Computations by Professor Kendall Houk and his group decipher rare enzymatic cope rearrangement

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The Houk group has elucidated how a novel enzyme catalyzes a reaction that was heretofore known only in the lab and not known to happen in nature.

They used computations to figure out the mechanism and basis for chemoselectivity of an unusual enzyme known as a Stig cyclase. Working in collaboration with the experimental group of Professor David Sherman at the University of Michigan, a team of computational chemists in the Houk group explored the various ways this reaction might happen. Their work, published in Nature Chemical Biology, combines X-ray crystallography and enzymatic assays performed in the Sherman group with state-of-the-art quantum mechanical computations and molecular dynamics simulations performed in the Houk group by postdoctoral researchers Dr. Marc Garcia-Borras and Dr. Jacob N. Sanders and graduate student Song Yang.

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Professor Kendall Houk, Dr. Marc Garcia-Borras, Dr. Jacob N. Sanders, and Song Yang.

Stig cyclases, which catalyze the biosynthesis of antibacterial and antifungal natural products known as hapalindole alkaloids, are part of a growing class of enzymes known as pericyclases, a term coined by Houk and collaborator Yi Tang, Professor of Chemical and Biomolecular Engineering and also Chemistry and Biochemistry. These enzymes catalyze pericyclic reactions, a class of organic reactions whose computational study the Houk group has pioneered for decades. While pericyclic reactions were previously considered rare in living systems, they are now being discovered with increasing frequency. The most well-known pericyclase is chorismate mutase, an enzyme that catalyzes a pericyclic reaction known as the Claisen rearrangement, in the biosynthesis of the amino acids phenylalanine and tyrosine. Stig cyclases are the first known enzymes to catalyze a related pericyclic reaction known as the Cope rearrangement.

Guided by state-of-the-art quantum mechanical computations, the Houk group discovered that Stig cyclase HpiC1 accelerates the Cope rearrangement via acid catalysis provided by an aspartic acid residue in the enzyme active site.  In addition, the Houk group used molecular dynamics simulations to identify the key amino acids that play a critical role in the subsequent steps of the enzymatic pathway, controlling the structure of the core ring system and precise stereochemistry of the final product that is formed.

Because hapalindoles have attractive biological properties, future collaboration between the Houk group and the Sherman group involves developing Stig cyclases into an enzymatic platform to synthesize related natural products with altered stereochemistry, different core ring systems, and varied functional groups.

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Snapshot from molecular dynamics simulations showing the substrate in the Stig cyclase enzyme active site.  As the snapshot shows, the active site maintains the substrate in an optimal near attack conformation for the Cope rearrangement, with C11 and C12 positioned to form a new bond (yellow dashed line) through a boat transition state.

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Snapshots from molecular dynamics simulations showing two different possible bond formation events (red dashed lines) in the reaction cascade that follows the Cope rearrangement. The identity of the amino acids in the active site can favor one bond formation event over the other, resulting in different core ring systems in the final product.

To learn more about the Houk group’s research, visit their website.