The emergence of the drug receptor theory

Quantitative receptor model for responses that are left- or right-shifted versus occupancy (are more or less concentration sensitive): the SABRE approach

Simple one-to three-parameter models routinely used to fit typical dose-response curves and calculate EC50 values using the Hill or Clark equation cannot provide the full picture connecting measured response to receptor occupancy, which can be quite complex due to the interplay between partial agonism and (pathway-dependent) signal amplification. The recently introduced SABRE quantitative receptor model is the first one that explicitly includes a parameter for signal amplification (γ) in addition to those for binding affinity (K d), receptor-activation efficacy (ε), constitutive activity (ε R0), and steepness of response (Hill slope, n). It can provide a unified framework to fit complex cases, where fractional response and occupancy do not match, as well as simple ones, where parameters constrained to specific values can be used (e.g., ε R0 = 0, γ = 1, or n = 1). Here, it is shown for the first time that SABRE can fit not only typical cases where response curves are left-shifted compared to occupancy (κ = K d/EC50 > 1) due to signal amplification (γ > 1), but also less common ones where they are right-shifted (i.e., less concentration-sensitive; κ = K d/EC50 < 1) by modeling them as apparent signal attenuation/loss (γ < 1). Illustrations are provided with μ-opioid receptor (MOPr) data from three different experiments with one left- and one right-shifted response (G protein activation and β-arrestin2 recruitment, respectively; EC50,Gprt < K d < EC50,βArr). For such cases of diverging pathways with differently shifted responses, partial agonists can cause very weak responses in the less concentration-sensitive pathway without having to be biased ligands due to the combination of low ligand efficacy and signal attenuation/loss-an illustration with SABRE-fitted oliceridine data is included.

Minding the gap: discovering the phenomenon of chemical transmission in the nervous system

The neuron doctrine, according to which nerves consist of discontinuous neurons, presented investigators with the challenge of determining what activities occurred between them or between them and muscles. One group of researchers, dubbed the sparks, viewed the electrical current in one neuron as inducing a current in the next neuron or in muscles. For them there was no gap between the activities of neurons or neurons and muscles that required filling with a new type of activity. A competing group, the soups, came to argue for chemicals, subsequently referred to neurotransmitters, as carrying out the activities between neurons or between neurons and muscles. But even for them the conclusion that chemicals performed this activity was only arrived over time. I examine the prolonged period in which proponents of chemical transmission developed their account and challenged the sparks. My goal is to illuminate the epistemic processes that led to the discovery of a new scientific phenomenon-chemical transmission between neurons.

Logic Nanodevice-Mediated Receptor Assembly for Nongenetic Regulation of Cell Behavior in Tumor-like Microenvironment

The reprogramming of cell signaling and behavior through the artificial control of cell surface receptor oligomerization shows great promise in biomedical research and cell-based therapy. However, it remains challenging to achieve combinatorial recognition in a complicated environment and logical regulation of receptors for desirable cellular behavior. Herein, we develop a logic-gated DNA nanodevice with responsiveness to multiple environmental inputs for logically controlled assembly of heterogeneous receptors to modulate signaling. The "AND" gate nanodevice uses an i-motif and an ATP-binding aptamer as environmental cue-responsive units, which can successfully implement a logic operation to manipulate receptors on the cell surface. In the presence of both protons and ATP, the DNA nanodevice is activated to selectively assemble MET and CD71, which modulate the HGF/MET signaling, resulting in cytoskeletal reorganization to inhibit cancer cell motility in a tumor-like microenvironment. Our strategy would be highly promising for precision therapeutics, including controlled drug release and cancer treatment.

Click Chemistry-Enabled Conjugation Strategy for Producing Dibenzodiazepinone-Type Fluorescent Probes To Target M2 Acetylcholine Receptors

The development of fluorescently labeled receptor-targeting compounds represents a powerful pharmacological tool to study and characterize ligand-receptor interactions. Despite significant advances in developing sub-type-specific antagonists for muscarinic acetylcholine receptors (mAChRs), reports on antagonists feasible for click chemistry are less common. Here, we designed and synthesized an antagonist suitable for probe attachment through click chemistry, namely, dibenzodiazepinone (DIBA)-alkyne, based on a previously reported DIBA scaffold with a high binding affinity to type-2 mAChR (M2R). To demonstrate the versatility of DIBA-alkyne as a building block for bioconjugates, we assembled DIBA-alkyne with Cyanine5 fluorophores (Cy5) and polyethylene glycol (PEG) biomolecules to obtain fluorescent DIBA antagonist (DIBA-Cy5) and fluorescent DIBA PEG derivatives. Flow cytometric analysis showed that DIBA-Cy5 possessed a high binding affinity to M2R (Kd = 1.80 nM), a two-order magnitude higher binding affinity than M1R. Fluorescent DIBA PEG derivatives maintained a potent binding to the M2R (Kd ≤ 4 nM), confirmed by confocal microscopic imaging. Additionally, DIBA-Cy5 can serve as a fluorescent ligand in the receptor-ligand competitive binding assay for other mAChR ligands, an attractive alternative to the traditional radioligand-based assay. The competitive binding mode between DIBA-Cy5 and orthosteric antagonist atropine/allosteric modulator LY2119620 indicated a dualsteric binding mode of the DIBA-type antagonist to M2R. Lastly, we demonstrated the direct staining of DIBA-Cy5 to M2R receptors in the sinoatrial node of a mouse heart. The adaptability of the clickable DIBA antagonist to a wide range of fluorophores and biomolecules can facilitate its use in various biomedical applications such as binding assays that screen compounds for M2R as the receptor target.

