Rational Design of Macrolides by Virtual Screening of Combinatorial Libraries Generated through in Silico Manipulation of Polyketide Synthases

Abstract

Bacterial secondary metabolites display diverse biological activities, thus having potential as pharmacological agents. Although most of these compounds are discovered by random screening, it is possible to predict and re-design their structures based on the information on their biosynthetic pathways. Biosynthesis of macrolides, governed by modular polyketide synthases (PKS), obeys certain rules, which can be simulated in silico. PKS mode of action theoretically allows for a huge number of macrolides to be produced upon combinatorial manipulation. Since engineering of all possible PKS variants is practically unfeasible, we created Biogenerator software, which simulates manipulation of PKS and generates virtual libraries of macrolides. These libraries can be screened by computer-aided prediction of biological activities, as exemplified by analysis of erythromycin and macrolactin libraries. This approach allows rational selection of macrolides with desired biological activities and provides instructions regarding the composition of the PKS gene clusters necessary for microbial production of such molecules.

Antibacterial Compounds-Macrolactin Alters the Soil Bacterial Community and Abundance of the Gene Encoding PKS

“…Macrolactins are a large group of macrolide antibiotics with a 24-member lactone ring first discovered in a marine Bacillus (Gustafson et al, 1989). Macrolactin showed numerous properties such as inhibiting the proliferation of cancer cells, a protective effect on T-lymphocyte from an HIV infection due to the phosphatase inhibitory activity (Gustafson et al, 1989), anti-inflammatory activity towards colon epithelial cells, and the inhibition of cell division by the reduction of the H + -transporting two-sector ATPase, which is essential for the viability of bacterial cells (Romero-Tabarez et al, 2006; Zotchev et al, 2006; Park et al, 2014). Recently, its biocontrol activity to suppress many bacterial pathogens has been reported (Arguelles-Arias et al, 2009; Chen et al, 2009; Wang et al, 2012; Yuan et al, 2012a).…”

Marine Drugs – Macrolactins

“…The PKS system is a primary and important element of the biosynthetics of macrolides. Macrolactins structurally belong to the macrolides, so it is assumed that macrolactins may assemble by PKS like macrolides [19]. The macrolactone rings of macrolides are formed via cyclization of polyketide chains assembled by the PKS type-I enzymes that perform repetitive decarboxylative condensations of carboxylic acids with an activated carboxylic acid starter unit [20].…”

“…The macrolactone rings of macrolides are formed via cyclization of polyketide chains assembled by the PKS type-I enzymes that perform repetitive decarboxylative condensations of carboxylic acids with an activated carboxylic acid starter unit [20]. On the basis of the PKS system, Zotchev et al [19] used PASS/PharmaExpert software to speculate on the antibacterial activity of macrolactins that it could be due to the inhibition of the H þ -transporting two-sector ATPase, which is essential for viability of bacterial cells. Antiviral activities of macrolactins could probably be attributed to the phosphatase inhibitory activity, and certain protein phosphatases were involved in regulation of HIV transcription.…”

ClustScan : an integrated program package for the semi-automatic annotation of modular biosynthetic gene clusters and in silico prediction of novel chemical structures

“…Another application of the new sequences is to use them to construct new polyketides based on known modules in silico ; i.e. use them as input for a program such as the Biogenerator program (35). ClustScan will help eliminate the bottleneck posed by the annotation of DNA sequences and allow the full utilization of the rapidly increasing DNA sequence data.…”