Applied Chemoinformatics

Achievements and Future Opportunities

Thomas Engel, Johann Gasteiger, Thomas Engel, Johann Gasteiger

• Publisher: Wiley-VCH
• Year: 2018
• ISBN:
  9783527806546
• Edition: 1
• Topic: Physical Sciences
• Subtopic: Physical & Theoretical Chemistry

Edited by world-famous pioneers in chemoinformatics, this is a clearly structured and applications-oriented approach to the topic, providing up-to-date and focused information on the wide range of applications in this exciting field.
The authors explain methods and software tools, such that the reader will not only learn the basics but also how to use the different software packages available. Experts describe applications in such different fields as structure-spectra correlations, virtual screening, prediction of active sites, library design, the prediction of the properties of chemicals, the development of new cosmetics products, quality control in food, the design of new materials with improved properties, toxicity modeling, assessment of the risk of chemicals, and the control of chemical processes.
The book is aimed at advanced students as well as lectures but also at scientists that want to learn how chemoinformatics could assist them in solving their daily scientific tasks.
Together with the corresponding textbook Chemoinformatics - Basic Concepts and Methods (ISBN 9783527331093) on the fundamentals of chemoinformatics readers will have a comprehensive overview of the field.

Chapter 1
Introduction

Thomas Engel¹ and Johann Gasteiger²

¹Ludwig-Maximilians-University Munich, Department of Chemistry, Butenandtstr. 5 - 13, 81377 Munich, Germany

²Computer-Chemie-Centrum, Universität Erlangen-Nürnberg, Nägelsbachstr. 25, 91052 Erlangen, Germany

1. 1.1 The Rationale for the Books
2. 1.2 Development of the Field
3. 1.3 The Basis of Chemoinformatics and the Diversity of Applications

1.1 The Rationale for the Books

In 2003 we issued the book

Chemoinformatics: A Textbook

(J. Gasteiger, T. Engel, Editors, Wiley-VCH Verlag GmbH, Weinheim, Germany, ISBN 13: 978-3-527-30681-7)

which was well accepted and contributed to the development of the field of chemoinformatics. However, with the enormous progress in chemoinformatics, it is now time for an update. As we started out on this endeavor, it became rapidly clear that all the developments require presenting the field in more than a single book. We have therefore edited two volumes:

• Chemoinformatics – Basic Concept and Methods [1]
• Applied Chemoinformatics – Achievements and Future Opportunities

In the first volume, “Basic Concept and Methods,” the essential foundations and methods that comprise the technology of chemoinformatics are presented. The links to this first volume are referenced in the present volume by “Methods Volume.”

The Application Volume – tagged as shortcut in the first volume – emerged from the single “Applications” chapter of the 2003 textbook. The fact that applications now merit a book of their own clearly demonstrates how enormously the field has grown. Chemoinformatics has certainly matured to a scientific discipline of its own with many applications in all areas of chemistry and in related fields.

Both volumes consist of chapters written by different authors. In order to somehow ensure that the material is not too heterogeneous, we have striven to adapt the contributions to an overall picture and inserted cross-references as mentioned above. We hope that this helps the reader to realize the interdependences of many of the methods and how they can work together in solving chemical problems.

Both volumes are conceived as textbooks for being used in teaching and self-learning of chemoinformatics. In particular, the first, “Methods Volume,” is addressed to students, explaining the basic approaches and supporting this with exercises. Altogether, we wanted to present with both books a comprehensive overview of the field of chemoinformatics for students, teachers, and scientists from all areas of chemistry, from biology, informatics, and medicine.

1.2 Development of the Field

We are happy to see – and demonstrate within this book – that chemoinformatics has ventured into and found applications in many fields other than drug discovery. Drug discovery is still the most important area of application of chemoinformatics methods (Chapter 6), but we expect that the other fields of applications will continue to grow.

Some comments on terminology are appropriate. The varying use of the terms chemoinformatics and cheminformatics seems to indicate a geographical (or perhaps cultural) divide, with “cheminformatics” mainly used in the United States and “chemoinformatics” originating and more widely used in Europe and the rest of the world.

Chemometrics is a field that originated in the early 1970s and is mainly associated with analytical chemistry, as is shown in Chapter 9. The two fields, chemometrics and chemoinformatics, have borrowed heavily from each other and use many of the same methods. As chemoinformatics has a much broader focus, it is fair to consider the data analysis methods in chemometrics as a part of chemoinformatics.

Molecular informatics has appeared as a term, but this is certainly too narrow a name to cover all potential chemoinformatics applications, as many tasks in chemistry deal with compounds and materials that are not limited to or cannot be identified with single molecular structures. The applications in materials science, presented in Chapter 12, are a case in point, as are the applications in process control illustrated in Chapter 13.

More fortunate developments have brought chemoinformatics closer together with other disciplines. The borders between chemoinformatics and bioinformatics are becoming quite transparent. Some important and challenging tasks in drug design, and cosmetics development, and in trying to understand living systems need approaches from both fields. We have taken account of this with Section 4.3 on biochemical pathways; Section 6.2 on drugs, targets, and diseases; and Chapter 11 on computational approaches in cosmetics products discovery.

In a similar manner, many tasks faced in chemistry and related fields are tackled by methods of both chemoinformatics and computational chemistry, thus blurring the borders between the two disciplines. We indicate the combined utilization of chemoinformatics and computational chemistry in Chapter 5 on structure–spectra correlations and computer-assisted structure elucidation (CASE), in Chapter 7 on computational approaches in agricultural research, and in Chapter 11 on computational approaches in cosmetics products discovery. Furthermore, the basic concepts of computational chemistry are described in Chapter 8 of the Methods Volume [1].

It is exciting to see that the use of computers in chemistry, by methods both of chemoinformatics and of computational chemistry, has gained more widespread recognition. This culminated in the awarding of the Nobel Prize in Chemistry in 2013 to Martin Karplus, Michael Levitt, and Arieh Warshel. The Swedish Academy of Sciences motivated its decision by stating:

“Today the computer is just as important a tool for chemists as the test tube.”

(https://www.nobelprize.org/nobel_prizes/chemistry/laureates/2013/press.html)

1.3 The Basis of Chemoinformatics and the Diversity of Applications

We were fortunate to gain many excellent scientists to demonstrate the various applications of chemoinformatics in chemistry and related fields by writing chapters for this book, but it should be emphasized from the very beginning that these applications are, by no means, all of the established or possible applications: the field is still expanding and growing.

1.3.1 Databases

Probably the most important achievement of chemoinformatics is the building of databases on chemical information. The development of chemoinformatics technologies made it possible to store and retrieve chemical information in a variety of databases. Interaction with these databases can be made by the international language of the chemist that is graphical in nature: structure diagrams and reaction equations. Databases are so routinely used in chemical research that it seems to have been forgotten that their construction was only possible by the work and developments by chemists, mathematicians, and computer scientists in the decades from 1960 to 1990. The building of databases on chemical information is presented in Chapter 6 of the Methods Volume [1]. In the present volume the exploitation of these databases will be shown in a variety of applications presented in the chapters.

Without these databases an overview of chemical information, which has grown enormously in recent decades, could not be maintained anymore. It is fair to say that modern chemical research can nowadays not be done without consulting databases on chemical information.

1.3.2 Fundamental Questions of a Chemist

In structuring the presentation of the applications of chemoinformatics methods, we were motivated by th...