Drug Hunting at the Nexus of Medicinal Chemistry and Chemical Biology and the Discovery of Novel Therapeutic Modalities

Small molecules designed to modulate protein function have been remarkably successful in advancing human health. As the frontiers of medicine and understanding of disease pathogenesis continue to expand, small molecule scientists must also pursue the development of novel therapeutic modalities beyond functional protein modulation to address diseases of unmet medical need. In this vein, this Perspective will highlight two emerging modalities, selective mRNA splice modulation and targeted protein degradation, as mechanisms that affect protein abundance, rather than protein function, to broaden the scope of low-molecular-weight treatable diseases. Key to the elucidation and development of these mechanisms was the interplay and contemporaneous efforts in medicinal chemistry and chemical biology. Continued research at the intersection of these two fields will be critical for the identification of novel targets and mechanisms toward the development of the next generation of small molecule therapeutics.

Free Drug Theory - No Longer Just a Hypothesis?

The Free Drug Hypothesis is a well-established concept within the scientific lexicon pervading many areas of Drug Discovery and Development, and yet it is poorly defined by virtue of many variations appearing in the literature. Clearly, unbound drug is in dynamic equilibrium with respect to absorption, distribution, metabolism, elimination, and indeed, interaction with the desired pharmacological target. Binding interactions be they specific (e.g. high affinity) or nonspecific (e.g. lower affinity/higher capacity) are governed by the same fundamental physicochemical tenets including Hill-Langmuir Isotherms, the Law of Mass Action and Drug Receptor Theory. With this in mind, it is time to recognise a more coherent version and consider it the Free Drug Theory and a hypothesis no longer. Today, we have the experimental and modelling capabilities, pharmacological knowledge, and an improved understanding of unbound drug distribution (e.g. Kp_uu) to raise the bar on our understanding and analysis of experimental data. The burden of proof should be to rule out mechanistic possibilities and/or experimental error before jumping to the conclusion that any observations contradict these fundamentals.

Spatiotemporally Controlled DNA Nanoclamps: Single-Molecule Imaging of Receptor Protein Oligomerization

Cell membrane surface receptor proteins play an important role in cellular biological processes. There are numerous methods to detect receptors, yet developing an artificially controlled and specific detection and treatment strategy remains a challenge. Herein, we develop such a strategy based on upconversion nanoparticles (UCNPs) loaded DNA probes that enable two-color ratiometric imaging excitated by a 980 nm laser. The light response controllable signal opening strategy avoids waste during probe transportation and improves sensitivity. Thereby the number of receptors on individual DU145 cell membranes is counted by single-molecule detection. Due to the different expression of specific receptor proteins, the number of single fluorescent dots counted can be used as a basis for distinguishing DU145 from other cells. This work is highly controllable to increase sensitivity, providing a platform for cancer diagnosis and treatment.

Application of computational methods in the analysis of pesticide target-site and resistance mechanisms

Meta-diamide insecticides including broflanilide have a high insecticidal activity by acting on RDL GABA receptors. Both membrane potential assays and docking studies suggest that the target site of meta-diamides is different from that of conventional noncompetitive inhibitors, such as fipronil. In fact, meta-diamides are effective against cyclodiene- and fipronil-resistant pests that carry target-site mutations. Dinotefuran uniquely possesses a tetrahydrofuran ring, whereas other neonicotinoids possess aromatic rings. Moreover, dinotefuran has been reported to be effective against imidacloprid-resistant strains. A docking study predicted the weak binding of dinotefuran to cytochrome P450s which are associated with imidacloprid resistance. Metabolic assays revealed that dinotefuran was not metabolized by these cytochrome P450s. These findings suggest that the lack of metabolic activity of P450s against dinotefuran causes a low level of cross-resistance.

Evolution of the drug-target residence time model

IntroductionThe pharmacological action of a drug is linked to its affinity for a specific molecular target as quantified by in vitro equilibrium measurements. However, it is clear that for many highly effective drugs, interactions with their molecular targets do not conform to simple, equilibrium conditions in vivo and this results in a temporal discordance between pharmacokinetics and pharmacodynamics. The drug-target residence time model was developed to provide a theoretical framework with which to understand cases in which very slow dissociation of the drug-target complex in vivo results in durable PD effects even after systemic concentrations of drug have waned.Area coveredIn this article, the author provides a brief description of the drug-target residence time model and focuses on the refinements that have been made to the original model to incorporate the influences of compound rebinding in cells and pharmacokinetic properties of drug molecules.Expert opinionThere is now overwhelming evidence for the utility of the drug-target residence time model as a framework for understanding in vivo drug action. The in vitro measured residence time (τ_R) must be used in concert with equilibrium measures of drug-target affinity (e.g. IC₅₀) and with in vivo measures of pharmacokinetic half-life, to afford the researcher a powerful approach to compound optimization for clinical effect. Despite the significant use and refinement of this model, continued studies are required to better understand the dynamic interplay between residence time, target pathobiology, drug distribution and drug pharmacokinetics.

