Ulf Madsen

Textbook of drug design and discovery

The US Food and Drug Administration (FDA) describes personalized medicine as “the right patient with the right drug at the right dose at the right time,” and it certainly is a timely and emerging medical practice. Personalized Medicine: Promises and Pitfalls, by Gloria Gronowicz, begins with a unique perspective: the author’s own personal anecdote about the very day she was diagnosed with stage 2 breast cancer. That day started the author’s own journey with personalized medicine. Gronowicz, a Professor Emeritus of Surgery, continues with a cogent overview and clearly demonstrates her love and broad knowledge of human biology. Packed into a slim 212 pages, with index and glossary of scientific terms, this book is filled with valuable information. The text is presented from the patient’s viewpoint and not, for example, pharmaceutical companies or hospital administrators. Not only are scientific concepts explained for the lay audience, but the material is also interspersed with individual true stories of patients, for a truly “personalized” approach. Each chapter covers an important aspect of personalized medicine, from genomics, proteomics, and epigenetics, to integrative medicine such as nutrition, meditation, and exercise, to an explanation of clinical trials and healthcare system costs. A long list of references finishes off each chapter, so that this book reads both like a condensed textbook and a collection of white papers. Concepts are often illustrated with black-and-white figures or tables. For example, the “Genomics” chapter features images of DNA and RNA and a diagram of DNA replication. The “Integrative medicine” chapter features useful tables on vitamins and minerals, and their corresponding functions and sources in food. Each chapter is divided into sections featuring current technologies and the science behind them, as well as the advantages and pitfalls. The author’s own voice and opinions are often interjected in first person throughout, so that the material becomes more relatable. In terms of breadth and depth, this is a comprehensive and well-researched text. Rarely will you find explanations of the placebo effect, CRISPR, peer review process, obesity maps from the CDC, and an analysis of Textbook of Drug Design and Discovery, Fifth Edition. By Kristian Strømgaard, Povl KrogsgaardLarsen, and Ulf Madsen. Boca Raton, Florida: CRC Press (Taylor & Francis Group); 2017. US

Resolution, absolute stereochemistry and molecular pharmacology of the enantiomers of ATPA.

94.04 (Hardcover). 436 p. ISBN: 978-1498702782

Lessons from more than 80 structures of the GluA2 ligand-binding domain in complex with agonists, antagonists and allosteric modulators

(RS)-2-Amino-3-(5-tert-butyl-3-hydroxy-4-isoxazolyl)propionic acid (ATPA), an analogue of (RS)-2-amino-3-(3-hydroxy-5-methyl-4-isoxazolyl)propionic acid (AMPA). has previously been shown to be a relatively weak AMPA receptor agonist and a very potent agonist at the GluR5 subtype of kainic acid-preferring (S)-glutamic acid ((S)-Glu) receptors. We report here the separation of (+)- and (-)-ATPA, obtained at high enantiomeric purity (enantiomeric excess values of 99.8% and > 99.8%, respectively) using chiral chromatography, and the unequivocal assignment of the stereochemistry of (S)-(+)-ATPA and (R)-(-)-ATPA. (S)- and (R)-ATPA were characterized in receptor binding studies using rat brain membranes, and electrophysiologically using the rat cortical wedge preparation and cloned AMPA-preferring (GluR1, GluR3, and GluR4) and kainic acid-preferring (GluR5, GluR6, and GluR6 + KA2) receptors expressed in Xenopus oocytes. In the cortical wedge, (S)-ATPA showed AMPA receptor agonist effects (EC50 = 23 microM) approximately twice as potent as those of ATPA. (R)-ATPA antagonized depolarizations induced by AMPA (Ki = 253 microM) and by (S)-ATPA (Ki = 376 microM), and (R)-ATPA antagonized the biphasic depolarizing effects induced by kainic acid (Ki = 301 microM and 1115 microM). At cloned AMPA receptors, (S)-ATPA showed agonist effects at GluR3 and GluR4 with EC50 values of approximately 8 microM and at GluR1 (EC50 = 22 microM), producing maximal steady state currents only 5.4-33% of those evoked by kainic acid. (R)-ATPA antagonized currents evoked by kainic acid at cloned AMPA receptor subtypes with Ki values of 33-75 microM. (S)-ATPA produced potent agonist effects at GluR5 (EC50 = 0.48 microM). Due to desensitization of GluR5 receptors, which could not be fully prevented by treatment with concanavalin A, (S)-ATPA-induced agonist effects were normalized to those of kainic acid. Under these circumstances, maximal currents produced by (S)-ATPA and kainic acid were not significantly different. (R)-ATPA did not attenuate currents produced by kainic acid at GluR5, and neither (S)- nor (R)-ATPA showed significant effects at GluR6. (S)-ATPA as well as AMPA showed weak agonist effects at heteromeric GluR6 + KA2 receptors, whereas (R)-ATPA was inactive. Thus, (S)- and (R)-ATPA may be useful tools for mechanistic studies of ionotropic non-NMDA (S)-Glu receptors, and lead structures for the design of new subtype-selective ligands for such receptors.

