lead (H2L) screening was performed to obtain analogues of the identified compounds. Using this multistep VS/H2L approach, 74 active compounds, 46 of which had K(i) values of ≤1000 nM, belonging to 16 structural classes, have been identified, and multiple compounds share no structural resemblance with known SERT binders.

Monoamine transporter structure, function, dynamics, and drug discovery: a computational perspective

With the breakthrough crystallization of the bacterial leucine transporter protein LeuT, the first available X-ray structure for the neurotransmitter/sodium symporter family, development of 3-D computational models is suddenly essential for structure-function studies on the plasmalemmal monoamine transporters (MATs). LeuT-based MAT models have been used to guide elucidation of substrate and inhibitor binding pockets, and molecular dynamics simulations using these models are providing insight into conformations involved in the substrate translocation cycle. With credible MAT models finally in hand, structure-based virtual screening for novel ligands is yielding lead compounds toward the development of new medications for psychostimulant dependence, attention deficit hyperactivity, depression, anxiety, schizophrenia, and other disorders associated with dopamine, norepinephrine, or serotonin dysregulation.

Diethyl 4-methoxyoxalyl-3,5-diphenylpyrrolidine-2,2-dicarboxylate

In the title compound, C₂₅H₂₇NO₇, the pyrrolidine ring exhibits an envelope conformation and the benzene rings form a dihedral angle of 33.47 (11)°. In the crystal, pairs of N—H⋯O hydrogen bonds link the mol­ecules into centrosymmetric dimers. Weak C—H⋯O inter­actions link the dimers into layers parallel to the bc plane.

2-Hy-droxy-11-methyl-16-[(E)-4-methyl-benzyl-idene]-13-(4-methyl-phen-yl)-1,11-diaza-penta-cyclo-[12.3.1.0.0.0]octa-deca-3(8),4,6-triene-9,15-dione

In the title compound, C(32)H(30)N(2)O(3), the piperidin-4-one and the two fused pyrrolidine rings adopt envelope conformations. The two methyl-phenyl rings are oriented at dihedral angle of 20.36 (7) and 56.24 (7)°, respectively, with respect to the indanone ring system. In the crystal structure, inter-molecular O-H⋯N and C-H⋯O hydrogen bonds link the mol-ecules into chains propagating along [001]. Weak C-H⋯π inter-actions are also observed.

Future directions for drug transporter modelling

Since the late 1980s computational methods such as quantitative structure-activity relationship (QSAR) and pharmacophore approaches have become more widely applied to assess interactions between drug-like molecules and transporters, starting with P-glycoprotein (P-gp). Identifying molecules that interact with P-gp and other transporters is important for drug discovery, but it is normally ascertained using laborious in vitro and in vivo studies. Computational QSAR and pharmacophore models can be used to screen commercial databases of molecules rapidly and suggest those likely to bind as substrates or inhibitors for transporters. These predictions can then be readily verified in vitro, thus representing a more efficient route to screening. Recently, the application of this approach has seen the identification of new substrates and inhibitors for several transporters. The successful application of computational models and pharmacophore models in particular to predict transporter binding accurately represents a way to anticipate drug-drug interactions of novel molecules from molecular structure. These models may also see incorporation in future pharmacokinetic-pharmacodynamic models to improve predictions of in vivo drug effects in patients. The implications of early assessment of transporter activity, current advances in QSAR, and other computational methods for future development of these and systems-based approaches will be discussed.

Pharmacophore design and database searching for selective monoamine neurotransmitter transporter ligands

Neuronal monoamine transporters (MATs) are involved in the pathophysiology and treatment of mental health conditions such as depression, attention deficit hyperactivity disorder, substance abuse and neurodegenerative disorders including Alzheimer's disease and Parkinson's disease. Various structural classes of compounds have been synthesized and tested in vitro for activity against transporters of three monoamine signaling molecules: noradrenaline (NET); serotonin (SERT) and dopamine (DAT). We have developed and validated a number of pharmacophore models describing the interaction of two classes of compounds with each of these three MATs. These pharmacophores explain the selectivity of binding to the MATs for various compound classes and have been used to search in silico databases for novel, potentially selective ligands. These ligands, after confirmation of their activities, will provide tools for investigating the function of MATs as well as the potential for new therapeutic agents in mental health applications. The database searches also retrieved close analogues of known MAT ligands, further validating the approach.

