The Pharmacological Basis of Therapeutics A Textbook of Pharmacology, Toxicology and Therapeutics for Physicians and Medical Students. By Prof. Louis Goodman and Prof. Alfred Gilman. Pp. xiii + 1383. (New York: The Macmillan Company, 1941.) 50s. net.

The Pharmacological Basis of Therapeutics

Years of cumulative research can result in the development of a clinically useful drug, providing either a cure for a particular disease or symptomatic relief from a physiological disorder. A lead compound with a desired pharmacological activity may have associated with it undesirable side effects, characteristics that limit its bioavailability, or structural features which adversely influence its metabolism and excretion from the body. Bioisosterism represents one approach used by the medicinal chemist for the rational modification of lead compounds into safer and more clinically effective agents. The concept of bioisosterism is often considered to be qualitative and intuitive.1 The prevalence of the use of bioisosteric replacements in drug design need not be emphasized. This topic has been reviewed in previous years.2-5 The objective of this review is to provide an overview of bioisosteres that incorporates sufficient detail to enable the reader to understand the concepts being delineated. While a few popular examples of the successful use of bioisosteres have been included, the George Patani graduated with a B.Pharm. in 1992 from the College of Pharmaceutical Sciences, Mangalore University at Manipal, India. In 1996, he received his M.S. in Pharmaceutical Science at Rutgers University under the direction of Professor Edmond J. LaVoie. He is presently pursuing graduate studies in pharmaceutics. His current research interests are focused on drug design and controlled drug delivery.

https://www.mch.estranky.sk/file/228/1996chemrev96-3147-76_bioisosterism.pdf

Bioisosterism: A Rational Approach in Drug Design.

The concentrations of bases, nucleosides, and nucleosides mono-, di- and tri-phosphate are compared for about 600 published values. The data are predominantly from mammalian cells and fluids. For the most important ribonucleotides average concentrations ±SD (μM) are: ATP, 3,152±1,698; GTP, 468±224; UTP, 567±460 and CTP, 278±242. For deoxynucleosidestriphosphate (dNTP), the concentrations in dividing cells are: dATP, 24±22; dGTP, 5.2±4.5; dCTP, 29±19 and dTTP 37±30. By comparison, dUTP is usually about 0.2 μM. For, the 4 dNTPs, tumor cells have concentrations of 6–11 fold over normal cells, and for the 4 NTPs, tumor cells also have concentrations 1.2–5 fold over the normal cells. By comparison, the concentrations of NTPs are significantly lower in various types of blood cells. The average concentration of bases and nucleosides in plasma and other extracellular fluids is generally in the range of 0.4–6 μM; these values are usually lower than corresponding intracellular concentrations. For phosphate compounds, average cellular concentrations are: Pi, 4400; ribose-1-P, 55; ribose-5-P, 70 and P-ribose-PP, 9.0. The metal ion magnesium, important for coordinating phosphates in nucleotides, has values (mM) of: free Mg2+, 1.1; complexed-Mg, 8.0. Consideration of experiments on the intracellular compartmentation of nucleotides shows support for this process between the cytoplasm and mitochondria, but not between the cytoplasm and the nucleus.

Physiological concentrations of purines and pyrimidines.

Chemistry of biologically important synthetic organoselenium compounds.

Molecular recognition in biological systems relies on the existence of specific attractive interactions between two partner molecules. Structure-based drug design seeks to identify and optimize such interactions between ligands and their host molecules, typically proteins, given their three-dimensional structures. This optimization process requires knowledge about interaction geometries and approximate affinity contributions of attractive interactions that can be gleaned from crystal structure and associated affinity data.

Here we compile and review the literature on molecular interactions as it pertains to medicinal chemistry through a combination of careful statistical analysis of the large body of publicly available X-ray structure data and experimental and theoretical studies of specific model systems. We attempt to extract key messages of practical value and complement references with our own searches of the CSDa,(1) and PDB databases.(2) The focus is on direct contacts between ligand and protein functional groups, and we restrict ourselves to those interactions that are most frequent in medicinal chemistry applications. Examples from supramolecular chemistry and quantum mechanical or molecular mechanics calculations are cited where they illustrate a specific point. The application of automated design processes is not covered nor is design of physicochemical properties of molecules such as permeability or solubility.

