Fragment-based design of small molecule PCSK9 inhibitors using simulated annealing of chemical potential simulations


Autoři: Frank Guarnieri aff001;  John L. Kulp, Jr. aff003;  John L. Kulp, III aff003;  Ian S. Cloudsdale aff003
Působiště autorů: Center for Drug Discovery, Northeastern University, Boston, MA, United States of America aff001;  PAKA Pulmonary Pharmaceuticals, Acton, MA, United States of America aff002;  Conifer Point Pharmaceuticals, Doylestown, PA, United States of America aff003;  Department of Chemistry, Baruch S. Blumberg Institute, Doylestown, PA, United States of America aff004
Vyšlo v časopise: PLoS ONE 14(12)
Kategorie: Research Article
prolekare.web.journal.doi_sk: 10.1371/journal.pone.0225780

Souhrn

PCSK9 is a protein secreted by the liver that binds to the low-density lipoprotein receptor (LDLR), causing LDLR internalization, decreasing the clearance of circulating LDL particles. Mutations in PCSK9 that strengthen its interactions with LDLR result in familial hypercholesterolemia (FH) and early onset atherosclerosis, while nonsense mutations of PCSK9 result in cardio-protective hypocholesterolemia. These observations led to PCSK9 inhibition for cholesterol lowering becoming a high-interest therapeutic target, with antibody drugs reaching the market. An orally-available small molecule drug is highly desirable, but inhibiting the PCSK9/LDLR protein-protein interaction (PPI) has proven challenging. Alternate approaches to finding good lead candidates are needed. Motivated by the FH mutation data on PCSK9, we found that modeling the PCSK9/LDLR interface revealed extensive electron delocalization between and within the protein partners. Based on this, we hypothesized that compounds assembled from chemical fragments could achieve the affinity required to inhibit the PCSK9/LDLR PPI if they were selected to interact with PCSK9 in a way that, like LDLR, also involves significant fractional charge transfer to form partially covalent bonds. To identify such fragments, Simulated Annealing of Chemical Potential (SACP) fragment simulations were run on multiple PCSK9 structures, using optimized partial charges for the protein. We designed a small molecule, composed of several fragments, predicted to interact at two sites on the PCSK9. This compound inhibits the PPI with 1 μM affinity. Further, we designed two similar small molecules where one allows charge delocalization though a linker and the other doesn’t. The first inhibitor with charge delocalization enhances LDLR surface expression by 60% at 10 nM, two orders of magnitude more potent than the EGF domain of LDLR. The other enhances LDLR expression by only 50% at 1 μM. This supports our conjecture that fragments can have surprisingly outsized efficacy in breaking PPI’s by achieving fractional charge transfer leading to partially covalent bonding.

Klíčová slova:

Biochemical simulations – Carbon – Drug discovery – Hydrogen bonding – Protein interactions – Salt bridges – Small molecules – Familial hypercholesterolemia


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2019 Číslo 12