Design and Synthesis of Novel Serotonin Receptor Ligands

Novel and potent ligands to the serotonin7 (5-HT7) receptor have been synthesized. The synthesized compounds include a set of substituted pyrimidines which show high affinity to the 5-HT7 receptor, synthesized by previously described methods [1,2] in high yield. Comparing the affinities of substituted pyrimidines to previously calculated models [3,4] yielded new hypotheses about the nature of interaction between the pyrimidine ligands and the 5-HT7 binding site. Several new series of compounds were synthesized by various methods to validate these hypotheses, including a conjugate addition to vinylpyrimidines [5]. These compounds include benzofurans, oximes, hydrazones, as well as a group of substituted piperazines. All series of compounds show affinity to the 5-HT7 receptor comparable to previously synthesized 5-HT7 ligands. Several of the synthesized ligands show affinity which exceeds that of currently available ligands. The synthesized compounds were evaluated quantitatively by calculating a three-dimensional quantitative structure-affinity relationship (3D-QSAR) for the 5-HT7 receptor. Evaluation of the calculated model validated qualitative assumptions about the data set as well as described regions of interaction in greater detail than previously available. These observations give further insight on the nature of ligand-binding site interactions with highly potent ligands such as 4-(3-furyl)-2-(N-methylpiperazino)pyrimidine which will lead to more potent 5-HT7 receptor ligands. Additionally, a model was calculated for affinity to the 5-HT2a receptor. Comparing this model to that calculated for affinity to the 5-HT7 receptor identified two regions which may be exploited in future sets of ligands to increase selectivity to the 5HT7 receptor

Mind the Gap - Deciphering GPCR Pharmacology Using 3D Pharmacophores and Artificial Intelligence

G protein-coupled receptors (GPCRs) are amongst the most pharmaceutically relevant and well-studied protein targets, yet unanswered questions in the field leave significant gaps in our understanding of their nuanced structure and function. Three-dimensional pharmacophore models are powerful computational tools in in silico drug discovery, presenting myriad opportunities for the integration of GPCR structural biology and cheminformatics. This review highlights success stories in the application of 3D pharmacophore modeling to de novo drug design, the discovery of biased and allosteric ligands, scaffold hopping, QSAR analysis, hit-to-lead optimization, GPCR de-orphanization, mechanistic understanding of GPCR pharmacology and the elucidation of ligand–receptor interactions. Furthermore, advances in the incorporation of dynamics and machine learning are highlighted. The review will analyze challenges in the field of GPCR drug discovery, detailing how 3D pharmacophore modeling can be used to address them. Finally, we will present opportunities afforded by 3D pharmacophore modeling in the advancement of our understanding and targeting of GPCRs

DESIGN, SYNTHESIS, AND PHARMACOLOGICAL EVALUATION OF A SERIES OF NOVEL, GUANIDINE AND AMIDINE-CONTAINING NEONICOTINOID-LIKE ANALOGS OF NICOTINE: SUBTYPE-SELECTIVE INTERACTIONS AT NEURONAL NICOTINIC-ACETYLCHOLINE RECEPTOR.

The current project examined the ability of a novel series of guandine and amidine-containing nicotine analogs to interact with several native and recombinantlyexpressed mammalian neuronal nicotinic-acetylcholine receptor (nAChR) subtypes. Rational drug design methods and parallel organic synthesis was used to generate a library of guanidine-containing nicotine (NIC) analogs (AH compounds). A smaller series of amidine-containing nicotine analogs (JC compounds) were also synthesized. In total, \u3e150 compounds were examined. Compounds were first assayed for affinity in a high-throughput [3H]epibatidine radioligand-binding screen. Lead compounds were evaluated in subtype-selective binding experiments to probe for affinity at the α4β2* and α7* neuronal nAChRs. Several compounds were identified which possess affinity and selectivity for the α4β2* subtype [AH-132 (Ki=27nm) and JC-3-9 (Ki=11nM)]. Schild analysis of binding suggests a complex one-site binding interaction at the desensitized high-affinity nAChR. Whole-cell functional fluorescence (FLIPR) assays revealed mixed subtype pharmacology. AH-compounds were identified which act as activators and inhibitors at nAChR subtypes, while lead JC-compounds were found which possess full agonist activity at α4β2* and α3β4* subtypes. Compounds were identified as partial agonists, full agonists and inhibitors of multiple nAChR subtypes. Several SAR-based, ligand-receptor pharmacophore models were developed to guide future ligand design. Second-generation lead compounds were identified

