Book reviews

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Computational Biochemistry and Biophysics

O. M. Becker, A. D. MacKerell, Jr.B. Roux and M. Watanabe, Marcel Dekker, USA, xii + 512 pp., price $195, ISBN 0-8247-0455-x Search PubMedAs the editors point out, almost every researcher now has ready access to computational resources that even a few years ago were restricted to specialists in the simulation of biological systems. Sophisticated molecular modelling methods and applications are moving into the mainstream, and there is a requirement for texts that will help those without extensive experience or training in this area to select and apply appropriate computational methodologies to their research interests. The stated aim of this book is to address the needs of such an audience, but also to provide chapters useful to the more advanced reader. Many of the chapters therefore combine elements of a traditional review of a subject area with a more tutorial approach to educating the reader.

The first chapter, Atomistic Models and Force Fields (Alexander MacKerell) provides a good general introduction to the basic concepts, before launching into a more detailed discussion of forcefield development. Next Oren Becker and Masakatsu Watanabe discuss Dynamics Methods, including trajectory analysis methods—more in this area would have been useful. Oren Becker then contributes a chapter on conformational analysis and structure optimisation. Tom Darden covers the treatment of long-range forces clearly and with some allowance for the less mathematically-minded reader. The following chapter, by Alexy Mazur on Internal Coordinate Simulation methods, is perhaps rather out of place; as a rather specialized area it probably belongs later in the book. The developing area of Implicit Solvation Methods is discussed by Benoit Roux, but this is perhaps less helpful as a tutorial text as it concentrates almost entirely on the theory without much discussion of the practicalities of the application of the methods. Steven Hayward provides an excellent introduction to Normal Mode Analysis methods, which will also prove very useful to those interested in related methods such as Principal Component Analysis. Free Energy Calculations are discussed by Thomas Simonson; this is a huge area but a good job has been done in concentrating on the basics and emphasising important but easily overlooked issues such as end-point corrections. The final two chapters move us on to cover chemical reactions: John Straub reviews computational approaches to the calculation of reaction rates and transition pathways (particularly the work from the laboratories of Karplus and Elber), and Paul Lyne and Owen Walsh provide a brief overview of QM-MM methods to study biochemical reactions, and then discuss three practical examples of the application of the method in some detail—an informative approach.

The remaining chapters cover what is classified as more advanced material, though in reality it is less easy to make a clear distinction from what has been dealt with earlier. Some chapters, for example Jeremy Smith on X-ray and Neutron Scattering, Roland Dunbrack on Bayesian Statistics, and Fumio Hirata and others on RISM-SCF/MCSCF approaches are clearly of specialist interest. The chapter on Simulations of Electron Transfer Proteins (Toshiko Ichiye) is probably more accessible to the non-specialist reader. Michael Nilges provides a lucid introductory-level overview of the applications of molecular modelling to NMR structure determination. The following chapter on Comparative Protein Structure Modelling (Andras Fiser and colleagues) is an excellent and detailed review of the current state of the area, if rather less of a tutorial text. The same is true of the chapter by Oren Becker on protein folding—it is a traditional review without a pedagogic approach. Computer Aided Drug Design is discussed by Alexander Tropsha and Weifan Zheng, in view of the enormous importance of this area it is a shame that page restrictions (I presume) limit this chapter to providing rather a brief overview. The penultimate chapter by Alexander MacKerell and Lennart Nilsson on Nucleic Acid Simulations provides a good starting review and an excellent practical guide to performing simulations in this area. Finally, Douglas Tobias covers Membrane Simulations, though this chapter is rather limited in scope, covering only simulations of pure lipid bilayers, and concentrating on the author’s own work. To complete the book, there is a fair-sized appendix of useful internet resources. This provides links to material associated with specific chapters, but also general resources—software, databases and on-line tutorials. Importantly in view of the fragile nature of such resources, there is a web page associated with the book via which this list (it is promised!) will be kept up-to-date.

All in all, the editors can be congratulated in putting together a useful resource that largely fulfils the aims set: providing not only a ‘one-stop-shop’ where non-specialists can quickly pick up the gist of the majority of general computational chemistry methods, but also a useful, if not comprehensive, source of information for the dedicated computational chemist.