Throughout this article, we wish to raise the readers’ awareness that formulating rules for molecular interactions is only possible within certain boundaries. The combination of 3D structure analysis with binding free energies does not yield a complete understanding of the energetic contributions of individual interactions. The reasons for this are widely known but not always fully appreciated. While it would be desirable to associate observed interactions with energy terms, we have to accept that molecular interactions behave in a highly nonadditive fashion.3,4 The same interaction may be worth different amounts of free energy in different contexts, and it is very hard to find an objective frame of reference for an interaction, since any change of a molecular structure will have multiple effects. One can easily fall victim to confirmation bias, focusing on what one has observed before and building causal relationships on too few observations. In reality, the multiplicity of interactions present in a single protein−ligand complex is a compromise of attractive and repulsive interactions that is almost impossible to deconvolute. By focusing on observed interactions, one neglects a large part of the thermodynamic cycle represented by a binding free energy: solvation processes, long-range interactions, conformational changes. Also, crystal structure coordinates give misleadingly static views of interactions. In reality a macromolecular complex is not characterized by a single structure but by an ensemble of structures. Changes in the degrees of freedom of both partners during the binding event have a large impact on binding free energy.

The text is organized in the following way. The first section treats general aspects of molecular design: enthalpic and entropic components of binding free energy, flexibility, solvation, and the treatment of individual water molecules, as well as repulsive interactions. The second half of the article is devoted to specific types of interactions, beginning with hydrogen bonds, moving on to weaker polar interactions, and ending with lipophilic interactions between aliphatic and aromatic systems. We show many examples of structure−activity relationships; these are meant as helpful illustrations but individually can never confirm a rule.

http://pubs.acs.org/doi/pdf/10.1021/jm100112j

A Medicinal Chemist’s Guide to Molecular Interactions

Potential chemotherapeutic targets in the purine metabolism of parasites.

Initial velocity and product inhibition studies of thymidine phosphorylase from mouse liver revealed that the basic reaction mechanism of this enzyme is a rapid equilibrium random bi-bi mechanism with an enzyme-phosphate-thymine dead-end complex. Thymine displayed both substrate inhibition and nonlinear product inhibition, Le., slope and intercept replots vs. 1 /(thymine) were nonlinear, indicating that there is more than one binding site on the enzyme for thymine and that when thymine is bound to one of these sites, the enzyme is inhibited, Furthermore, both thymidine and phosphate showed "cooperative effects" in the presence of thymine at concentrations above 60 pM, suggesting that the enzyme may have multiple interacting allosteric and/or catalytic sites. The deoxyribosyl transferase reaction catalyzed by this enzyme is phosphate-dependent, requires nonstoichiometric amounts of phosphate, and can proceed by an "enzyme-bound" 2-deoxyribose 1-phosphate intermediate. These findings are in accord with the rapid equilibrium random bi-bi mechanism and demonstrate that deoxyribosyl transfer by this enzyme involves an indirect-transfer mechanism. These results strongly suggest that phosphorolysis and deoxyribosyl transfer are catalyzed by the same site on thymidine phosphorylase. % y midine phosphorylase (thymidine:orthophosphate deox- yribosyltransferase, EC 2.4.2.4) catalyzes the reversible phosphorolysis of thymidine (dThd),' deoxyuridine, and their analogues (but not deoxycytidine) to their respective bases and 2-deoxyribose 1-phosphate (dRib-1-P):

Kinetic studies of thymidine phosphorylase from mouse liver.

Structure-activity relationship of ligands of the pyrimidine nucleoside phosphorylases

5-benzylacyclouridine and 5-benzyloxybenzylacyclouridine, potent inhibitors of uridine phosphorylase.