Partial Agonism and Antagonism of the Ionotropic Glutamate Receptor iGLuR5 STRUCTURES OF THE LIGAND-BINDING CORE IN COMPLEX WITH DOMOIC ACID AND 2-AMINO-3-[5-tert-BUTYL-3-(PHOSPHONOMETHOXY)-4-ISOXAZOLYL]PROPIONIC ACID

Ionotropic glutamate receptors (iGluRs) constitute a family of ligand-gated ion channels that are essential for mediating fast synaptic transmission in the central nervous system. These receptors play an important role for the development and function of the nervous system, and are essential in learning and memory. However, iGluRs are also implicated in or have causal roles for several brain disorders, e.g. epilepsy, Alzheimers disease, Parkinsons disease and schizophrenia. Their involvement in neurological diseases has stimulated widespread interest in their structure and function. Since the first publication in 1998 of the structure of a recombinant soluble protein comprising the ligand-binding domain of GluA2 extensive studies have afforded numerous crystal structures of wildtype and mutant proteins including different ligands. The structural information obtained combined with functional data have led to models for receptor activation and desensitization by agonists, inhibition by antagonists and block of desensitization by positive allosteric modulators. Furthermore, the structural and functional studies have formed a powerful platform for the design of new selective compounds.

Design, synthesis and pharmacology of model compounds for indirect elucidation of the topography of AMPA receptor sites

More than 50 structures have been reported on the ligand-binding core of the ionotropic glutamate receptor iGluR2 that belongs to the 2-amino-3-(3-hydroxy-5-methyl-4-isoxazolyl)propionic acid-type of receptors. In contrast, the ligand-binding core of the kainic acid-type receptor iGluR5 has only been crystallized with three different ligands. Hence, additional structures of iGluR5 are needed to broaden the understanding of the ligand-binding properties of iGluR5, and the conformational changes leading to channel opening and closing. Here, we present two structures of the ligand-binding core of iGluR5; one as a complex with the partial agonist (2S,3S,4S)-3-carboxymethyl-4-[(1Z,3E,5R)-5-carboxy-1-methyl-hexa-1,3-dienyl]-pyrrolidine-2-carboxylic acid (domoic acid) and one as a complex with the antagonist (S)-2-amino-3-[5-tert-butyl-3-(phosphonomethoxy)-4-isoxazolyl]propionic acid ((S)-ATPO). In agreement with the partial agonist activity of domoic acid, the ligand-binding core of the iGluR5 complex is stabilized by domoic acid in a conformation that is 11° more open than the conformation observed in the full agonist (S)-glutamic acid complex. This is primarily caused by the 5-carboxy-1-methyl-hexa-1,3-dienyl moiety of domoic acid and residues Val685-Thr690 of iGluR5. An even larger domain opening of 28° is introduced upon binding of the antagonist (S)-ATPO. It appears that the span of domain opening is much larger in the ligand-binding core of iGluR5 (30°) compared with what has been observed in iGluR2 (19°). Similarly, much larger variation in the distances between transmembrane linker residues in the two protomers comprising the dimer is observed in iGluR5 as compared with iGluR2.