Pediatric Drug-Drug Interaction Evaluation: Drug, Patient Population, and Methodological Considerations

Hospitalized pediatric patients and those with complex or chronic conditions treated on an outpatient basis are commonly prescribed multiple drugs, resulting in increased risk for drug-drug interactions (DDIs). Although dedicated DDI evaluations are routinely performed in healthy adult volunteers during drug development, they are rarely performed in pediatric patients because of ethical, logistical, and methodological challenges. In the absence of pediatric DDI evaluations, adult DDI data are often extrapolated to pediatric patients. However, the magnitude of a DDI in pediatric patients may differ from adults because of age-dependent physiological changes that can impact drug disposition or response and because of other factors related to the drug (eg, dose, formulation) and the patient population (eg, disease state, obesity). Therefore, the DDI magnitude needs to be assessed in children separately from adults, although a lack of clinical DDI data in pediatric populations makes this evaluation challenging. As a result, pediatric DDI assessment relies on the predictive performance of the pharmacometric approaches used, such as population and physiologically based pharmacokinetic modeling. Therefore, careful consideration needs to be given to adequately account for the age-dependent physiological changes in these models to build high confidence for such untested DDI scenarios. This review article summarizes the key considerations related to the drug, patient population, and methodology, and how they can impact DDI evaluation in the pediatric population.

Structural analogues in herbal medicine ginseng hit a shared target to achieve cumulative bioactivity

By a pilot trial on investigating immunomodulatory activity and target of ginsenosides, the major bioactive components of ginseng, here we report that structural analogues in herbal medicines hit a shared target to achieve cumulative bioactivity. A ginsenoside analogues combination with definite immunomodulatory activity in vivo was designed by integrating pharmacodynamics, serum pharmacochemistry and pharmacokinetics approaches. The cumulative bioactivity of the ginsenoside analogues was validated on LPS/ATP-induced RAW264.7 macrophages. The potentially shared target NLRP3 involved in this immunomodulatory activity was predicted by systems pharmacology. The steady binding affinity between each ginsenoside and NLRP3 was defined by molecular docking and bio-layer interferometry assay. The activation of NLRP3 inflammasomes in LPS/ATP-induced RAW264.7 was significantly suppressed by the combination, but not by any individual, and the overexpression of NLRP3 counteracted the immunomodulatory activity of the combination. All these results demonstrate that the ginsenoside analogues jointly hit NLRP3 to achieve cumulative immunomodulatory activity.

Zhang et al. design ginsenoside structural analogues and demonstrate that their combination shows more potent immunomodulatory activities than individual ginsenosides used alone at the same dosages. They predict that these analogues act on the joint target NLRP3 and consequently suggest that structural analogues hit a shared target to achieve cumulative bioactivity.

Antisense technology: A review

Antisense technology is beginning to deliver on the broad promise of the technology. Ten RNA-targeted drugs including eight single-strand antisense drugs (ASOs) and two double-strand ASOs (siRNAs) have now been approved for commercial use, and the ASOs in phase 2/3 trials are innovative, delivered by multiple routes of administration and focused on both rare and common diseases. In fact, two ASOs are used in cardiovascular outcome studies and several others in very large trials. Interest in the technology continues to grow, and the field has been subject to a significant number of reviews. In this review, we focus on the molecular events that result in the effects observed and use recent clinical results involving several different ASOs to exemplify specific molecular mechanisms and specific issues. We conclude with the prospective on the technology.

Geoffrey Burnstock - An accidental pharmacologist

Geoffrey Burnstock, the founder of the field of purinergic signaling research passed away in Melbourne, Australia on June 3rd, 2020, at the age of 91. With his death, the world of biomedical research lost one of its most passionate, creative and unconventional thought leaders. He was an inspiration to the many researchers he interacted with for more than 50 years and a frequent irritation to those in the administrative establishment. Geoff never considered himself a pharmacologist having being trained as a zoologist and becoming an autonomic neurophysiologist based on his evolving interests in systems and disease-related research. By the end of his life he had: published some 1550 papers; been cited more than 125,000 times; had an h-index of 156 and had supervised over 100 Ph.D. students. His indelible legacy, based on a holistic, data-based, multidisciplinary, unconventional "outside the box" approach to research was reflected in two of the seminal findings in late 20th century biomedical research: the purinergic neurotransmitter hypothesis and the concept of co-neurotransmission, both of which were initially received by his peers with considerable skepticism that at times verged on disdain. Nonetheless, while raising hackles and threatening the status quo, Geoff persevered and prevailed, becoming a mentor for several generations of biomedical researchers. In this review we provide a joint perspective on Geoff Burnstock's legacy in research.

Oxytocin Receptor Signaling in Vascular Function and Stroke

The oxytocin receptor (OXTR) is a G protein-coupled receptor with a diverse repertoire of intracellular signaling pathways, which are activated in response to binding oxytocin (OXT) and a similar nonapeptide, vasopressin. This review summarizes the cell and molecular biology of the OXTR and its downstream signaling cascades, particularly focusing on the vasoactive functions of OXTR signaling in humans and animal models, as well as the clinical applications of OXTR targeting cerebrovascular accidents.

