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

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 earl...

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Main Authors: Frank Guarnieri, John L Kulp, Ian S Cloudsdale
Format: Article
Language:English
Published: Public Library of Science (PLoS) 2019-01-01
Series:PLoS ONE
Online Access:https://doi.org/10.1371/journal.pone.0225780
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spelling doaj-7f1a149b5ef447d2a4ea43d60b2784562021-03-04T11:20:44ZengPublic Library of Science (PLoS)PLoS ONE1932-62032019-01-011412e022578010.1371/journal.pone.0225780Fragment-based design of small molecule PCSK9 inhibitors using simulated annealing of chemical potential simulations.Frank GuarnieriJohn L KulpJohn L KulpIan S CloudsdalePCSK9 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.https://doi.org/10.1371/journal.pone.0225780
collection DOAJ
language English
format Article
sources DOAJ
author Frank Guarnieri
John L Kulp
John L Kulp
Ian S Cloudsdale
spellingShingle Frank Guarnieri
John L Kulp
John L Kulp
Ian S Cloudsdale
Fragment-based design of small molecule PCSK9 inhibitors using simulated annealing of chemical potential simulations.
PLoS ONE
author_facet Frank Guarnieri
John L Kulp
John L Kulp
Ian S Cloudsdale
author_sort Frank Guarnieri
title Fragment-based design of small molecule PCSK9 inhibitors using simulated annealing of chemical potential simulations.
title_short Fragment-based design of small molecule PCSK9 inhibitors using simulated annealing of chemical potential simulations.
title_full Fragment-based design of small molecule PCSK9 inhibitors using simulated annealing of chemical potential simulations.
title_fullStr Fragment-based design of small molecule PCSK9 inhibitors using simulated annealing of chemical potential simulations.
title_full_unstemmed Fragment-based design of small molecule PCSK9 inhibitors using simulated annealing of chemical potential simulations.
title_sort fragment-based design of small molecule pcsk9 inhibitors using simulated annealing of chemical potential simulations.
publisher Public Library of Science (PLoS)
series PLoS ONE
issn 1932-6203
publishDate 2019-01-01
description 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.
url https://doi.org/10.1371/journal.pone.0225780
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