Agonist discrimination between AMPA receptor subtypes.

Abstract Based on structure-activity studies on excitatory amino acids with specific agonist effect at ( RS )-2-amino-3-(3-hydroxy-5-methyl-4-isoxazolyl)propionic acid (AMPA) receptors we have earlier proposed a simple model of the AMPA receptor pharmacophore. In order to judge the capacity of this empirical model we have now synthesized and tested 3 model compounds derived from the AMPA receptor agonists, AMPA and ( RS )-3-hydroxy-4,5,6,7-tetrahydroisoxazolo[5,4- c ]pyridine-7-carboxylic acid (7-HPCA). These model compounds, ( RS )-2-amino-3-(5-ethyl-3-hydroxy-4-isoxazolyl)propionic acid (Et-AMPA), ( RS )-2-amino-4-(3-hydroxy-5-methyl-4-isoxazolyl)butyric acid (Homo-AMPA) and ( RS )-3-hydroxy-5,6,7,8-tetrahydro-4 H -isoxazolo[5,4- c ]azepine-8-carboxylic acid (Homo-7-HPCA) were tested electrophysiologically and in receptor binding assays. Et-AMPA was slightly more potent than AMPA as an AMPA agonist (EC 50 = 2.3 μM compared to 3.5 μM for AMPA) and as a specific inhibitor of [ 3 H]AMPA binding (IC 50 = 0.030 μM compared with 0.040 μM for AMPA), whereas Homo-AMPA was essentially inactive. Homo-7-HPCA was much weaker than 7-HPCA. These data support the view that the AMPA recognition site(s) comprise a confined region, which tightly binds the charged structure-elements of agonists molecules, and a cavity capable of accommodating bulky lipophilic groups in such compounds.

The AMPA Receptor Binding Site: Focus on Agonists and Competitive Antagonists

The lack of subtype-selective compounds for AMPA receptors (AMPA-R) led us to search for compounds with such selectivity. Homoibotenic acid analogues were investigated at recombinant GluR1o, GluR2o(R), GluR3o and GluR1o+ 3o receptors expressed in Sf9 insect cells and affinities determined in [3H]AMPA radioligand binding experiments. (S)-4-bromohomoibotenic acid (BrHIBO) exhibited a 126-fold selectivity for GluR1o compared to GluR3o. Xenopus laevis oocytes were used to express functional homomeric and heteromeric recombinant AMPA-R and to determine BrHIBO potency (EC50) at these channels. (R,S)-BrHIBO exhibited a 37-fold selectivity range amongst the AMPA-R. It is hoped that BrHIBO can be used as a lead structure for the development of other subtype-selective compounds.

Excitatory amino-acid receptor agonists. Synthesis and pharmacology of analogues of 2-amino-3-(3-hydroxy-5-methylisoxazol-4-yl)propionic acid

It is generally agreed that (S)-glutamic acid (Glu) receptors are involved in the development of a number of diseases in the central nervous system (CNS), and ligands that interact with these receptors are of significant interest. Selective ligands are indispensable as tools for the elucidation of the physiological role of AMPA receptors and as leads for the development of therapeutic agents. Over the last decade a wide variety of such ligands have been developed and studies on the structure-activity relationships of these compounds have contributed to our understanding of the mechanisms involved in AMPA receptor activation and blockade. Series of selective agonists using the 3-isoxazolol amino acid ibotenic acid (2) as a lead compound have been designed and developed. Other heterocycles, such as the uracil moiety of willardiine (6), have also proved to be highly effective bioisosteres for the distal carboxyl group of Glu. For a number of reasons, the development of competitive antagonists with therapeutic potential has been hampered for example due to the limited solubility of key heterocyclic compounds structurally unrelated to Glu. However, some problems have been overcome, and series of water-soluble, potent and selective quinoxalinediones, indenoimidazones and isatine oximes have now been developed. At the turn of the millennium the crystal structure of GluR2 co-crystallized with different AMPA receptor ligands became available, opening a new era in the design of AMPA receptor ligands on a rational basis.