A single unified model for fitting simple to complex receptor response data

The fitting of complex receptor-response data where fractional response and occupancy do not match is challenging. They encompass important cases including (a) the presence of "receptor reserve" and/or partial agonism, (b) multiple responses assessed at different vantage points along a pathway, (c) responses that are different along diverging downstream pathways (biased agonism), and (d) constitutive activity. For these, simple models such as the well-known Clark or Hill equations cannot be used. Those that can, such as the operational (Black&Leff) model, do not provide a unified approach, have multiple nonintuitive parameters that are challenging to fit in well-defined manner, have difficulties incorporating binding data, and cannot be reduced or connected to simpler forms. We have recently introduced a quantitative receptor model (SABRE) that includes parameters for Signal Amplification (γ), Binding affinity (Kd), Receptor activation Efficacy (ε), and constitutive activity (εR0). It provides a single equation to fit complex cases within a full two-state framework with the possibility of incorporating receptor occupancy data (i.e., experimental Kds). Simpler cases can be fit by using consecutively reduced forms obtained by constraining parameters to specific values, e.g., εR0 = 0: no constitutive activity, γ = 1: no amplification (Emax-type fitting), and ε = 1: no partial agonism (Clark equation). Here, a Hill-type extension is introduced (n ≠ 1), and simulated and experimental receptor-response data from simple to increasingly complex cases are fitted within the unified framework of SABRE with differently constrained parameters.

100 years of modelling ligand-receptor binding and response: A focus on GPCRs

Experimental pharmacologists rely on the application of models to describe biological observations in order to learn about a drug's effective concentration, the strength with which it binds its target and drives a response (at either molecular or system level), and the nature of more complex drug actions (allosterism/functional selectivity). Models in current use build upon decades of basic principles, going back to the beginning of the last century. Yet often, researchers are only partially familiar with these underlying principles, creating the potential for confusion due to failure to recognise the underpinning assumptions of the models that are used. Here, we describe the history of receptor theory as it underpins receptor stimulus-response models in use today, emphasising particularly attributes and models relevant to GPCRs-and point to some current aims of model development.

Nongenetic engineering strategies for regulating receptor oligomerization in living cells

Nongenetic strategies for regulating receptor oligomerization in living cells based on DNA, protein, small molecules and physical stimuli.

Attractor - a new turning point in drug discovery

Drug discovery for complex diseases can be viewed as a challenging problem in which the influence of compounds on dynamic features of disease system should be considered, especially the strategies escaping from the disease attractors. Moreover, escaping from the disease-related attractors has been proved to be a cue for the treatment of the complex diseases. The drug discovery methodology based on the attractor theory indicates new solutions for target identification, drug discovery and drug combination design. The methodology is based on the holism level of the organism and the features of system dynamics, so it has advantages for the classification of complex diseases and drug discovery. Currently, research results of this method have increased, which expand the insight scope for drug discovery. This article introduces the major drug discovery methods in the history of pharmacy development and their characteristics, so as to illustrate the reasons and inevitability of the appearance of attractor method, its position in the history of pharmacy development, and its advantages for drug discovery and design, thereby to prove that the attractor method can indeed become the next major drug development method. In addition, it provides a comprehensive description about the concept of attractor, the pipeline of attractor analysis, the common methods of each process and its research progress, so as to provide a macroscopic framework and optional methods and tools for the follow-up researchers.

Quantitative structural assessment of graded receptor agonism

Ligand-receptor interactions, which are ubiquitous in physiology, are described by theoretical models of receptor pharmacology. Structural evidence for graded efficacy receptor conformations predicted by receptor theory has been limited but is critical to fully validate theoretical models. We applied quantitative structure-function approaches to characterize the effects of structurally similar and structurally diverse agonists on the conformational ensemble of nuclear receptor peroxisome proliferator-activated receptor γ (PPARγ). For all ligands, agonist functional efficacy is correlated to a shift in the conformational ensemble equilibrium from a ground state toward an active state, which is detected by NMR spectroscopy but not observed in crystal structures. For the structurally similar ligands, ligand potency and affinity are also correlated to efficacy and conformation, indicating ligand residence times among related analogs may influence receptor conformation and function. Our results derived from quantitative graded activity-conformation correlations provide experimental evidence and a platform with which to extend and test theoretical models of receptor pharmacology to more accurately describe and predict ligand-dependent receptor activity.

A Receptor Model With Binding Affinity, Activation Efficacy, and Signal Amplification Parameters for Complex Fractional Response Versus Occupancy Data

