Narayan Lab @ UMich

CATNIP for chemists: New data-driven tool broadens access to greener chemistry University of Michigan and Carnegie Mellon University researchers have developed a new tool that makes greener chemistry more accessible.

Camille Dreyfus Teacher-Scholar Alison Narayan (Alison Narayan, Narayan Lab @ UMich, University of Michigan) and colleagues have developed "a new tool that makes greener chemistry more accessible."

https://news.umich.edu/catnip-for-chemists-new-data-driven-tool-broadens-access-to-greener-chemistry/

A round of applause for the amazing Dr. José!!! The P450 and non-heme king is moving on and we are so excited to watch you succeed!!! 👑

#GoBlue #Biocats @joserhm.bsky.social

Uncovering the Origins of Selectivity in Non-Heme Iron Dioxygenase-Catalyzed Tropolone Biosynthesis Non-heme iron (NHI) enzymes perform diverse oxidative transformations with precise control, which can be challenging to achieve with small molecule catalysts, such as the biosynthesis of tropolone. Among them, Anc3, a reconstructed ancestral α-ketoglutarate (α-KG)-dependent NHI dioxygenase, catalyzes a ring-expansion in fungal tropolone biosynthesis from a cyclohexadienone to afford the tropolone natural product stipitaldehyde (ring-expansion product) alongside 3-hydroxyorcinaldehyde (shunt product). This study reveals how the enzyme environment guides the reaction to the ring-expansion product preferably over the shunt product, where the precise selectivity ratio depends on just a handful of Anc3 residues. In particular, molecular dynamics (MD) and quantum mechanical/molecular mechanical (QM/MM) simulations describe how the substrate binds within the NHI active site and can proceed through two distinct mechanisms, ring-expansion or rebound hydroxylation, to yield the two experimentally observed products. Discovery of a linear relationship of ΔEa values and hydrogen bond distances between Arg191 and the Fe(III)–OH group reveals that inhibition of the rebound hydroxylation step increases selectivity toward ring-expansion. Our findings suggest that the rebound hydroxylation rate is further tuned through the Fe(III)–OH bond strength, as influenced by specific secondary sphere coordination effects around the active site. These influences are largely orthogonal to the ring-expansion mechanism, which is shown to prefer to proceed through a radical pathway. In addition, a cationic pathway initiated by electron transfer from substrate to iron is shown to be unfavorable based upon thermodynamic considerations. Altogether, the atomistic details and reaction mechanisms delineated in this work have the potential to guide the tuning of the reaction pathway in related NHI enzymes for selective oxidation reactions.

Uncovering the Origins of Selectivity in Non-Heme Iron Dioxygenase-Catalyzed Tropolone Biosynthesis

doi.org/10.1021/acs....

Ancestral Sequence Reconstruction to Accelerate Non-heme Iron-dependent Biocatalyst Engineering Nature provides access to biological catalysts that can expand the chemical transformations accessible to synthetic chemists. Among these, α-ketoglutarate, non-heme iron-dependent (NHI) enzymes stand out as scalable biocatalysts for catalyzing selective oxidation reactions. Many NHI enzymes require protein engineering to improve their activity, selectivity, or stability. However, the reliance of this strategy on the innate stability of the enzyme can thwart the success of the engineering campaign. Harnessing innately stable enzymes can overcome these challenges and accelerate biocatalyst engineering. Herein, we highlight the use of ancestral sequence reconstruction (ASR) to mine for thermostable enzymes that can serve as superior starting points for protein engineering. In our effort to develop a biocatalytic route to tropolones, we identified an NHI enzyme that demonstrated poor stability, diminished activity at high substrate concentrations, and a limited substrate scope. We compared the in-lab evolution of the modern NHI enzyme and its ancestor, demonstrating the improved evolvability profile of the latter. By engineering the ancestral protein, we accessed variants with enhanced thermostability and expression, increased rates, and a substrate scope broader than those of their modern counterparts. Altogether, this work provides a strategy to rapidly access enzyme backbones that can accelerate engineering of more robust and synthetically useful NHI enzymes.

Check out our work utilizing ancestral sequence reconstruction to accelerate protein engineering! @joserhm.bsky.social

doi.org/10.1021/acsc...

CATNIP for the win! Read our newest work with the Gomes group- doi.org/10.1038/s415...

