The role of combichem in antibiotic discovery - …

To demonstrate the efficacy of the method to identify novel antimicrobial compounds, a large naive combinatorial library was tested by using the modified method. An available library of triazines was chosen for its size and composition, as there was no evidence in the literature to suggest that triazines could function as antimicrobial agents (therefore the triazine library could be considered a “naive” library with respect to antimicrobial screening). The complete triazine library of 46,656 compounds (Fig. ) was chosen to test the concept of identifying active compounds among thousands of inactive compounds. For purposes of this study, the 36 pools of beads generated in the final round of synthesis were preserved as individual samples, meaning that each pool of 1,296 compounds has one building block in common (Fig. ). Antibacterial screening was performed on aliquots of the individual pools. For each of the 36 pools, more than one pool equivalent (1,400 to 1,900 beads; approximately 5 to 7 mg of beads) was screened for antibacterial activity by using the more sensitive format described above. GIZs, as shown in Fig. , appeared as white zones in contrast to the red lawn and are clearly associated with individual beads. As might be expected from the synthesis strategy and their common chemical signature, individual pools presented unique antibacterial qualities, as measured by the number and relative intensities of GIZs observed in each screen. For example, pool 25 revealed no strong GIZs (not shown) in contrast to pool 16, which had a few small well-defined GIZs (Fig. A), and pool 10, which generated numerous GIZs of various intensities (Fig. B).

The role of combichem in antibiotic discovery

Combinatorial synthesis — the design of compound libraries and their application to drug discovery

The role of combichem in antibiotic discovery.

Turning to the second method of identifying new antibiotics—mining orphan secondary metabolic pathways— Khosla explained that his group has used whole-genome sequencing and other technologies to identify close to 900 distinct assembly-line polyketide synthases, of which fewer than 20 percent have well-characterized substrates and products. To his knowledge, there is no ongoing large-scale effort to mine this family of polyketide assembly lines despite the fact that more than a dozen commercially important antibiotics come from the 20 percent of assembly lines that are well characterized and that make known molecules. His group has been developing techniques for refactoring these assembly-line pathways in heterologous hosts to produce novel compounds from glucose and propionic acid. In one project using such a system, Khosla’s team and collaborators from Kosan Biosciences were able to produce commercial quantities of the anticancer agent epothilone D within three years after this compound’s discovery.

initiating a ‘New Age of Antibiotic Discovery’

Looking to the future, Khosla said that it will one day be possible to engineer these assembly lines to make entirely new molecules, the third approach to antibiotic discovery. His group and others have developed a number of methods of engineering assembly-line polyketide biosynthetic pathways, but more work is needed to truly realize the promise of this approach. The main challenge to address is conceptual rather than technical, he explained. “We do not yet understand fully how these assembly lines work, and we certainly do not yet understand the structural basis for the modularity of these assembly lines,” he said. “Until we do, it is premature to predict where this approach will take us.”

Natural products possess a pedigree to justify quality and appreciation in drug discovery and development.
However, I'm stumped for a mnemonic to remember antibiotic spectrum of activity, so a list it must be.

Combinatorial Chemistry |authorSTREAM

In another example, of Scripps Research Institute Florida and , now at Dartmouth College, developed a way to synthesize chirally and conformationally constrained compounds resembling natural products made by bacterial polyketide synthase enzymes—a class of compounds that displays antibiotic and anticancer properties. And and coworkers at the University of Illinois, Urbana-Champaign, developed a way to start with actual natural products and chemically modify their rings and functional groups to create new molecules.

Preparation of Hydrazones and Discovery of an Antibiotic Compound using Combinatorial techniques .

Natural product-like combinatorial libraries - SciELO

One point raised during the discussion period was that when organisms are screened for the purpose of antibiotic discovery, they are often grown under benign conditions rather than in circumstances in which they might turn on orphan pathway or metabolic defense mechanisms and produce novel compounds. Shaw and others in the audience noted that it is becoming more common to add either various stimulatory compounds, such as lipopolysaccharide, or other organisms to the culturing system, but this has yet to be done in a sufficiently organized way to determine if that approach makes a difference in terms of the antibacterial compounds the organisms produce. Regarding this last point, Silver argued that bacteria have been waging war against each other for millions of years and that it is unlikely that experiments of this sort would yield anything that has not been identified already in natural product screens from soil and other bacterial environments.

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PPT - Combinatorial Chemistry PowerPoint …

Large encoded combinatorial libraries on beads present a major challenge to the assayer: how to screen thousands of compounds efficiently while maintaining separation of the beads. Jayawickreme et al. presented the first evidence that single-bead activity from peptides could be detected on acid-cleavable beads in a lawn format assay (). The work presented here demonstrates how we developed and implemented a system to simultaneously screen thousands of compounds against bacterial cells in a lawn assay. In a primary demonstration, penicillin V (PenV), a known antibiotic, was coupled to beads via a photolinker to test the concept and develop the method. Ultimately, a 36 × 36 × 36 (46,656-member) library of triazines was screened by using a two-dimensional (2D) agar-based whole-cell format, showing that the lawn-based format can be applied to large naive libraries as a first step in the application of combinatorial chemistry to antimicrobial lead discovery.