In quantitative pharmacology, multi-parameter receptor models are needed to account for the complex nonlinear relationship between fractional occupancy and response that can occur due to the intermixing of the effects of partial receptor activation and post-receptor signal amplification. Here, a general two-state receptor model and corresponding quantitative forms are proposed that unify three distinct processes, each characterized with its own parameter: 1) receptor binding, characterized by K_d, the equilibrium dissociation constant used for binding affinity; 2) receptor activation, characterized by an (intrinsic) efficacy parameter ε; and 3) post-activation signal transduction (amplification), characterized by a gain parameter γ. Constitutive activity is accommodated via an additional ε_R0 parameter quantifying the activation of the ligand-free receptor. Receptors can be active or inactive in both their ligand-free and ligand-bound states (two-state receptor theory), but ligand binding alters the likelihood of activation (induced fit). Because structural data now confirm that for most receptors in their active conformation, the small-molecule ligand-binding site is buried inside, straightforward binding to the active form (direct conformational selection) is unlikely. The proposed general equation has parameters that are more intuitive and better suited for optimization by nonlinear regression than those of the operational (Black and Leff) or del Castillo–Katz model. The model provides a unified framework for fitting complex data including a) fractional responses that do not match independently measured fractional occupancies, b) responses measured after partial irreversible inactivation of the “receptor reserve” (Furchgott method), c) fractional responses that are different along distinct downstream pathways (biased agonism), and d) responses with constitutive receptor activity. Furthermore, unlike previous models, the present one can be reduced back for special cases of its parameters to consecutively nested simplified forms that can be used on their own when adequate (e.g., ε_R0 = 0, no constitutive activity; γ = 1: E_max model for partial agonism; ε = 1: Clark equation).

Neuropeptide PEN and Its Receptor GPR83: Distribution, Signaling, and Regulation

Neuropeptides are chemical messengers that act to regulate a number of physiological processes, including feeding, reward, pain, and memory, among others. PEN is one of the most abundant hypothalamic neuropeptides; however, until recently, its target receptor remained unknown. In this Review, we summarize recent developments in research focusing on PEN and its receptor GPR83. We describe the studies leading to the deorphanization of GPR83 as the receptor for PEN. We also describe the signaling mediated by the PEN-GPR83 system, as well as the physiological roles in which PEN-GPR83 has been implicated. As studies have suggested a role for the PEN-GPR83 system in food intake and body weight regulation, as well as in drug addiction and reward disorders, a thorough understanding of this novel neuropeptide-receptor system will help identify novel therapeutic targets to treat pathophysiological conditions involving PEN-GPR83.

A Pharmacological Perspective on the Study of Taste

The study of taste has been guided throughout much of its history by the conceptual framework of psychophysics, where the focus was on quantification of the subjective experience of the taste sensations. By the mid-20th century, data from physiologic studies had accumulated sufficiently to assemble a model for the function of receptors that must mediate the initial stimulus of tastant molecules in contact with the tongue. But the study of taste as a receptor-mediated event did not gain momentum until decades later when the actual receptor proteins and attendant signaling mechanisms were identified and localized to the highly specialized taste-responsive cells of the tongue. With those discoveries a new opportunity to examine taste as a function of receptor activity has come into focus. Pharmacology is the science designed specifically for the experimental interrogation and quantitative characterization of receptor function at all levels of inquiry from molecules to behavior. This review covers the history of some of the major concepts that have shaped thinking and experimental approaches to taste, the seminal discoveries that have led to elucidation of receptors for taste, and how applying principles of receptor pharmacology can enhance understanding of the mechanisms of taste physiology and perception.

The Pharmacophore Concept and Its Applications in Computer-Aided Drug Design

Pharmacophore-based techniques currently are an integral part of many computer-aided drug design workflows and have been successfully and extensively applied for tasks such as virtual screening, de novo design, and lead optimization. Pharmacophore models can be derived both in a receptor-based and in a ligand-based manner, and provide an abstract description of essential non-bonded interactions that typically occur between small-molecule ligands and macromolecular targets. Due to their simplistic and abstract nature, pharmacophores are both perfectly suited for efficient computer processing and easy to comprehend by life and physical scientists. As a consequence, they have also proven to be a valuable tool for communicating between computational and medicinal chemists.This chapter aims to provide a short overview of the pharmacophore concept and its applications in modern computer-aided drug design. The chapter is divided into three distinct parts. The first section contains a brief introduction to the pharmacophore concept. The second section provides a description of the most common nonbonded interaction types and their representation as pharmacophoric features. Furthermore, it gives an overview of the various methods for pharmacophore generation and important pharmacophore-based techniques in drug design. This part concludes with examples for recent pharmacophore concept-related research and development. The last section is dedicated to a review of research in the field of natural product chemistry as carried out by employing pharmacophore-based drug design methods.

Ecological Roles and Biological Activities of Specialized Metabolites from the Genus Nicotiana

Species of Nicotiana grow naturally in different parts of the world and have long been used both medicinally and recreationally by human societies. More recently in our history, Nicotiana tabacum has attracted interest as one of the most economically important industrial crops. Nicotiana species are frequently investigated for their bioactive natural products, and the ecological role of their specialized metabolites in responses to abiotic stress or biotic stress factors like pathogens and herbivores. The interest of tobacco companies in genetic information as well as the success of a few wild tobacco species as experimental model organisms have resulted in growing knowledge about the molecular biology and ecology of these plants and functional studies of the plant's natural products. Although a large number of reviews and books on biologically active natural products already exists, mostly from N. tabacum, we focus our attention on the ecological roles and biological activity of natural products, versus products from cured and processed material, in this Review. The studied compounds include alkaloids, aromatic compounds, flavonoids, volatiles, sesquiterpenoids, diterpenes alcohols, and sugar esters from trichomes of the plants, and recently characterized acyclic hydroxygeranyllinalool diterpene glycosides (HGL-DTGs). In this Review (1800s-2017), we describe the above-mentioned classes of natural products, emphasizing their biological activities and functions as they have been determined either in bioassay-guided purification approaches or in bioassays with plants in which the expression of specific biosynthetic genes has been genetically manipulated. Additionally, a review on the history, taxonomy, ecology, and medicinal application of different Nicotiana species growing around the globe presented in this Review may be of interest for pharmacognosists, natural products, and ecological chemists.