@gabegomes.bsky.social @alisonnarayan.bsky.social @aepaton.bsky.social

Profiling of Diverse Pyridoxal-5′-Phosphate Dependent Enzymes Reveals Promiscuous Aldolase Activity with (2-Azaaryl)methanamines The elaboration of amine substrates through C–C bond-forming reactions is important in the synthesis of bioactive small molecules. Pyridoxal-5′-phosphate (PLP)-dependent enzymes have emerged as valuable biocatalysts for this class of reactions, due to their high stereoselectivity and ability to forge new C–C bonds on unprotected α-amino acid substrates. However, the use of abiological primary amines as pronucleophiles with enzymes such as threonine aldolase has been unexplored, moderating the utility of a biocatalytic approach in the synthesis of diverse 1,2-amino alcohols. In this report, we disclose the discovery and engineering of a PLP-dependent aldolase that accepts (2-azaaryl)methanamines in an aldol-type transformation. The 1,2-amino alcohol products generated, which contain representative heteroaromatic pharmacophores, are delivered with control over both the diastereoselectivity and enantioselectivity in the C–C bond-forming event. Protein engineering provided variants with improved binding affinity for the abiological substrate and decreased affinity for the native α-amino acid, overcoming inhibition of the abiotic reaction by components of lysate, a major challenge in reaction discovery with PLP-dependent enzymes such as threonine aldolases. This work represents the first known example of C–C bond formation on nonamino acid substrates with threonine aldolase and provides a platform for further development of complexity-building biocatalytic reactions with abiotic amine substrates.

I'm very excited to share the newest publication from team PLP. I've been working with this PLP library since my summer rotation in 2021 and it's so exciting to see the first paper finally out! #PLProud @narayanlab.bsky.social
pubs.acs.org/doi/10.1021/...

Site-, Stereo-, and Chemoselective Enzymatic Halogenation of Terpenoids by a Substrate Masquerade Enzymatic halogenation of C–H bonds is a promising approach to synthesize chlorine-containing compounds. However, few halogenases chlorinate C(sp3)–H bonds of molecules lacking a carrier protein, and ...

This is such a neat idea from the @narayanlab.bsky.social and the @hartwiggroup.bsky.social now in #JACSasap fooling enzymes with a removable binding ligand to accept non-native substrates #ChemSky

Abstract representation of the connections between chemical space and protein space

A team from @umich.edu and @cmu.edu has developed CATNIP for chemists — a data-driven open-access platform that removes a major barrier to wider adoption of #biocatalysis, making greener chemistry more accessible.
Read more: myumi.ch/dgp2Z
@narayanlab.bsky.social
@alisonnarayan.bsky.social

Congrats to our newest doctor Anthony!!! so proud of our tropolone king 👑

#GoBlue #Biocats #Chemsky

The Narayan lab birthday elves struck again! Happy 16th birthday @alisonnarayan.bsky.social ! 🥳

#Sweet16 #Biocats #GoBlue

Ryan passed his candidacy exam! PLP for the win 🤩

#Biocat #GoBlue

Yesterday our PLP queen became a PhD candidate! Congratulations Maddie on a fantastic gateway exam!

#PLP #Biocats #GoBlue

Congratulations to our new PhD candidate Caroline! The Mapp and Narayan labs are so proud of you!

#Biocat #GoBlue @annamapp.bsky.social @alisonnarayan.bsky.social @umlifesciences.bsky.social

The application deadline has been extended to April 11th! For more information on the workshop look here - sites.google.com/umich.edu/cc...

Today is the last day to apply!

#Biocats #GoBlue

Chemists create matchmaking app for biocatalysis Machine learning model Catnip helps chemists find biocatalysts to try in synthesis

Excited to share this article from @cenmag.bsky.social! Such a nice highlight of the work we've been doing between @narayanlab.bsky.social and @gabegomes.bsky.social

cen.acs.org/acs-news/acs...

Calling everyone interested in learning biocatalysis! Come to the Narayan lab to learn the biocat basics. Please apply here - docs.google.com/forms/d/e/1F...

#Biocat #GoBlue

🚨New merch Friday🚨

Our newest PhD candidate! Congratulations Jolie on your amazing work!

#Biocats #Flavinista #GoBlue

We are a lab full of musicians 🎤

Tomorrow is our last day of spirit week! Stay tuned for our new Narayan lab merch …

WIGS !!!

See you tomorrow for favorite musician Thursday!

We have the Michigan spirit! 〽️ 〽️〽️

Wig Wednesday is up next …

Comfy Monday was a success! Excited for Michigan Tuesday today 〽️

This week marks the first annual Narayan Lab spirit week! Join us in the fun leading up to our new merch for this year!

#Biocats #GoBlue

Congratulations to our new PhD candidate @umax-umich.bsky.social ! We are so excited to see all of your amazing work 🥳

#Biocat #GoBlue