Inhibitors of Polyhydroxyalkanoate (PHA) Synthases: Synthesis, Molecular Docking, and Implications

Abstract

Polyhydroxyalkanoate (PHA) synthases (PhaCs) catalyze the formation of biodegradable PHAs that are considered as an ideal alternative to nonbiodegradable synthetic plastics. However, study of PhaC has been challenging because the rate of PHA chain elongation is much faster than that of initiation. This difficulty along with lack of a structure has become the main hurdle to understand and engineer PhaCs for economical PHA production. Here we reported the synthesis of two carbadethia CoA analogs, sT-CH2-CoA 26a and sTet-CH2-CoA 26b as well as sT-aldehyde 29 as new PhaC inhibitors. Study of these analogs with PhaECAv revealed that 26a/b and 29 are competitive and mixed inhibitors, respectively. It was observed that CoA moiety and PHA chain extension can increase binding affinity, which is consistent with the docking study. Estimation from Kic of 26a/b predicts that a CoA analog attached with an octameric-HB chain may facilitate the formation of a kinetically well-behaved synthase.

Polyhydroxyalkanoate (PHA) Production in Pseudomonas sp. phDV1 Strain Grown on Phenol as Carbon Sources

“…However, a frame shift is detected in its coding region probably due to a sequencing error (GenBank accession number: CP031606.1, locus tag: DZC76_02275) [ 12 ]. PHA synthase are grouped into four classes based on substrate specificity, and their preference in forming short-chain-length (scl) or medium-chain-length (mcl) polymers: Class I, Class III and Class IV produce principally scl-PHAs, while Class II PHA synthase synthesize mcl-PHAs [ 18 , 19 ]. A recent comprehensive analysis of the proteome of Pseudomonas sp.…”

Role of PhaC Type I and Type II Enzymes during PHA Biosynthesis

“…possessing Class II PHA polymerizing enzymes. PhaC synthases are grouped into four classes based on substrate specificity, and the preference in forming short-chain-length (scl) or medium-chain-length (mcl) polymers: Class I, Class III and Class IV produce principally scl-PHAs, while Class II PhaC synthesize mcl-PHAs [7,15].…”

“…Class III PHA synthases are made of two subunits, namely, a catalytic subunit PhaC (40–53 kDa) and a second subunit PhaE (ranging from 20 to 40 kDa), which form the PhaEC complex, in which the PhaE subunit is necessary for PHA polymerization. Class III PhaC are structured as tetramers, such as phaEC from Chromatium vinosum (with catalytic triad Cys 149 , Asp 302 , His 331 ), whose enzyme activity has been studied using substrate analogs [15]. The authors performed molecular docking and in-silico studies that are in agreement with the crystal structure of synthases available [15], based on homology models built using CPHmodels3.0, SWISS-MODEL and I-TASSER, performing structure-guided sequence profiles.…”

“…Class III PhaC are structured as tetramers, such as phaEC from Chromatium vinosum (with catalytic triad Cys 149 , Asp 302 , His 331 ), whose enzyme activity has been studied using substrate analogs [15]. The authors performed molecular docking and in-silico studies that are in agreement with the crystal structure of synthases available [15], based on homology models built using CPHmodels3.0, SWISS-MODEL and I-TASSER, performing structure-guided sequence profiles. The results of their analysis, referring to PhaC Cn and PhaC Class III from Chromatium vinosum , describe the presence of an active site of cysteine that is buried in a pocket.…”

“…The results of their analysis, referring to PhaC Cn and PhaC Class III from Chromatium vinosum , describe the presence of an active site of cysteine that is buried in a pocket. The authors, by comparison with other enzymes with known crystal structures (lipases), postulated the presence of the substrate-entrance and product-exit channels [15].…”