Charles Laughton
University of Nottingham, UK

Enzymes in Nonaqueous Solvents, Methods and Protocols

Ed. Evgeny N. Vulfson, Peter J. Halling and Herbert L. Holland, Humana Press, 2001, 649 pp., price $139.50, ISBN 0-89603-929-3 Search PubMedBiocatalysts are most often regio- and stereo-selective, active in mild conditions, and catalyze reactions that may be inaccessible or difficult to achieve by traditional synthesis. These qualities have motivated the use of enzymes in the preparation of various chemicals. The increasing need for enantiopure chemicals in fields such as drug discovery and food science is partially responsible for the growing interest in enzymatic asymmetric synthesis. However, the use of biocatalysts still poses serious challenges such as product inhibition, substrate solubility, enzyme stability issues, and cofactor requirements. Water is also difficult to eliminate and may undergo unwanted side reactions. Unquestionably, the early belief that enzymes could work solely in aqueous media has restrained the scope of their applications. However, it is now well established that numerous enzymes can function perfectly well under nearly anhydrous conditions. Furthermore, enzymes in organic solvents often display useful properties such as highly enhanced stability, molecular imprinting, and modified selectivity. Numerous techniques have been developed to optimize the use of enzymes in nonaqueous media. The goal of Enzymes in Nonaqueous Solvents, Methods and Protocols is to present some theory and detailed protocols to the reader interested in using enzymes in synthesis.

The first chapter of this volume addresses the issues that affect the activity, specificity, and stability of low water enzymes, namely, temperature, substrate concentration, acid/base effects, solvent, and residual water. Suitable preparation of the biocatalyst is critical to the behavior and activity that it exhibits. For example, the precise conditions of lyophilization, which are rarely specified clearly, have a significant effect on activity and can be improved by drying in the presence of salts or a suitable imprinting agent. Small variations in the residual water of anhydrous systems can have dramatic effects on the enzyme behavior. A variety of methods to precisely quantify and control the water content are described at great length in this book. In addition, the authors point out many specific considerations that apply to the determination of enzyme activity and selectivity in organic solvents.

Proteins with increased activity and stability in organic media can be obtained by immobilization of the biocatalyst. The authors outline three important techniques to immobilize enzymes: 1) entrapment within a polymer network (e.g. polyethylene glycol), 2) microencapsulation within permeable polymeric microcapsules, and 3) the use of hydrogel supports, which are cross-linked polymeric structures that can imbibe large quantities of water. Because enzymes in anhydrous media form heterogeneous mixtures, finer dispersions generally translate into higher synthetic yields. More homogeneous solutions are often achieved by covalent attachment of polyethylene glycol or hydrophobic modifiers, or non-covalent modification with polyethylene glycol or synthetic lipids. Interestingly, the addition of crown ethers has been reported to enhance the activity of many enzymes in anhydrous conditions. Also addressed is the study of enzymes by calorimetric, fluorescence, and CD measurements, followed by specific examples of enzymatic synthesis in the second chapter.

The ability to form esters and amides without competing hydrolysis, the manipulation of regio- and stereo-selectivity, and the higher solubility of substrates and products have all contributed to the spread of enzyme applications in nearly anhydrous conditions. Organic solvents can be advantageous for oxidation reactions which are severely limited by oxygen solubility in water. The series of empirical rules provided in this volume for selection of a hydrolase with optimum activity and selectivity is a highly valuable resource. Although most of the work in this field has involved hydrolytic enzymes, many other reactions are amenable to biocatalysis including reductions, oxidations, preparation of chiral alcohols by transesterification, as well as several transformations of hydrophobic organosilicon substrates.

Low water systems are equally useful with whole-cell biocatalysts. Organic solvents, water–organic solvent biphasic systems, and reverse micelles have been used successfully to optimize specific transformations by whole cells. A number of interface bioreactors adapted to nearly anhydrous mixtures are described in great detail. Yeast, one of the most popular biocatalysts, can catalyze a wide range of reactions. It is commonly used as an actively growing culture and, therefore, all of its biochemical pathways are active. This methodology is well established and often affords high selectivity, but the same problems encountered with enzymes in aqueous media apply. In addition, product isolation is impeded by the complex nature of the fermentation media. These can be overcome using a recently reported methodology which uses dried Baker’s yeast in an organic solvent. Since the yeast is not fermenting, very few of the natural metabolites are produced and no food source is required.

Organic solvents are not the only alternative to aqueous media. Numerous other low water systems have been successfully used in enzymatic catalysis, and the third chapter focuses on them. Supercritical fluids, solvent-free, gas phase, solid-to-solid, and solid-to-gas systems are some of the extreme conditions reported. Also useful are frozen aqueous solutions, supersaturated substrate solutions, reverse micelles, and microemulsions. In general, the appropriate type of conditions to be used with the bioreactor is determined by the properties of the substrate.

