Natural diversity library

Because of their ease of synthesis and their structural similarity to peptides, many laboratories have used peptoids as the basis for combinatorial drug discovery. Peptoids were among the first non-natural compounds used to establish the basic principles and practical methods of combinatorial discovery [17]. Typically, diverse libraries of relatively short peptoids (< 10 residues) are synthesized by the mix-and-split method and then screened for biological activity. Individual active compounds can then be identified by iterative re-synthesis, sequencing of compounds on individual beads, or indirect deduction by the preparation of positional scanning libraries. 

While in the recent past it was extremely difficult, time consuming and labour intensive to build such a library from purified natural products, with the advent of newer and improved technologies related to separation, isolation and identification of natural products the situation has improved remarkably. Now, it is possible to build a high quality and chemically diverse natural product library that can be suitable for any modern HTS programmes. Natural product libraries can also be of crude extracts, chromatographic fractions or semi-purified compounds. However, the best result can be obtained from a fully identified pure natural product library as it provides scientists with the opportunity to handle the lead rapidly for further developmental work, e.g. total or partial synthesis, dealing with formulation factors, in vivo assays and clinical trials. 

Directed evolution is an iterative process that mimics the natural evolution process in vitro, by generating a diverse library of enzymes and selecting those with the desired features. Natural evolution is very effective in the long term (bacteria adapt to every environment, living even in so-called black smokers, deep-ocean vents where temperatures can reach 350°C and the pressure is 200bar [93]). Unfortunately, it typically takes millions of years. Happily, directed evolution can be carried out within weeks or months and with an unlimited number of parents. Importantly, and unlike rational design, directed evolution is a stochastic method. It does not require any structural or mechanistic information on the enzyme of interest (although such information can help). 

Nitrilases (E.C. 3.5.5.1) promote the mild hydrolytic conversion of organonitriles directly to the corresponding carboxylic acids.19 However, less than 20 microbially derived nitrilases had been characterized at the start of this work, despite their potential synthetic value. The paucity of enzymes and the limited substrate scope of the handful of enzymes available have limited practical commercial development of nitrilase-catalyzed conversions, except in a few cases. Accordingly, we engaged in a discovery effort centered around exploiting the natural diversity available within our environmental DNA libraries and have discovered and characterized more than 200 new sequence unique nitrilases.20 All of the newly discovered nitrilases possess the conserved catalytic triad Glu-Lys-Cys that is characteristic for this enzyme class.19... 

The preparation of prefractionated natural product libraries for drug discovery can be made more efficient by automation. Automation reduces manpower requirements, improves efficiency and increases productivity. In addition, human errors are reduced and reproducibility is improved. Overall, automation increases throughput and can produce larger and more diverse screening libraries. 

In terms of HTS campaigns, there has been a move toward screening purified natural products libraries.6,7 Although more chemical diversity can be sampled from crude extract libraries or partially purified natural product libraries, pure... 

Figure 3.7 Potential coupling sites on a natural product-related core-based diversity library. (Reprinted from [25] with permission, copyright 1999, American Chemical Society).

The first success was demonstration in 1994, with the report of a large, diverse library of decapeptides displayed and selected while associated with E. coli S30 polysomes and RNA.262 The key to Dower s success was the application of natural product antibiotics that were known to interfere with protein synthesis by stabilizing the ribosome-mRNA-protein complex. Thus, rifampicin and chloramphenicol (for prokaryotic system) or cycloheximide (for eukaryotic system) were used.2 3 Because these antibiotics halt the translation at random locations, the ensuing libraries were composed of mostly truncated peptides and thus not really suitable for the generation of cDNA libraries. Later, removal of the stop codon from mRNA was used to stall the translation at the end of the mRNA.264,265 Several improvements have been made more recently to stabilize the... 

Products/technologies The company has diverse libraries of natural compounds prepared from plant, fungal, and microbial sources and proprietary... 

To synthesize highly diverse libraries, carrying more than six degenerated sequence positions (X), several methods using premixed mixtures of amino acids for the introduction of X positions in the sequence have been described [12]. Obviously, the frequency of each amino acid in a X position is influenced by the composition of the premixed amino acid mixture, the chemistry applied for coupling as well as by the nature of the solid support. The synthetic peptide libraries have been analyzed by electrospray mass spectrometry and pool sequencing [13,14]. Due to their stoichiometry, peptides from extremely diverse combinatorial collections are only partially accessible for biological assays [12]. 

Libraries used for lead finding are, by nature, diverse, but screening places the added demand that this diversity be describable we need to be able to register and store a variety of characteristics associated with each individual compound, as well as collate chemical and biological information. Not only is it necessary to keep track of each compound, the... 

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