Enzyme inhibition studies on extracts from human liver, mouse liver, and human placenta indicate that there are considerable differences between human and murine hepatic uridine phosphorylases (UrdPase, EC 2.4.2.3) and thymidine phosphorylases (dThdPase, EC 2.4.2.4.) with regard to their specificities and roles in the phosphorolysis of natural and 5-fluoropyrimidine nucleosides. To confirm further these differences between human and murine pyrimidine nucleoside phosphorylases, UrdPase and dThdPase were isolated from human liver, mouse liver, and human placenta using diethylaminoethyl-cellulose ion exchange chromatography. The pattern of elution from the column suggests that the hydrophobicity or charges on the human enzymes at pH 8 are different from those on their murine counterparts. The amount of each enzyme present differed between tissues and species. The apparent Km, Vmax, and efficiency of catalysis (VmaxKmax) values were determined for each enzyme using uridine, thymidine, deoxyuridine, 5-fluorouridine (FUrd), 5-fluoro-2′-deoxyuridine (FdUrd), and 5′-deoxy-5-fluorouridine (5′-dFUrd) as substrates. Kinetic parameters and inhibition studies were used to ascertain the binding affinity, substrate specificity, and contributions of UrdPase and dThdPase to the phosphorolysis of the various nucleosides in the 3 tissues. The roles of UrdPase and dThdPase in human liver were quite distinct from those of their counterparts from human placenta and mouse liver. In human liver, UrdPase appears to be highly specific to uridine. Human hepatic UrdPase contributes only 15% to the cleavage of FUrd and does not contribute to the cleavage of the deoxyribosides (thymidine, deoxyuridine, FdUrd, and 5′-dFUrd). In mouse liver, UrdPase has a broader specificity as it cleaves over 85% of FUrd, 15% of FdUrd, and 25% of 5′-dFUrd. On the other hand, human hepatic dThdPase has a broader specificity than murine hepatic dThdPase. Human hepatic dThdPase cleaves all nucleosides tested including the ribosides, uridine, and FUrd. Approximately 15% of uridine and 85% of FUrd phosphorolysis in human liver is carried out by dThdPase. This contrasts with the murine hepatic dThdPase, which is more specific to deoxyribosides, as it does not contribute to the phosphorolysis of uridine, and contributes only 15% toward the cleavage of FUrd. dThdPase is the principal enzyme responsible for the phosphorolysis of 5′-dFUrd in both human and murine livers. The specificities of UrdPase and dThdPase from human placenta resembled the enzymes from the murine liver more than those from human liver. Thus, it appears that the specificities of human hepatic pyrimidine nucleoside phosphorylases are distinct from those from extrahepatic tissues. This suggests the existence of tissue-specific isozymes of pyrimidine nucleoside phosphorylases in humans. The inter- and intraspecies differences in substrate specificities and activities between human and murine pyrimidine nucleoside phosphorylases may have an important impact on the validity of attempts to introduce inhibitors of these enzymes into the clinic or on drawing conclusions about the metabolism and the chemotherapeutic use of pyrimidine analogues in humans based on studies in mice.

/pdf/differences-in-activities-and-substrate-specificity-of-human-3zfp652f72.pdf

Differences in Activities and Substrate Specificity of Human and Murine Pyrimidine Nucleoside Phosphorylases: Implications for Chemotherapy with 5-Fluoropyrimidines

Mahmoud H. el Kouni

Papers

Potential chemotherapeutic targets in the purine metabolism of parasites.

Kinetic studies of thymidine phosphorylase from mouse liver.

Structure-activity relationship of ligands of the pyrimidine nucleoside phosphorylases

5-benzylacyclouridine and 5-benzyloxybenzylacyclouridine, potent inhibitors of uridine phosphorylase.

Differences in Activities and Substrate Specificity of Human and Murine Pyrimidine Nucleoside Phosphorylases: Implications for Chemotherapy with 5-Fluoropyrimidines