Development of functional protein microarrays for drug discovery: progress and challenges

Functional protein microarrays promise new approaches to address longstanding challenges in drug discovery and development, with applications ranging from target identification to clinical trial design. However, their widespread adoption will be contingent upon a robust ability to develop and manufacture arrays in support of these applications. This review will address the major areas of relevance to the development of functional protein microarrays; protein content, surface chemistry, manufacture and assay development. Successful development will empower multiple drug research applications, help fill future HTS pipelines and guide next generation combinatorial chemistry efforts.     

Leslie W. Tari (ed.): Structure-based drug discovery. Volume 841 in methods in molecular biology

Structural Chemistry -     

High-throughput protein crystallography and drug discovery

Single crystal X-ray diffraction is the technique of choice for studying the interactions of small organic molecules with proteins by determining their three-dimensional structures; however the requirement for highly purified protein and lack of process automation have traditionally limited its use in this field. Despite these shortcomings, the use of crystal structures of therapeutically relevant drug targets in pharmaceutical research has increased significantly over the last decade. The application of structure-based drug design has resulted in several marketed drugs and is now an established discipline in most pharmaceutical companies. Furthermore, the recently published full genome sequences of Homo sapiens and a number of micro-organisms have provided a plethora of new potential drug targets that could be utilised in structure-based drug design programs. In order to take maximum advantage of this explosion of information, techniques have been developed to automate and speed up the various procedures required to obtain protein crystals of suitable quality, to collect and process the raw X-ray diffraction data into usable structural information, and to use three-dimensional protein structure as a basis for drug discovery and lead optimisation.This tutorial review covers the various technologies involved in the process pipeline for high-throughput protein crystallography as it is currently being applied to drug discovery. It is aimed at synthetic and computational chemists, as well as structural biologists, in both academia and industry, who are interested in structure-based drug design.     

Flash vacuum pyrolysis (F.V.P.) of 1,2,4-benzotriazine derivatives

Flash vacuum pyrolysis of 3-methylsulfanyl-1,2,4-benzotriazine N-oxide, 3-methylsulfanyl-1,2,4-benzotriazine, and 3-phenyl-1,2,4-benzotriazine are described. The N-oxide derivative underwent deoxygenation between 500 and 600°C, whereas at higher temperatures both methylsulfanyl compounds, besides yielding the same products, also gave benzimidazole formed by an independent mechanism. Transformation of these derivatives between 600 and 750°C led to formation of a complex reaction mixture indicating the radical nature of the processes. The phenyl substituted derivative was studied between 575 and 650°C and afforded benzonitrile and traces of biphenylene.     

Functional nucleic acids in high throughput screening and drug discovery

In vitro selection can be used to generate functional nucleic acids such as aptamers and ribozymes that can recognize a variety of molecules with high affinity and specificity. Most often these recognition events are associated with structural alterations that can be converted into detectable signals. Several signaling aptamers and ribozymes constructed by both design and selection have been successfully utilized as sensitive detection reagents. Here we summarize the development of different types of signaling nucleic acids, and approaches that have been implemented in the screening format.