Triple uptake inhibitors: therapeutic potential in depression and beyond

Drugs that interfere with the uptake and/or metabolism of biogenic amines have been used to treat depression for > 4 decades. Early medications such as tricyclic antidepressants and monoamine oxidase inhibitors are effective but possess many side effects that limit their usefulness. Selective serotonin reuptake inhibitors (SSRIs) or selective noradrenaline reuptake inhibitors (SNRIs) are the results of rational design to find drugs that are as effective as the tricyclic antidepressants, but with more selectivity towards a single monoamine transporter. The SSRI class of drugs, which includes fluoxetine, paroxetine and sertraline, were previously viewed as the agents of choice for treating major depression. Recently, inhibitors of both serotonin and noradrenaline uptake ('dual uptake inhibitors'; SSRI/SNRI such as venlafaxine, duloxetine and milnacipran) have gained acceptance in the market. However, neither the SSRIs nor the SSRI/SNRI are fully satisfactory due to a delayed onset of action, low rate of response and side effect that can affect compliance. An important recent development has been the emergence of the triple uptake inhibitors (SSRI/SNRI/selective dopamine reuptake inhibitor), which inhibit the uptake of all three neurotransmitters that are most closely linked to depression: serotonin, noradrenaline and dopamine. Preclinical studies and clinical trials indicate that a drug inhibiting the uptake of all three of these neurotransmitters could produce a more rapid onset of action and possess greater efficacy than traditional antidepressants. This review discusses the evolution of biogenic amine-based therapies, the emerging strategies involved in the design and synthesis of novel triple uptake inhibitors as antidepressants and the therapeutic potential of triple uptake inhibitors.

QSAR studies and pharmacophore identification for arylsubstituted cycloalkenecarboxylic acid methyl esters with affinity for the human dopamine transporter

Data from a series of 29 monoamine transport inhibitors were used to generate 2D and 3D QSAR models for their binding affinity to the human dopamine transporter (hDAT). Among the inhibitors were many non-nitrogen containing compounds. The 2D QSAR analysis resulted in the equation -logK(i)=4.00-3.93E(LUMO)-0.67E(HOMO)-3.24sigma(p), which predicted the importance of electron withdrawing groups in the aromatic moiety. However, the model failed to predict the observed poor binding of nitro-substituted compounds. In contrast, a derived 3D QSAR model was capable of predicting these more correctly.

Application of data mining approaches to drug delivery

Computational approaches play a key role in all areas of the pharmaceutical industry from data mining, experimental and clinical data capture to pharmacoeconomics and adverse events monitoring. They will likely continue to be indispensable assets along with a growing library of software applications. This is primarily due to the increasingly massive amount of biology, chemistry and clinical data, which is now entering the public domain mainly as a result of NIH and commercially funded projects. We are therefore in need of new methods for mining this mountain of data in order to enable new hypothesis generation. The computational approaches include, but are not limited to, database compilation, quantitative structure activity relationships (QSAR), pharmacophores, network visualization models, decision trees, machine learning algorithms and multidimensional data visualization software that could be used to improve drug delivery after mining public and/or proprietary data. We will discuss some areas of unmet needs in the area of data mining for drug delivery that can be addressed with new software tools or databases of relevance to future pharmaceutical projects.

Pharmacophore-based discovery of ligands for drug transporters

The ability to identify ligands for drug transporters is an important step in drug discovery and development. It can both improve accurate profiling of lead pharmacokinetic properties and assist in the discovery of new chemical entities targeting transporters. In silico approaches, especially pharmacophore-based database screening methods have great potential in improving the throughput of current transporter ligand identification assays, leading to a higher hit rate by focusing in vitro testing to the most promising hits. In this review, the potential of different in silico methods in transporter ligand identification studies are compared and summarized with an emphasis on pharmacophore modeling. Various implementations of pharmacophore model generation, database compilation and flexible screening algorithms are also introduced. Recent successful utilization of database searching with pharmacophores to identify novel ligands for the pharmaceutically significant transporters hPepT1, P-gp, BCRP, MRP1 and DAT are reviewed and the challenges encountered with current approaches are discussed.