Above the critical point of the phase diagram, a substance is said to be supercritical (SC) and is described as a dense gas or an expanded liquid. Close to the critical point, small changes in temperature or pressure can result in large changes in density and solvation ability of the fluid. These media also show lower viscosity and higher diffusivity as compared to organic solvents. This is a major advantage since diffusion is often rate-limiting when enzyme and substrates are not in the same phase. In addition, supercritical fluids represent a less toxic and less flammable alternative to organic solvents and can be easily separated from the product. As a result, SC-CO₂ and SC-SO₂ are increasingly popular media for enzymes that have been freeze-dried, immobilized, or crystallized.

Solid-to-solid peptide synthesis consists of up to 20% (w/w) of enzyme in water mixed with solid substrates. In all cases, some substrate remains undissolved. Similarly, enzymatic reactions can be performed in the liquid phase using low-melting-point eutectic mixtures of supersaturated substrates. Such systems can be prepared by mixing molten substrates together at elevated temperature followed by slow cooling to room temperature. This procedure has been employed in the preparation of numerous peptide derivatives, glycosides, and disaccharides. The advantages of using this technique include: a better volumetric productivity, higher yields of products, and change in stereoselectivity of glycosylations from primary to secondary hydroxy groups.

Micellar enzymology was initially developed as a model for biomembranes, yet reverse micelles are attractive media for many other reasons including: driving the equilibrium towards the formation of products, allowing for accurate control of the water content, and permitting the dissolution of both hydrophilic and hydrophobic substrates while providing an isotropic solution which can be monitored by spectroscopy.

Enzymes in Nonaqueous Solvents, Methods and Protocols includes detailed descriptions of the latest technologies used for biocatalysis in nearly anhydrous systems. Numerous specific enzymatic reactions, bioreactors, and useful techniques are carefully explained in a format intelligible to most readers in spite of the great diversity of the fields covered. This work of reference will be extremely valuable to those interested in enzymatic and asymmetric synthesis. One drawback however is its high cost.

Karine Auclair
McGill University, Montreal, Canada

Bioactive Compounds from Natural Sources

Ed. Corrada Tringali, Taylor & Francis, 2000, x + 693 pp., price £65, ISBN 0-7484-0890-8 Search PubMedChapter 1 provides a good summary of various methods of detecting bioactive compounds, a topic not covered in most books on natural products. As is the case in most of the chapters there is an excellent set of references.

Chapter 2 discusses the application of various types of coupled chromatography (LC/UV; LC/MS; LC/NMR) to separate compounds, one of the key parts to natural products chemistry.

Chapter 3 is devoted to the uses of NMR in natural products chemistry. A good brief discussion of the theoretical aspects is followed by examples of the application of the various aspects of the method to practical problems.

Chapter 4 discusses the aspects of bioactive compounds of Mexican origin. Many examples are discussed. Chapter 5 provides a brief look at flavonoids of importance in cancer chemotherapy.

Chapters 5 to 17 provide brief looks at various classes of natural products. Most chapters give a brief discussion of the class followed by an example of each class (e.g., taxoid compounds, antimalarial drugs). The alkaloids, of which many are bioactive (e.g., morphine, quinine), are not discussed in the book.

All in all, the book, including the excellent references, provides a good introduction to the methods and classes of natural products. It is an excellent starting point for new graduate students, and a useful reference for practitioners in the natural products field. It is unfortunate that the alkaloids are not included.

W. Ayer
University of Alberta

Natural Compounds in Cancer Chemotherapy

John Boik, Oregon Medical Press, 2001, xiii + 521 pp., price $32, ISBN 0-9648280-1-4 Search PubMedSomething like 50% of the drugs used in cancer chemotherapy are natural compounds. Well known examples include the Vinca alkaloids vinblastine and vincristine, the podophyllins, and of course Taxol (Paclitaxel). But these are not the natural compounds described in this book—they are the compounds present in the herbal remedies used (it is claimed) by 40–60% of cancer patients in the USA. I have to admit that my prejudice against this type of pseudo-science led me to anticipate the worst as I began to read the book. I was, however, entirely wrong. The book is full of carefully explained science and comes as close as one can imagine to giving a balanced view of the efficacy of plant extracts in cancer therapy.