Receptor visualization and the atomic bomb. A historical account of the development of the chemical neuroanatomy of receptors for neurotransmitters and drugs during the Cold War

This is a historical account of how receptors for neurotransmitters and drugs got to be seen at the regional, cellular, and subcellular levels in brain, in the years going from the end of the World War II until the collapse of the Soviet Union, the Cold War (1945-1991). The realization in the US of the problem of mental health care, as a consequence of the results of medical evaluation for military service during the war, let the US Government to act creating among other things the National Institute for Mental Health (NIMH). Coincident with that, new drug treatments for these disorders were introduced. War science also created an important number of tools and instruments, such as the radioisotopes, that played a significant role in the development of our story. The scientific context was marked by the development of Biochemistry, Molecular Biology and the introduction in the early 80's of the DNA recombinant technologies. The concepts of chemical neurotransmission in the brain and of receptors for drugs and transmitters, although proposed before the war, where not generally accepted. Neurotransmitters were identified and the mechanisms of biosynthesis, storage, release and termination of action by mechanisms such as reuptake, elucidated. Furthermore, the synapse was seen with the electron microscope and more important for our account, neurons and their processes visualized in the brain first by fluorescence histochemistry, then using radioisotopes and autoradiography, and later by immunohistochemistry (IHC), originating the Chemical Neuroanatomy. The concept of chemical neurotransmission evolved from the amines, expanded to excitatory and inhibitory amino acids, then to neuropeptides and finally to gases and other "atypical" neurotransmitters. In addition, coexpression of more than one transmitter in a neuron, changed the initial ideas of neurotransmission. The concept of receptors for these and other messengers underwent a significant evolution from an abstract chemical concept to their physical reality as gene products. Important steps were the introduction in the 70's of radioligand binding techniques and the cloning of receptor genes in the 80's. Receptors were first visualized using radioligands and autoradiography, and analyzed with the newly developed computer-assisted image analysis systems. Using Positron Emission Tomography transmitters and receptors were visualized in living human brain. The cloning of receptor genes allowed the use of in situ hybridization histochemistry and immunohistochemistry to visualize with the light and electron microscopes the receptor mRNAs and proteins. The results showed the wide heterogeneity of receptors and the diversity of mode of signal transmission, synaptic and extra-synaptic, again radically modifying the early views of neurotransmission. During the entire period the interplay between basic science and Psychopharmacology and Psychiatry generated different transmitter or receptor-based theories of brain drug action. These concepts and technologies also changed the way new drugs were discovered and developed. At the end of the period, a number of declines in these theories, the use of certain tools and the ability to generate new diagnostics and treatments, the end of an era and the beginning of a new one in the research of how the brain functions.

A three-parameter two-state model of receptor function that incorporates affinity, efficacy, and signal amplification

A generalized model of receptor function is proposed that relies on the essential assumptions of the minimal two-state receptor theory (i.e., ligand binding followed by receptor activation), but uses a different parametrization and allows nonlinear response (transduction) for possible signal amplification. For the most general case, three parameters are used: Kd, the classic equilibrium dissociation constant to characterize binding affinity; ε, an intrinsic efficacy to characterize the ability of the bound ligand to activate the receptor (ranging from 0 for an antagonist to 1 for a full agonist); and γ, a gain (amplification) parameter to characterize the nonlinearity of postactivation signal transduction (ranging from 1 for no amplification to infinity). The obtained equation, E/Emax=εγLεγ+1-εL+Kd, resembles that of the operational (Black and Leff) or minimal two-state (del Castillo-Katz) models, E/Emax=τLτ+1L+Kd, with εγ playing a role somewhat similar to that of the τ efficacy parameter of those models, but has several advantages. Its parameters are more intuitive as they are conceptually clearly related to the different steps of binding, activation, and signal transduction (amplification), and they are also better suited for optimization by nonlinear regression. It allows fitting of complex data where receptor binding and response are measured separately and the fractional occupancy and response are mismatched. Unlike the previous models, it is a true generalized model as simplified forms can be reproduced with special cases of its parameters. Such simplified forms can be used on their own to characterize partial agonism, competing partial and full agonists, or signal amplification.

Full and Partial Agonism of a Designed Enzyme Switch

Chemical biology has long sought to build protein switches for use in molecular diagnostics, imaging, and synthetic biology. The overarching challenge for any type of engineered protein switch is the ability to respond in a selective and predictable manner that caters to the specific environments and time scales needed for the application at hand. We previously described a general method to design switchable proteins, called "chemical rescue of structure", that builds de novo allosteric control sites directly into a protein's functional domain. This approach entails first carving out a buried cavity in a protein via mutation, such that the protein's structure is disrupted and activity is lost. An exogenous ligand is subsequently added to substitute for the atoms that were removed by mutation, restoring the protein's structure and thus its activity. Here, we begin to ask what principles dictate such switches' response to different activating ligands. Using a redesigned β-glycosidase enzyme as our model system, we find that the designed effector site is quite malleable and can accommodate both larger and smaller ligands, but that optimal rescue comes only from a ligand that perfectly replaces the deleted atoms. Guided by these principles, we then altered the shape of this cavity by using different cavity-forming mutations, and predicted different ligands that would better complement these new cavities. These findings demonstrate how the protein switch's response can be tuned via small changes to the ligand with respect to the binding cavity, and ultimately enabled us to design an improved switch. We anticipate that these insights will help enable the design of future systems that tune other aspects of protein activity, whereby, like evolved protein receptors, remolding the effector site can also adjust additional outputs such as substrate selectivity and activation of downstream signaling pathways.

