Length 170 pages

Date published March 2009

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Medicinal Chemistry for Drug Discovery: Significance of Recent Trends Overview


coverMedicinal Chemistry for Drug Discovery: Significance of Recent Trends

Author: Ken Rubenstein, PhD




A thorough analysis of recent trends in medicinal chemistry and evaluation of their significance for advancing productivity in drug discovery is presented. This report includes:

  • A critical evaluation of chemical and computational technological modalities, their current and potential value, and their commercial manifestations.
  • A consideration of market dynamics with an emphasis on outsourcing and user views on the implications of current practices in drug discovery organizations.
  • Insights gleaned from an extensive literature review, discussions with industry experts, and an opinion survey of personnel active in medicinal chemistry for drug discovery.

Medicinal Chemistry for Drug Discovery: Significance of Recent Trends reviews the state of the art and aims to determine the significance of technology and market trends in medicinal chemistry for advancing productivity in drug discovery. Although the fundamental task of medicinal chemists has not changed drastically over time, the chemical and computational tools and perspectives at their disposal have advanced significantly. One in particular, fragment-based drug design, stands out as promising major improvements in research productivity.

We examine medicinal chemistry-related approaches and methodologies that drug discovery organizations employ in an effort to increase productivity in early drug discovery and decrease attrition at later pipeline stages. Key topics considered include structure-based drug design, fragment-based drug design, natural products-based drug design, diversity-oriented synthesis, and chemogenomics. An overall assessment of the current and potential value of these approaches is presented. Various flavors of computer-aided drug design are also considered, as the complexity and limitations of drug discovery programs that are based on biochemical screens of large compound collections have been major factors in stimulating the growth of this modality.


Each of the aforementioned technological modalities is viewed in terms of practical examples and commercial activity. Outsourcing arises as a prominent theme in the applications realm, with special emphasis on companies with primary operations in countries with developing economies, notably China, India, and Russia. Among 32 companies considered, structure-based drug design is the most prevalent activity with most players emphasizing the fragment-based variation. Virtual screening is the second-most prevalent modality, whereas natural products, diversity-oriented synthesis, and chemogenomics appear in only a small minority of cases.

Outsourcing vendors are viewed according to participation in hit discovery, hit-to-lead synthesis, lead optimization, library synthesis, in-house drug discovery, and virtual drug design. More than one-third of the companies considered have operations primarily located in countries with emerging economies. A large majority of companies offer computer-based services, hit-to-lead, lead optimization, and library synthesis. Fewer engage in hit discovery, and a small minority do their own drug discovery.

Medicinal Chemistry for Drug Discovery: Significance of Recent Trends next examines deal activity and the influence of outsourcing on research productivity. Results from a survey of managers and researchers active in the field provide a multifaceted picture of practices and attitudes prevalent in drug discovery organizations today. Conclusions from the user survey highlight which modalities are viewed as having greater potential to make an impact on productivity. Finally, the complete transcripts of seven interviews with experts in the field are provided.

About the Author:Ken Rubenstein, PhD, a biochemist and molecular biologist, received his PhD at the University of Wisconsin and postdoctoral training at the University of Pennsylvania School of Medicine. He was a key innovator and research manager for Syva Company, the diagnostics branch of Syntex Corporation. During his 13 years with Syva, Dr. Rubenstein became vice president, scientific affairs, a function that included strategic planning. Since 1983, he has served as a technology and marketing consultant to biomedical companies and an industry analyst, with more than 40 published studies to his credit.