The first two parts of the book describe the development and progression of cancer, complete with diagrams and explanations of cell-signalling cascades, apoptosis, and transcription of DNA. The biology is quite demanding in places and would certainly require a science degree in order to appreciate it fully. Indeed many chemists would not appreciate the subtleties of ras proteins, vascular endothelial growth factors, cyclin dependent kinases, etc. Yet the target audience for the book is claimed to be “the patient, the doctor, and the researcher”. I fear that most of the contents of parts I and II will certainly be lost on the first two categories of readers.

Part III will, however, be much more intelligible, and covers trace metals, vitamins, flavonoids, terpenes, polysaccharides, amino acids etc., their sources and therapeutic value. The numerous appendices contain technical material like dosing levels of compounds, some chemical structures, data on particular plants and constituents, and there are literally hundreds of research references.

Overall, I am left with the impression that this is a highly scientific treatment of a subject that is usually left in the hands of the herbalists. It will probably be of most value to oncologists looking for additional therapies for their patients. The herbalists will unfortunately find additional justification for prescribing large amounts of inter alia horse chestnut, butcher’s broom, feverfew, melatonin, and vitamins A to E.

John Mann
Queen’s University, Belfast

Medicinal Chemistry – Into the Millennium

M. M. Campbell and I. S. Blagbrough, The Royal Society of Chemistry, UK, x + 398 pp., price £69.50, ISBN 0-85404-769-7 Search PubMedDespite enormous developments over the past decade or so, design and discovery of new biologically active molecules for use as pharmaceutical agents is an ongoing challenge. Advances in genomics have identified new molecular targets for investigation, while on the synthetic side, production of large chemical libraries has increased efficiency in lead generation and optimisation. Converting these technological developments into new efficient pharmaceutical agents poses a significant challenge to scientists in the pharmaceutical sector.

In this book, the Proceedings of the European Federation of Medicinal Chemistry Symposium held in September 1998, contributions from scientists in the pharmaceutical sector and academic researchers offer an interesting blend of insights into recent (in 1998) developments in Medicinal Chemistry. Organisation of the material into a number of themes each consisting of between two and five individual contributions is particularly useful.

The first section covering New Technologies in Drug Discovery reflects recent activity in the areas of library construction and design, and informatics. The first contribution by Paul Bartlett’s group discusses design of macrocyclic peptidase inhibitors, while the second by Daniel Rich’s group focuses on protease inhibitors. Both articles highlight the interplay between rational design and combinatorial approaches. This section is completed by a contribution form Ken Siddle and Tom Blundell’s groups showing the use of structural genomics and protein superfamilies in drug discovery.

The next section on Ion Channels features two contributions, the first from Paul Leeson at AstraZeneca focusing on ligand-gated ion channels as targets, in particular the NMDA receptor as a target for CNS disorders, while the chapter by Frank Slok and co-workers discusses the design of selective ligands for Excitatory Amino Acid (EAA) receptors. This is followed by two contributions on Glycine Antagonists, with the first by David Jane exploring the therapeutic potential of these antagonists acting at the NMDA receptor complex, while the second by G. Gaviraghi and co-workers at GlaxoWellcome describes the discovery and development of novel indole-2-carboxylates as potent and selective glycine antagonists for use as neuroprotective agents in brain ischaemia.

The section on 7TM receptors commences with a contribution from David Horwell and co-workers from Parke-Davis describing the use of ligand based design to modify neuropeptides to give therapeutically useful peptoids as antagonists, focusing on bombesin and tachykinins. Interestingly this article also explores the use of dendroids as a non-peptide motif as mimetics of protein–protein interactions. Following this a contribution from Steven Bromidge of SmithKline Beecham describes the discovery by high throughput screening of a lead bis-aryl sulfonamide as a ligand for the 5-HT₆ receptor and subsequent optimisation of the bioactivity through structural modification. Autoradiography studies using a highly specific radioligand demonstrated for the first time that 5-HT₆ receptors are present in the human brain. F. Ince from Astra Charnwood then describes the discovery of a family of dual D₂-receptor and β₂-adrenoceptor agonists for application in the treatment of airway disorders such as asthma and COPD.

Two contributions on Growth Factors commence with an article by J. I. Luengo and co-workers at SmithKline Beecham and Ligand Pharmaceuticals on the discovery of a small, non-peptidyl mimic of granulocyte-colony stimulating factor showing for the first time that a small non-peptidyl molecule can trigger the selective activation of a cytokine receptor. The second chapter by Andrew Barker, Zeneca, describes the use of 4-anilinoquinazolines as inhibitors of epidermal growth factor receptor tyrosine kinase for application in cancer therapy.