Inhaled protein/peptide-based therapies for respiratory disease

Asthma, chronic obstructive pulmonary disease (COPD), and cystic fibrosis (CF) are all chronic pulmonary diseases, albeit with different etiologies, that are characterized by airflow limitation, chronic inflammation, and abnormal mucus production/rheology. Small synthetic molecule-based therapies are commonly prescribed for all three diseases. However, there has been increased interest in “biologicals” to treat these diseases. Biologicals typically constitute protein- or peptide-based therapies and are often more potent than small molecule-based drugs. In this review, we shall describe the pros and cons of several different biological-based therapies for respiratory disease, including dornase alfa, a recombinant DNAase that reduces mucus viscosity and short palate lung and nasal epithelial clone 1 (SPLUNC1)-derived peptides that treat Na⁺ hyperabsorption and rebalance CF airway surface liquid homeostasis.

Imaging Agonist-Induced D2/D3 Receptor Desensitization and Internalization In Vivo with PET/fMRI

This study investigated the dynamics of dopamine receptor desensitization and internalization, thereby proposing a new technique for non-invasive, in vivo measurements of receptor adaptations. The D2/D3 agonist quinpirole, which induces receptor internalization in vitro, was administered at graded doses in non-human primates while imaging with simultaneous positron emission tomography (PET) and functional magnetic resonance imaging (fMRI). A pronounced temporal divergence between receptor occupancy and fMRI signal was observed: occupancy remained elevated while fMRI responded transiently. Analogous experiments with an antagonist (prochlorperazine) and a lower-affinity agonist (ropinirole) exhibited reduced temporal dissociation between occupancy and function, consistent with a mechanism of desensitization and internalization that depends upon drug efficacy and affinity. We postulated a model that incorporates internalization into a neurovascular-coupling relationship. This model yielded in vivo desensitization/internalization rates (0.2/min for quinpirole) consistent with published in vitro measurements. Overall, these results suggest that simultaneous PET/fMRI enables characterization of dynamic neuroreceptor adaptations in vivo, and may offer a first non-invasive method for assessing receptor desensitization and internalization.

Polypharmacology in Precision Oncology: Current Applications and Future Prospects

Over the past decade, a more comprehensive, large-scale approach to studying cancer genetics and biology has revealed the challenges of tumor heterogeneity, adaption, evolution and drug resistance, while systems-based pharmacology and chemical biology strategies have uncovered a much more complex interaction between drugs and the human proteome than was previously anticipated. In this mini-review we assess the progress and potential of drug polypharmacology in biomarker-driven precision oncology. Polypharmacology not only provides great opportunities for drug repurposing to exploit off-target effects in a new single-target indication but through simultaneous blockade of multiple targets or pathways offers exciting opportunities to slow, overcome or even prevent inherent or adaptive drug resistance. We highlight the many challenges associated with exploiting known or desired polypharmacology in drug design and development, and assess computational and experimental methods to uncover unknown polypharmacology. A comprehensive understanding of the intricate links between polypharmacology, efficacy and safety is urgently needed if we are to tackle the enduring challenge of cancer drug resistance and to fully exploit polypharmacology for the ultimate benefit of cancer patients.

What is biased efficacy? Defining the relationship between intrinsic efficacy and free energy coupling

A G protein-coupled receptor (GPCR) is only biologically active when associated with a transduction protein, but it can also switch function by interacting with different types of transduction proteins. Biased agonism arises when the ligand induces the receptor to engage distinct transduction proteins with different efficacies. We briefly review the concept of ligand efficacy, from the classical empirical idea to the current mechanistic views of allosteric regulation in proteins. A combination of these theoretically distinct ideas and methodologies allows us to distinguish true ligand bias from divergences of signalling caused by the system. We also demonstrate a rigorous mathematical connection between the intrinsic efficacy of classical receptor theory and the energetic effect that makes a ligand capable of stabilizing receptor-transducer association in the ternary complex model. This relationship unifies different definitions of efficacy and provides a rational basis for quantifying biased agonism.

Biology is more theoretical than physics

The word "theory" is used in at least two senses--to denote a body of widely accepted laws or principles, as in "Darwinian theory" or "quantum theory," and to suggest a speculative hypothesis, often relying on mathematical analysis, that has not been experimentally confirmed. It is often said that there is no place for the second kind of theory in biology and that biology is not theoretical but based on interpretation of data. Here, ideas from a previous essay are expanded upon to suggest, to the contrary, that the second kind of theory has always played a critical role and that biology, therefore, is a good deal more theoretical than physics.