PHARMACOPHORIC EVALUATION OF 5-HT2A AND 5-HT2B SEROTONIN RECPEPTORS

Serotonin (5-HT) receptors represent a class of receptors involved in a variety of physiological processes including regulation of mood, perception, cognition, appetite, and heart function, and thus serve as drug targets of several drugs such as antipsychotic agents, hallucinogenic drugs, and appetite suppressant drugs. Due to the structural similarity of certain 5-HT receptor subtypes, particularly 5-HT2 receptors (5-HT2A, 5-HT2B receptors) determination and refinement of pharmacophore models of these receptor subtypes can greatly improve the therapeutic efficacy of drugs that target them. The goals of this study were to define and/or refine existing pharmacophore models for 5-HT2A and 5-HT2B receptors. Investigation of 5-HT2A receptors involved analysis of a previously published pharmacophore for 5-HT2A receptors based on the structure of the atypical antipsychotic risperidone. Investigation of a 5-HT2A receptor agonist quipazine and its positional isomers/analogues also aided in the elaboration of 5-HT2A receptor binding. Finally, to determine structural requirements for 5-HT2B agonist action, a series of phenyl-substituted amphetamine analogues and a series of 4-substituted-2,5-dimethoxyamphetamines (DOX-type phenylisopropylamine compounds) were analyzed for their 5-HT2B receptor functional activity. In the present study, a previously known pharmacophoric 5-HT2A antagonist compound was synthesized along with its N-propyl analogue. The pharmacophoric compound, along with several others in a series in which the piperidine substituent varies in both length and bulk, were screened across serotonin, dopamine, and adrenergic receptors to determine if high affinity and selectivity can be achieved for 5-HT2A receptors. The affinity screen revealed that, as the size and bulk of the piperidine substituent increases, affinity and selectivity for 5-HT2A receptors increased albeit with an accompanying increase in D2 receptor affinity – antagonism at D2 receptors is responsible for extrapyramidal stimulation (EPS) symptoms associated with several antipsychotics. Because D2 receptor affinity could not be abolished, it was determined that extending the chain size of the piperidine substituent is not an effective method for achieving more selective 5-HT2A antagonists. Computational analysis of quipazine and its analogues was conducted to determine their binding modes at 5-HT2A receptor crystal structures. Higher affinity ligands 1-NP and 2-NP were found to bind in a distinct pocket relative to the lower affinity ligands quipazine and isoquipazine. It was predicted that the binding pocket occupied by 1-NP and 2-NP contains numerous hydrophobic amino acids and that hydrophobic interactions with these residues confer the high affinity for this class of compounds. Finally, evaluation of 5-HT2B receptors involved analyzing several 5-HT2B ligands in a Ca2+-release assay to determine their functional activity. In particular, analogues of norfenfluramine (nFen) and DOB were analyzed and it was determined that the agonist activity of nFen is driven by hydrophobic interactions of its 3-CF3 substituent. To determine the SAR of related phenylisopropylamines at 5-HT2B receptors, a series of DOX analogues was analyzed for their functional activity. It was discovered that larger, more lipophilic 4-position halogens such as bromine (DOB) and iodine (DOI) are more accommodated than smaller less lipophilic halogens such as fluorine (DOF). Supporting the importance of a hydrophobic interaction with the 4-position substituent, DOPR and DOTB containing propyl and t-butyl 4-position substituents, respectively, produced potencies on par with that of DOI. These studies resulted in formulation of the first ever pharmacophore for agonist activity at 5-HT2B receptors

Biochemistry of opioid (morphine) receptors : binding, structure and molecular modelling

Morphine is the most widely used compound among narcotic analgesics and remains the gold standard when the effects of other analgetic drugs are compared. The most characteristic effect of morphine is the modulation of pain perception resulting in an increase in the threshold of noxious stimuli. Antinociception induced by morphine is mediated via opioid receptors, namely the μ-type opioid receptor. Apart from the μ-opioid receptor, two other classical opioid receptors κ- and δ- and one non-classical opioid receptor, the nociceptin receptor was discovered and cloned so far. At the same time endogenous opioids were also discovered, such as enkephalins, endorphins, and dynorphins. The opioid receptors together with the endogenous opioids form the so called endogenous opioid system, which is highly distributed throughout the body and apart from analgesia it has several other important physiological functions. In this article we will review the historical milestones of opioid research − in detail with morphine. The review will also cover the upmost knowledge in the molecular structure and physiological effects of opioid receptors and endogenous opioids and we will discuss opioid receptor modelling − a rapidly evolving field in opioid receptor research

Computational Ligand-Based CNS Therapeutic Design: The Search for Novel-Scaffold Norepinephrine Transporter Inhibitors