Molecular pharmacology of the AMPA agonist, (S)-2-amino-3-(3-hydroxy-5-phenyl-4-isoxazolyl)propionic acid [(S)-APPA] and the AMPA antagonist, (R)-APPA ☆

Summary We have previously proposed the existence of a lipophilic cavity of the 2-amino-3-(3-hydroxy-5-methylisoxazol-4-yl)propionic acid (AMPA) receptor recognition site capable of accommodating alkyl substituents of limited size in the 5-position of the isoxazole ring. In order to indirectly elucidate the approximate extent of this proposed cavity we have synthesized and pharmacologically characterized a number of AMPA analogues. For most of these AMPA analogues, a positive correlation between AMPA receptor affinity and agonist effect was observed. The only exception was demethyl-AMPA ( 8a ), which showed relatively high AMPA receptor affinity (IC 50 = 0.27 μM) but remarkably weak agonist potency (EC 50 = 900 μM). Whereas the ethyl analogue of AMPA (Et-AMPA) (IC 50 = 0.030 μM; EC 50 = 2.3 μM) has previously been shown to be slightly more potent than AMPA (IC 50 = 0.040 μM; EC 50 = 3.5 μM), substitutions of a propyl or a butyl group for the methyl group of AMPA to give 8b (IC 50 = 0.090 μM; EC 50 = 5.0 μM) or 8f (IC 50 = 1.0 μM; EC 50 = 32 μM), respectively, result in progressive loss of the AMPA agonist effect. Analogues containing larger groups, such as isopentyl ( 8e ), 1-propylbutyl ( 8g ), 2,2-dimethylpropyl ( 8h ), or benzyl ( 14 ) groups, were very weak or totally inactive as AMPA receptor ligands.

Resolution, absolute stereochemistry, and enantiopharmacology of the GluR1–4 and GluR5 antagonist 2-amino-3-[5-tert-butyl-3-(phosphonomethoxy)-4-isoxazolyl]propionic acid

The heterocyclic analogue of (S)-glutamic acid, (S)-2-amino-3-(3-hydroxy-5-methyl-4-isoxazolyl)propionic acid [(S)-AMPA] is a potent and selective AMPA receptor agonist, whereas the enantiomeric compound, (R)-AMPA, is virtually inactive. We have previously characterized (RS)-2-amino-3-(3-hydroxy-5-phenyl-4-isoxazolyl)propionic acid [(RS)-APPA] as a partial AMPA receptor agonist showing about 60% of the efficacy of (RS)-AMPA. This partial agonism produced by (RS)-APPA is, however, only apparent, since resolution of (RS)-APPA has now been shown to provide the full AMPA receptor agonist, (S)-APPA, whereas (R)-APPA is a non-N-methyl-D-aspartic acid (non-NMDA) receptor antagonist showing preferential AMPA blocking effects. In agreement with classical theories for competitive interaction between agonists and antagonists, the efficacy of depolarizations produced by (S)-APPA in the rat cortical wedge preparation was shown to be progressively reduced with increasing molar ratios of (R)-APPA/(S)-APPA. These compounds and the competitive antagonists (RS)-2-amino-3-(3-carboxymethoxy-5-methyl-4-isoxazolyl)propionic acid [(RS)-AMOA], 6-cyano-7-nitroquinoxalin-2,3-dione (CNQX) and 6-nitro-7-sulfamoylbenzo(f)quinoxalin-2,3-dione (NBQX) were also tested in [3H]AMPA and [3H]CNQX binding systems, the latter ligand being used in the absence or presence of thiocyanate ions. On the basis of these studies it is suggested that (RS)-AMPA and the AMPA agonist (S)-APPA interact with a high-affinity receptor conformation, whereas the competitive antagonists (RS)-AMOA and (R)-APPA, derived from these agonists, preferentially bind to a low-affinity AMPA receptor conformation.(ABSTRACT TRUNCATED AT 250 WORDS)