SE5:E2: The Macrocyclic Mullet

Part 1 laid out the strategy. Now, it’s time to make the molecule. Four enzymes, one vessel, and plenty of competing amines. What could possibly go wrong? Dani and LC return with Stephanie Galanie, Director in Biocatalysis, and Artis Klapars, Distinguished Scientist in Process Chemistry, for a closer look at the chemistry behind MK-0616 manufacturing. We start with the northern fragment, where making three bonds selectively means getting four engineered enzymes to play well together, ATP recycling included. Then we tackle fragment ligation with an evolved thioesterase and a hydrogen-borrowing cascade that closes a macrocycle. How do you drive an uphill reaction toward completion? And why would you start engineering an enzyme with the “wrong” substrate? Stephanie and Artis explain the solutions behind the synthesis. Finally, traditional coupling chemistry gets its moment alongside enzymatic macrocyclization, and a “counterion dance” gets MK-0616 out of solution in the right purity and salt form. We wrap up with what it takes to turn ambitious chemistry into a manufacturing process, and why protecting-group-free fragment coupling, concentrated macrocyclizations, and crystallization could change how we make complex peptides.

How do you design a manufacturing process for a molecule as complex as MK-0616? In Part 1 of this Pharm to Table series, Dani and LC join Stephanie Galanie, Director in Biocatalysis, and Artis Klapars, Distinguished Scientist in Process Chemistry, to discuss the manufacturing route behind their Science paper on biocatalytic cascades for this macrocyclic peptide. We start with a central question: why develop a new synthesis when an existing route already delivers hundreds of kilograms? Artis and Stephanie explain how the team worked backward from MK-0616’s complex structure to choose key disconnections, then developed three interconnected cascades to assemble it. Along the way, we unpack the tools behind those decisions, including directed evolution and enzymes that selectively form amide bonds without relying on protecting groups. Part 2 takes us inside the cascades, from four enzymes working in one vessel to fragment ligation and macrocyclization, then tackles the final challenge: isolating MK-0616 in the right purity and salt form. Read some of the papers we discussed today: Biocatalytic cascades enable manufacture of the macrocyclic peptide MK-0616 - ⁠Science⁠ More on Pharm to Table Follow the Pharm to Table podcast on X - ⁠⁠⁠⁠@PharmtoTablePod ‘Pharm to Table’ podcast duo bridges the academia-industry divide' - C&EN Should You Start a Chemistry Podcast? - Organic Letters The Future of Science Communication - ACS BrandLab ⁠⁠⁠⁠Visit our website at ⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠https://podcasters.spotify.com/pod/show/pharm-to-table⁠⁠⁠⁠⁠⁠

Last episode, we watched medicinal chemistry dream up enclitide (MK-0616) — this week we find out what happens when someone actually has to make it. Dani and LC are joined by David Thaisrivongs and Gao Shang to unpack their recent JACS paper on the total synthesis of enlicitide, a macrocyclic peptide complex enough to keep company with taxol, vancomycin, and eribulin. Along the way they get into the pivot from solid-phase to solution-phase peptide synthesis, the perpetual headache of sourcing non-canonical amino acids and how biocatalysis cracked it open, and the crystallization detective work that let the team ditch chromatography entirely. There's also a great discussion on why a late-stage macrolactamization became a late-stage RCM — the kind of route decision that looks obvious only in hindsight. Fair warning: this one was among JACS's top-accessed papers of 2025, so you're in good company! If you enjoyed this chapter of the enlicitide story, stay tuned—we've got plenty more peptide chemistry, process development adventures, and behind-the-scenes drug discovery stories coming your way this season.

To kick off Season 5, Dani and LC discuss a recent perspective published in the Journal of Organic Chemistry that highlights innovations in synthetic chemistry which trace their origins to the work of discovering, developing and commercializing novel therapeutics. This publication was the most accessed paper published in JOC in 2025! Dani and LC explore the motivations on writing it, its main thesis and lesson learned from reexamining nearly 75 years of chemistry innovations at Merck. Be sure to listen through to the very end for a special Season 5 theme reveal!

In Part 2 of our Pharm to Table deep dive on MK‑7845, Dani and LC shift from invention to implementation, welcoming process chemists Nastaran Salehi Marzijarani and Ben Turnbull to the pod. We explore how the team re‑imagined the synthesis to enable robust, scalable supply—and why a classic multicomponent reaction you probably remember from school, the Joullié–Ugi reaction, ended up stealing the show. Along the way, we unpack route selection trade‑offs, lifecycle thinking in process chemistry, and what it really takes to bring an antiviral to life at scale. Read and listen to some of the papers we discussed today: Asymmetric Synthesis of MK-7845, an Investigational Treatment for COVID-19 - Org. Lett. Part 1 of MK-7845 series: SE4:E7: From Discovery to Process, Part 1: Building a 3CL Protease Inhibitor Through Smart Fluorine Placement and Design Intuition