Monoamine transporter (MAT) proteins are responsible for regulating cellular signal transduction through control of neurotransmitter reuptake in the synapse, and are therefore relevant to diseases including addiction, psychosis, anxiety and depression. MATs, specifically the serotonin transporter (SERT or 5-HTT), norepinephrine transporter (NET), and dopamine transporter (DAT), serve as the principal targets for antidepressant drugs, such as SSRIs (selective serotonin reuptake inhibitors), NRIs (norepinephrine reuptake inhibitors) and TCAs (tricyclic antidepressants), as well as psychostimulant drugs of abuse such as cocaine and the amphetamines. Due to a lack of crystallographic MAT data, it is unclear as to which of two MAT protein ligand binding sites these drugs bind, hindering knowledge of the specific binding modes of MAT ligands. In this study an in silico pharmacophore model was created using a ligand-based method aimed at drug screening for the ability to specifically inhibit NET, using Molecular Operating Environment software. A group of four structurally-diverse compounds with high NET binding affinities comprised the training set used to generate the model. A test set, which included ten compounds with a range of known NET affinities, served in the validation of the model. The constructed pharmacophore model selected all high affinity NET inhibitors and one relatively inactive compound from the test set. Following model validation, the ZINC small molecule structural database was virtually screened to identify novel MAT inhibitor candidates. Hit compounds were ranked by an overlay score, which calculated how well novel compounds aligned to the original training set alignment. Six top-ranking compounds were purchased and evaluated via in vitro pharmacology to determine the binding affinity at the MATs. Although no significant inhibition was observed at the MATs, compound AC-1 showed a 15% inhibition at the DAT in radioligand binding assays. This result suggests that with further refinement of key pharmacophore features or alteration of the AC-1 structure, more potent MAT inhibitors could be discovered. Pharmacophore-based drug design has become one of the most important tools in drug discovery. Using the molecular modeling approaches described in this study, it is possible to rationally design novel and more selective central nervous system drugs

Part I, Unified Pharmacophore Protein Models of the Benzodiazepine Receptor Subtypes ; Part II, Subtype

Part I. New models of unified pharmacophore/receptors have been constructed guided by the synthesis of subtype selective compounds in light of recent developments both in ligand synthesis and structural studies of the binding site itself. The evaluation of experimental data in combination with comparative models of the α1β2γ2, α2β2γ2, α3β2γ2 and α5β2γ2 GABA(A) receptors has led to an orientation of the pharmacophore model within the benzodiazepine binding site (Bz BS). These results not only are important for the rational design of new selective ligands, but also for the identification and evaluation of possible roles which specific residues may have within the benzodiazepine binding pocket. More importantly, the process summarized here may be used as a general template to help scientists develop novel ligands for receptors for which the three dimensional structure has not yet been confirmed by X-ray crystallography or cryo-electron microscopy. Presented here are new models of the α1β2γ2, α2β2γ2, α3β2γ2 and α5β2γ2 GABA(A) receptors which have incorporated homology models built based on the acetylcholine binding protein. These new models will further our ability to understand structural characteristics of ligands which act as agonists, antagonists, or inverse agonists to the Bz BS of the GABA(A) receptor. This approach will also serve as a powerful model for structure based approaches carried out using ligand-protein docking methods. Part II. An effective strategy to alleviate memory deficits would be to enhance memory and cognitive processes by augmenting the impact of acetylcholine released from cholinergic neurons of the hippocampus. Using the included volume pharmacophore presented in Part I, a number of a5 selective compounds were synthesized, notably PWZ-029. PWZ-029 was examined in rats in the passive and active avoidance, spontaneous locomotor activity, elevated plus maze and grip strength tests which are indicative of the effects on memory acquisition, locomotor activity, anxiety, and muscle tone. Improvement of task learning was shown at a dose of 5mg/kg in passive avoidance test without effect on anxiety or muscle tone. Moderate negative modulation at GABA(A) receptors containing the α5 subunit using a moderate inverse agonist such as PWZ-029, is a sufficient condition for eliciting enhanced encoding/consolidation of declarative memory. Using low temperature NMR and X-ray analysis, it was shown that enhanced selectivity and potent in vitro affinity of α5 selective benzodiazepine dimers was possible with aliphatic linkers of 3 to 5 carbons in length. Although originally proposed to enhance solubility, oxygen-containing linkers caused the dimer to fold back on itself leading to the inability of dimers to enter the binding pocket. In addition, studies of a series of PWZ-029 analogs found that the electrostatic potential near the ligands\u27 terminal substituent correlated with its binding selectivity toward the α5β2γ2 versus α1β2γ2 Bzr/GABA(A) ergic isoform. Investigations further found that compound PWZ-029, which exhibits reasonable binding selectivity toward GABA(A) receptors containing the a5 subunit and possesses a favorable electrophysiological profile, was able to attenuate scopolamine induced contextual memory impairment in mice. This compound appears to be useful (Harris, Delorey et al.) for the treatment of cognitive deficits in rodents as well as primates (Rowlett et al.) and may well be a compound for the treatment of patients with Alzheimers disease