CoMFA Study of Piperidine Analogues of Cocaine at the Dopamine Transporter: Exploring the Binding Mode of the 3α-Substituent of the Piperidine Ring Using Pharmacophore-Based Flexible Alignment

A 3D-QSAR CoMFA study of piperidine-based analogues of cocaine with flexible 3 alpha-substituents is described. A series of pharmacophore models were generated based on three representative compounds 1p, 2i, and 3c using the Genetic Algorithm Similarity Program (GASP) method. The flexible superposition of all studied compounds was performed for each pharmacophore model using the FlexS algorithm and the three-dimensional structure of 2i as a template. All sets of the overlaid structures with the top-ranked conformers were used for CoMFA modeling. Two best initial CoMFA models were selected and further optimized by identifying the best-fitting conformer of each compound. Compared with the initial models, the conventional correlation coefficients r(2) for the optimized models 1 and 2 were improved from 0.90 and 0.837 to 0.997 and 0.993, respectively. The leave-one-out cross-validated coefficients q(2) for the optimized models 1 and 2 were improved from 0.515 and 0.296 to 0.828 and 0.849, respectively. The results of the two CoMFA models suggest that both steric and electrostatic interactions play important roles in the binding of the 3 alpha-substituents of the piperidine-based analogues of cocaine. The contributions from steric and electrostatic fields for model 1 were 0.621 and 0.379, respectively. The contributions from steric and electrostatic fields for model 2 were 0.493 and 0.507, respectively. The two highly predictive CoMFA models indicate that the 3 alpha-substituent has two possible binding modes at the DAT. The CoMFA contour maps provide a visual representation of prospective binding modes of the 3 alpha-substituent of the piperidine-based analogues of cocaine and can be used to design novel DAT inhibitors that may be useful for the treatment of cocaine abuse and certain neurological disorders.

Synthesis, molecular modeling, and biological studies of novel piperidine-based analogues of cocaine: evidence of unfavorable interactions proximal to the 3alpha-position of the piperidine ring

A qualitative model for the binding pocket proximal to the 3alpha-substituent of the piperidine-based monoamine transporter ligands was proposed and tested. Based on this model, a new series of druglike 3alpha-modified piperidine-based analogues of cocaine were designed, synthesized, and studied for their ability to inhibit reuptake of DA, 5-HT, and NE by the DA, 5-HT, and NE transporters. We found that the insertion of at least one additional methylene group between the piperidine ring and the polar group in the 3alpha-substituent dramatically improves the activity of the compounds that are generally inactive without this additional linker. Molecular modeling analysis showed that the more flexible 3alpha-substituents can avoid unfavorable interactions with the binding sites of DAT, SERT, and NET. The present results may have important implications for the elucidation of the structural differences between DA, 5-HT, and NE transporters and for the further design of new leads for development of cocaine abuse medication as well as certain neurological disorders such as ADHD and depression.

2,3-Disubstituted quinuclidines as a novel class of dopamine transporter inhibitors

There is considerable interest in developing dopamine transporter (DAT) inhibitors as potential therapies for the treatment of cocaine abuse. We report herein our pharmacophore-based discovery and molecular modeling-assisted rational design of 2,3-disubstituted quinuclidines as potent DAT inhibitors with a novel chemical scaffold. Through 3-D-database pharmacophore searching, compound 12 was identified as a very weak DAT inhibitor with K(i) values of 7.3 and 8.9 microM in [3H]mazindol binding and in inhibition of dopamine reuptake, respectively. Molecular modeling-assisted rational design and chemical modifications led to identification of potent analogues (-)-29 and 34 with K(i) values of 14 and 32 nM for both compounds in binding affinity and inhibition of dopamine reuptake, respectively. Behavioral pharmacological evaluations in rodents showed that 34 has a profile very different from cocaine. While 34 is substantially more potent than cocaine as a DAT inhibitor, it is approximately four times less potent than cocaine in mimicking the discriminative stimulus properties of cocaine in rat. On the other hand, 34 (3-30 mg/kg) lacks either the locomotor stimulant or stereotypic properties of cocaine in mice. Importantly, 34 blocks locomotor stimulant activity induced by 20 mg/kg cocaine in mice, with an estimated ED(50) of 19 mg/kg. Taken together, our data suggest that 34 represents a class of potent DAT inhibitors with a novel chemical scaffold and a behavioral pharmacological profile different from that of cocaine in rodents. Thus, 34 may serve as a novel lead compound in the ultimate development of therapeutic entities for cocaine abuse and/or addiction.

