We asked the global drug discovery community to nominate and vote on their favorite molecule from 2023, and the results are in. The 2023 winner, with the most votes between ten molecules, is Merck’s oral macrocyclic peptide inhibitor of PCSK9, MK-0616, derived from mRNA display technology and shown to have clinical efficacy. Herein, we highlight what makes MK-0616 so impressive to the drug discovery community.

MK-1084 is an oral covalent inhibitor of KRAS(G12C) being developed by Merck (as part of a collaboration with Taiho and Astex), which is currently in a Ph. I trial (NCT05067283) for the treatment of solid tumors either as a monotherapy or in combination with their checkpoint inhibitor immunotherapy pembrolizumab (Keytruda™). The medicinal chemistry story was recently presented at the ACS Spring 2024 meeting in New Orleans, following a presentation of the Ph. I interim results by Merck at ESMO in Oct. 2023.

Nuvalent’s lead compound, NVL-520, is an oral, brain-penetrant, TRK-sparing, and potential best-in-class ROS1 kinase inhibitor that recently entered Ph. II of the ARROS-1 trial (NCT05118789) in patients with advanced ROS1-positive NSCLC. This article highlights what makes the Nuvalent’s NVL-520 program scientifically notable, including what gives it a potential best-in-class profile as a ROS1 inhibitor, the emerging toxicology of hard-to-avoid off-targets, an interesting synthetic route to the small macrocycle, and more.

LUNA18 is an orally bioavailable, cell-penetrant, macrocyclic peptide pan-RAS inhibitor (Chugai ’21Q3 earnings call) intended for the treatment of KRAS-mutant cancers. It disrupts the protein-protein interaction between KRAS and SOS, preventing RAS activation.

Merck’s macrocyclic PCSK9 protein-protein interaction (PPI) inhibitor, MK-0616, is a once-daily PCSK9-lowering and LDL-cholesterol-lowering small molecule that has recently demonstrated antibody-like efficacy as an oral agent in the clinic. The program highlights numerous technical achievements at the forefront of modern drug discovery, and will set a standard for modern “classics in drug discovery” for some time.

“Compound 6f” is a potent macrocyclic factor XIa inhibitor (<1 nM) that is highly selective against other serine proteases and has excellent oral PK (high bioavailability, low clearance). The BMS team was able to troubleshoot metabolic instability through met. ID, which revealed a hotspot outside of the macrocycle.

Overview. Cyclin-dependent kinase ( CDK2 ) is a target of recent interest , but selectivity has been challenging to obtain. This molecule provides an interesting example of AI being applied to lead generation. Macrocycles can be challenging to design rationally, but can lead to a variety of favorable properties (e.g. in addressing resistance [...]

In 2022, Turning Point Therapeutics ($TPTX) was acquired by BMS for a whopping $4.1 billion in cash. In November 2023, the most advanced molecule from Turning Point, repotrectinib, was approved for the treatment of ROS1+ NSCLC. This article explores the science behind repotrectinib, what made Turning Point so valuable, how we know, and what's next. [...]

Merck’s oral, macrocyclic PCSK9 inhibitors are among the 12 candidates for 2021's "Molecule of the Year" and have already gotten quite a few votes for 2021’s “Molecule of the Year.” They’ve been called “gamechangers” by readers, with impressive human proof-of-concept. MK-0616 is a macrocyclic PCSK9 inhibitor with demonstrated once-daily [...]

MK-0616 is a macrocyclic PCSK9 inhibitor with demonstrated once-daily PCSK9-lowering and LDL-cholesterol-lowering activities in a human clinical trial (<300 mg QD). Currently PCSK9-targeting therapies are only available by injection, and the cost-benefit of using large molecules to lower cholesterol has been hotly debated. Identification of [...]

The Turning Point Therapeutics oral, brain-penetrant ALK/ROS1/TRK kinase inhibitor, repotrectinib (TPX-0005), is a macrocyclic molecule with a small size intended to limit adverse interactions with resistance mutation hotspots near kinase active sites. TRK fusion proteins are driver mutations in certain cancers (which respond well to [...]

The Merck bicyclic macrocyclic peptide PCSK9 inhibitor, “ compound 44 ,” is a highly potent (Ki = 0.00239 nM) and orally bioavailable (cyno %F = 2.9, t1/2 = 10 h) agent against a notoriously difficult target for small molecules, demonstrating target engagement comparable to approved PCSK9 antibodies. The discovery of this molecule is an [...]

The BMS factor XIa inhibitor, milvexian (BMS-986177), is an oral antithrombotic with a Ki of 0.11 nM. A member of this macrocyclic series was previously highlighted as one of 2020’s Molecules of the Year . Poor pharmaceutic properties from previous preclinical molecules such as solubility were addressed resulting in this candidate. Milvexian [...]

ASP5286 is an analog of the natural product cyclosporin A that maintains the anti-HCV activity of cyclosporin A by binding to cyclophilin, but was optimized to be less immunosuppresive than cyclosporin A. The macrocycle was identified through semisynthetic derivitization of a related natural product, FR901459. The Astellas team was able to [...]

“Compound 6f” is a potent macrocyclic factor XIa inhibitor (<1 nM) that is highly selective against other serine proteases and has excellent oral PK (high bioavailability, low clearance). The BMS team was able to troubleshoot metabolic instability through met. ID, which revealed a hotspot outside of the macrocycle.