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The rise of molecular simulations in fragment-based drug design (FBDD): an overview.

ABSTRACT: Fragment-based drug discovery (FBDD) is an innovative approach, progressively more applied in the academic and industrial context, to enhance hit identification for previously considered undruggable biological targets. In particular, FBDD discovers low-molecular-weight (LMW) ligands (<300Da) able to bind to therapeutically relevant macromolecules in an affinity range from the micromolar (?M) to millimolar (mM). X-ray crystallography (XRC) and nuclear magnetic resonance (NMR) spectroscopy are commonly the methods of choice to obtain 3D information about the bound ligand-protein complex, but this can occasionally be problematic, mainly for early, low-affinity fragments. The recent development of computational fragment-based approaches provides a further strategy for improving the identification of fragment hits. In this review, we summarize the state of the art of molecular dynamics simulations approaches used in FBDD, and discuss limitations and future perspectives for these approaches.

SUBMITTER: Bissaro M

PROVIDER: S-EPMC7314695 | biostudies-literature | 2020 Jun

REPOSITORIES: biostudies-literature

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The rise of molecular simulations in fragment-based drug design (FBDD): an overview.

Bissaro Maicol M Sturlese Mattia M Moro Stefano S

Drug discovery today 20200625 9

Fragment-based drug discovery (FBDD) is an innovative approach, progressively more applied in the academic and industrial context, to enhance hit identification for previously considered undruggable biological targets. In particular, FBDD discovers low-molecular-weight (LMW) ligands (<300Da) able to bind to therapeutically relevant macromolecules in an affinity range from the micromolar (μM) to millimolar (mM). X-ray crystallography (XRC) and nuclear magnetic resonance (NMR) spectroscopy are com ...[more]

PMID: 32592867

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Project 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 ?M 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 ?M. 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.

Dataset Information

The rise of molecular simulations in fragment-based drug design (FBDD): an overview.

Publications

The rise of molecular simulations in fragment-based drug design (FBDD): an overview.

Similar Datasets

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