Time-scale separation--Michaelis and Menten's old idea, still bearing fruit

Michaelis and Menten introduced to biochemistry the idea of time-scale separation, in which part of a system is assumed to be operating sufficiently fast compared to the rest so that it may be taken to have reached a steady state. This allows, in principle, the fast components to be eliminated, resulting in a simplified description of the system's behaviour. Similar ideas have been widely used in different areas of biology, including enzyme kinetics, protein allostery, receptor pharmacology, gene regulation and post-translational modification. However, the methods used have been independent and ad hoc. In the present study, we review the use of time-scale separation as a means to simplify the description of molecular complexity and discuss recent work setting out a single framework that unifies these separate calculations. The framework offers new capabilities for mathematical analysis and helps to do justice to Michaelis and Menten's insights about individual enzymes in the context of multi-enzyme biological systems.

The fall and rise of pharmacology--(re-)defining the discipline?

Pharmacology is an integrative discipline that originated from activities, now nearly 7000 years old, to identify therapeutics from natural product sources. Research in the 19th Century that focused on the Law of Mass Action (LMA) demonstrated that compound effects were dose-/concentration-dependent eventually leading to the receptor concept, now a century old, that remains the key to understanding disease causality and drug action. As pharmacology evolved in the 20th Century through successive biochemical, molecular and genomic eras, the precision in understanding receptor function at the molecular level increased and while providing important insights, led to an overtly reductionistic emphasis. This resulted in the generation of data lacking physiological context that ignored the LMA and was not integrated at the tissue/whole organism level. As reductionism became a primary focus in biomedical research, it led to the fall of pharmacology. However, concerns regarding the disconnect between basic research efforts and the approval of new drugs to treat 21st Century disease tsunamis, e.g., neurodegeneration, metabolic syndrome, etc. has led to the reemergence of pharmacology, its rise, often in the semantic guise of systems biology. Against a background of limited training in pharmacology, this has resulted in issues in experimental replication with a bioinformatics emphasis that often has a limited relationship to reality. The integration of newer technologies within a pharmacological context where research is driven by testable hypotheses rather than technology, together with renewed efforts in teaching pharmacology, is anticipated to improve the focus and relevance of biomedical research and lead to novel therapeutics that will contain health care costs.

Pharmacological traits of delta opioid receptors: pitfalls or opportunities?

RATIONALE

Delta opioid receptors (DORs) have been considered as a potential target to relieve pain as well as treat depression and anxiety disorders and are known to modulate other physiological responses, including ethanol and food consumption. A small number of DOR-selective drugs are in clinical trials, but no DOR-selective drugs have been approved by the Federal Drug Administration and some candidates have failed in phase II clinical trials, highlighting current difficulties producing effective delta opioid-based therapies. Recent studies have provided new insights into the pharmacology of the DOR, which is often complex and at times paradoxical.

OBJECTIVE

This review will discuss the existing literature focusing on four aspects: (1) Two DOR subtypes have been postulated based on differences in pharmacological effects of existing DOR-selective ligands. (2) DORs are expressed ubiquitously throughout the body and central nervous system and are, thus, positioned to play a role in a multitude of diseases. (3) DOR expression is often dynamic, with many reports of increased expression during exposure to chronic stimuli, such as stress, inflammation, neuropathy, morphine, or changes in endogenous opioid tone. (4) A large structural variety in DOR ligands implies potential different mechanisms of activating the receptor.

CONCLUSION

The reviewed features of DOR pharmacology illustrate the potential benefit of designing tailored or biased DOR ligands.

Medicinal chemistry and the pharmacy curriculum

The origins and advancements of pharmacy, medicinal chemistry, and drug discovery are interwoven in nature. Medicinal chemistry provides pharmacy students with a thorough understanding of drug mechanisms of action, structure-activity relationships (SAR), acid-base and physicochemical properties, and absorption, distribution, metabolism, excretion, and toxicity (ADMET) profiles. A comprehensive understanding of the chemical basis of drug action equips pharmacy students with the ability to answer rationally the "why" and "how" questions related to drug action and it sets the pharmacist apart as the chemical expert among health care professionals. By imparting an exclusive knowledge base, medicinal chemistry plays a vital role in providing critical thinking and evidence-based problem-solving skills to pharmacy students, enabling them to make optimal patient-specific therapeutic decisions. This review highlights the parallel nature of the history of pharmacy and medicinal chemistry, as well as the key elements of medicinal chemistry and drug discovery that make it an indispensable component of the pharmacy curriculum.

Systems pharmacology

We examine how physiology and pathophysiology are studied from a systems perspective, using high-throughput experiments and computational analysis of regulatory networks. We describe the integration of these analyses with pharmacology, which leads to new understanding of drug action and enables drug discovery for complex diseases. Network studies of drug-target relationships can serve as an indication on the general trends in the approved drugs and the drug-discovery progress. There is a growing number of targeted therapies approved and in the pipeline, which meets a new set of problems with efficacy and adverse effects. The pitfalls of these mechanistically based drugs are described, along with how a systems view of drug action is increasingly important to uncover intricate signaling mechanisms that play an important part in drug action, resistance mechanisms, and off-target effects. Computational methodologies enable the classification of drugs according to their structures and to which proteins they bind. Recent studies have combined the structural analyses with analysis of regulatory networks to make predictions about the therapeutic effects of drugs for complex diseases and possible off-target effects.