The section on Intracellular Signalling consists of five articles, the first by A. J. Bridges and co-workers at Parke-Davis describes the development of highly selective, irreversible epidermal growth factor receptor tyrosine kinase inhibitors, again based on the anilinoquinazoline pharmacophore, for cancer therapy. Jerry Adams and co-workers at SmithKline Beecham then describe the development of pyrimidinylimidazoles as p38 MAP kinase inhibitors for anti-inflammatory application. Peter Davis and co-workers from Celltech Chiroscience discuss the development and optimisation of inhibitors of T-cell specific tyrosine kinases. Alan Lewis and Anthony Manning of Signal Pharmaceuticals discussed the role of gene regulating kinases in inflammatory diseases and strategies for designing inhibitors. The final contribution in this section from David Gani’s group describes the mechanism of catalytic hydrolysis of inositol-1-phosphate by inositol monophosphatase; design and solid phase synthesis of inhibitors based on the catalytic mechanism is discussed. Novel aspects of the solid phase synthesis include new protocols for quantifying resin loading using ¹⁹F gel-phase NMR spectroscopy.

The next topic in the book is Protease Inhibitors – Michael Venuti and co-workers from Axys Pharmaceuticals describe the discovery of small molecules for zinc-dependent serine protease inhibition, including use of X-ray crystallography to explore the zinc binding. P. S. Dragovich, Agouron Pharmaceuticals, describe the structure based design of irreversible inhibitors of human rhinovirus 3C protease based on ketomethylene dipeptide isosteres. Furthermore optimisation of tripeptide derived inhibitors of the same target using solid phase synthesis and high-throughput assay is reported. Daniel Veber and co-workers describe the design of 1,3-bis(acylamino)propan-2-ones as new potent, reversible inhibitors of the cysteine protease cathepsin K, with a view to developing treatment for osteoporosis.

Five varied contributions in the area of Glycochemistry and Glycobiology form an interesting section of the book, starting with an article by Horst Kunz and co-workers describing the synthesis and use of glycoconjugates as tumour-associated antigens and ligands in regulatory processes. The next contribution by Elizabeth Hounsell and David V. Renouf outlines new potential drug targets based in glycochemistry focusing in particular on protein glycosylation in immuno- and neuro-pathology. The next contribution by Per-Erik Jansson incorporating a multiinternational group of co-workers, describes investigation of the chemistry of lipopolysaccharides—biologically active surface polymers—from Helicobacter pylori and Vibrio cholerae. Structure–activity relationships in synthetic heparin-like oligosaccharides are described by C. M. Dreef-Tromp and co-workers from Organon, leading to well defined synthetic antithrombotics with tailor made profiles with respect to anti-factor Xa and anti-thrombin activities. The final contribution from P. M. St Hilaire and co-workers describes the use of automated techniques for the synthesis of glycopeptides and use of these structures for investigation of protein-carbohydrate interactions.

Richard Silverman’s group describe the design of selective inhibitors of three isozymes of Nitric Oxide Synthase, demonstrating that relatively minor structural modifications can produce very different results, implying that subtle differences exist in the active sites of the three isozymes.

Converting lead compounds based on molecular targets into commercial drugs is one of the major challenges in the pharmaceutical sector. In particular the areas of drug metabolism and pharmacokinetics (DMPK), which are often investigated late in the discovery process, lack predictivity, and can be a major stumbling block. Accordingly there are currently significant efforts invested in attempting to develop predictive methods for DMPK, and earlier use of these in the cycle of drug discovery. The final section of the book involves four contributions in the area of Predicting DMPK highlighting some of the problems and solutions in this regard. Dennis Smith, Pfizer, describes absorption and distribution as factors in drug design, and demonstrates how structural features which provide good dissolution properties, such as inclusion of an ionised group, can markedly improve the duration of the compound in vivo. Bernard Testa then highlights the importance of detailed understanding of drug metabolism. Marc Bertrand and co-workers from Technologie Servier describe techniques for rapid screening and assessment of drug metabolism long before clinical trials, allowing understanding of the fate of a potential drug in vivo. The final contribution from Nico Vermeulen and co-workers describes the investigation of the active sites of cytochrome P450s using modelling techniques.

In a collection of this nature inevitably the selection of molecular targets included can never be comprehensive. However, those included cover many therapeutically significant areas. Inclusion of the opening section on New Technologies for Drug Discovery and the closing section on Predicting DMPK ensure that the book provides a useful overview of the process of drug discovery. This book will be of interest to all involved in medicinal chemistry, especially to those in the pharmaceutical sector.

Anita R. Maguire
University College Cork, Ireland

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