Pharmacophore-based discovery of substituted pyridines as novel dopamine transporter inhibitors

Abnormal dopamine signaling in brain has been implicated in several conditions such as cocaine abuse, Parkinson's disease and depression. Potent and selective dopamine transporter inhibitors may be useful as pharmacological tools and therapeutic agents. Simple substituted pyridines were discovered as novel dopamine transporter (DAT) inhibitors through pharmacophore-based 3D-database search. The most potent compound 18 has a K(i) value of 79 nM in inhibition of WIN35,248 binding to dopamine transporter and 255 nM in inhibition of dopamine reuptake, respectively, as potent as cocaine. Preliminary structure-activity relationship studies show that the geometry and the nature of the substituents on the pyridine ring determine the inhibitory activity and selectivity toward the three monoamine transporters. The substituted pyridines described herein represent a class of novel DAT inhibitors with simple chemical structures and their discovery provides additional insights into the binding site of DAT.

SAR studies of piperidine-based analogues of cocaine. 4. Effect of N-modification and ester replacement

A series of novel N- and 3alpha-modified piperidine-based analogues of cocaine were synthesized and tested for their ability to inhibit reuptake of DA, 5-HT, and NE by the DA, 5-HT, and NE transporters. N-Demethylation of trans-(+)-3alpha-piperidine-based ligands leads to improved activity at the SERT and NET and modest changes at the DAT. Replacement of the N-methyl group in trans-(+)-ester 1a with phenylalkyl groups leads to a modest 2.3-fold improvement in activity at the SERT (K(i) < or = 3.27 microM), insignificant changes at the NET, and a 3.5-fold loss in activity at the DAT (K(i) > or = 810 nM); however, such replacement in cis-(-)-ester 4, the more potent isomer of 1a, leads, in general, to a significant decrease in activity at all monoamine transporters (K(i) > 1 microM). Other N-modified ligands, including the ligands with polar groups incorporated in the N-alkyl substituent (3e-g) and ligands lacking the basic nitrogen (3i and 6d), show decreased activity at all monoamine transporters, though ligands 3e-g are similar in potency at the NET to 1a. N-Norester 2a, a possible metabolite of the lead compound 1a, and alcohol 1c, a compound with a 3alpha-substituent that is more stable to metabolism than 1a, were selected for further behavioral tests in animals. Alcohol 1c and ester 2a are similar in potency at the DAT to cocaine, ester 1a, and oxadiazole 1b, and both fully substitute for cocaine and have potency similar to that of cocaine in drug discrimination tests. Like cocaine, 1c increased locomotor activity (LMA) monotonically with time, whereas 2a produces biphasic effects consisting of initial locomotor depression followed by delayed locomotor stimulation. An interesting difference between cocaine, ester 1a, alcohol 1c, and N-norester 2a is that 1c and 2a are significantly longer acting in LMA tests. Although this result was anticipated for alcohol 1c, it is rather surprising for 2a which has an ester function susceptible to hydrolysis, a pathway of in vivo deactivation of cocaine and its ester analogues. The present results may have important implications for our understanding of the pharmacological mechanisms underlying the behavioral actions of cocaine and of the structural features needed for the design of the new leads in the discovery of a cocaine abuse medication.

Discovery of substituted 3,4-diphenyl-thiazoles as a novel class of monoamine transporter inhibitors through 3-D pharmacophore search using a new pharmacophore model derived from mazindol

Substituted 3,4-diphenyl-1,3-thiazols were identified as a class of novel and potent monoamine transporter inhibitors through a 3-D pharmacophore search using a new pharmacophore model derived from mazindol. The most potent compound (13) has K(i) values of 24 and 23 nM in binding to dopamine transporter and inhibition of dopamine reuptake, respectively.

Thiophene derivatives: a new series of potent norepinephrine and serotonin reuptake inhibitors

A series of (1S,3S,6R,10S)-(Z)-9-(thienylmethylene- or substituted thienylmethylene)-7-azatricyclo[4.3.1.0(3,7)]decanes was prepared and evaluated for the ability to block dopamine, serotonin, and norepinephrine reuptake by their respective transporters. Compound 5b is a NET-selective inhibitor, 5c is a mixed NET- and SERT-selective inhibitor, while 11 is a SERT-selective inhibitor.