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Receptor residence time trumps drug-likeness and oral bioavailability in determining efficacy of complement C5a antagonists.

Seow V, Lim J, Cotterell AJ, Yau MK, Xu W, Lohman RJ, Kok WM, Stoermer MJ, Sweet MJ, Reid RC, Suen JY, Fairlie DP - Sci Rep (2016)

Bottom Line: The unusually long residence time of 3D53 on its receptor was mechanistically probed by molecular dynamics simulations, which revealed long-lasting interactions that trap the antagonist within the receptor.Despite negligible oral bioavailability, 3D53 was much more orally efficacious than W54011 or JJ47 in preventing repeated agonist insults to induce rat paw oedema over 24 h.Thus, residence time on a receptor can trump drug-likeness in determining efficacy, even oral efficacy, of pharmacological agents.

View Article: PubMed Central - PubMed

Affiliation: Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia.

ABSTRACT
Drug discovery and translation are normally based on optimizing efficacy by increasing receptor affinity, functional potency, drug-likeness (rule-of-five compliance) and oral bioavailability. Here we demonstrate that residence time of a compound on its receptor has an overriding influence on efficacy, exemplified for antagonists of inflammatory protein complement C5a that activates immune cells and promotes disease. Three equipotent antagonists (3D53, W54011, JJ47) of inflammatory responses to C5a (3 nM) were compared for drug-likeness, receptor affinity and antagonist potency in human macrophages, and anti-inflammatory efficacy in rats. Only the least drug-like antagonist (3D53) maintained potency in cells against higher C5a concentrations and had a much longer duration of action (t1/2 ~ 20 h) than W54011 or JJ47 (t1/2 ~ 1 -3 h) in inhibiting macrophage responses. The unusually long residence time of 3D53 on its receptor was mechanistically probed by molecular dynamics simulations, which revealed long-lasting interactions that trap the antagonist within the receptor. Despite negligible oral bioavailability, 3D53 was much more orally efficacious than W54011 or JJ47 in preventing repeated agonist insults to induce rat paw oedema over 24 h. Thus, residence time on a receptor can trump drug-likeness in determining efficacy, even oral efficacy, of pharmacological agents.

No MeSH data available.


Related in: MedlinePlus

Representation of C5aR-3D53 interactions at multiple time points in MD simulations.C5aR-3D53 complex at (A) 10 ns: Arg6 of 3D53 faced towards ECL2 and made a short-lived contact with the Cys188 backbone carbonyl oxygen. (B) 50 ns: Arg6 underwent a large shift involving re-location and formation of an electrostatic interaction with Asp282, accompanied by movement of the top region of TM2 to shorten the distance to TM7. (C) 80 ns: similar protein-ligand interactions as at 50 ns, reflecting stable and long-lasting interactions between 3D53 and C5aR. Hydrogen bonds are depicted as dotted lines. (D) Distance measurements between stated residues and TM helices throughout MD simulations. (E) Root mean square fluctuation (RMSF) of C5aR residue sidechains throughout MD simulations.
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f6: Representation of C5aR-3D53 interactions at multiple time points in MD simulations.C5aR-3D53 complex at (A) 10 ns: Arg6 of 3D53 faced towards ECL2 and made a short-lived contact with the Cys188 backbone carbonyl oxygen. (B) 50 ns: Arg6 underwent a large shift involving re-location and formation of an electrostatic interaction with Asp282, accompanied by movement of the top region of TM2 to shorten the distance to TM7. (C) 80 ns: similar protein-ligand interactions as at 50 ns, reflecting stable and long-lasting interactions between 3D53 and C5aR. Hydrogen bonds are depicted as dotted lines. (D) Distance measurements between stated residues and TM helices throughout MD simulations. (E) Root mean square fluctuation (RMSF) of C5aR residue sidechains throughout MD simulations.

Mentions: To investigate a possible mechanism accounting for the long residence time of 3D53 on the receptor C5aR, molecular dynamics (MD) simulations were performed for the C5aR-3D53 complex derived from a homology model of C5aR built from an antagonist-CXCR4 crystal structure21 (PDB code: 3ODU). After 0–10 ns simulation (Fig. 6A), Arg6 of 3D53 faced extracellular loop 2 (ECL2) of C5aR making a short-lived contact with the Cys188 backbone carbonyl oxygen. After 15 ns, Arg6 moved closer to transmembrane helix TM7 and began to form hydrogen bonds with Asp282 (Fig. 6B). This interaction remarkably closed the distance between the sidechains of these residues from 15 Å to 2 Å (Fig. 6B,D). During intermediate MD simulations, Arg6 of 3D53 sandwiched between TM2 and TM7 (TM2-TM7dist 13 Å to 6.5 Å, Fig. 6D), forming stable hydrogen bonds with the backbone oxygen of Ile91 and the sidechain of Asp282 (Fig. 6C). This led to a stable salt-bridge throughout the later 85 ns and constituted the most stable protein-ligand contact observed (Supplementary Fig. 1). Previous results supported an interaction between Arg6 of 3D53 and Asp282, since Asp282Ala mutation caused a 10-fold loss in affinity of 3D5322. In MD simulations, Arg175 and Glu199 also maintained hydrogen bond contact (Fig. 6B,C), suggesting stabilization of an inactive C5aR conformation. Trp5 of 3D53 was found to switch between aromatic pi-interactions and a H-bond interaction with Tyr290, the distance between the NH from the indole ring and the hydroxyl group of Tyr290 being monitored in Fig. 6D.


Receptor residence time trumps drug-likeness and oral bioavailability in determining efficacy of complement C5a antagonists.

Seow V, Lim J, Cotterell AJ, Yau MK, Xu W, Lohman RJ, Kok WM, Stoermer MJ, Sweet MJ, Reid RC, Suen JY, Fairlie DP - Sci Rep (2016)

Representation of C5aR-3D53 interactions at multiple time points in MD simulations.C5aR-3D53 complex at (A) 10 ns: Arg6 of 3D53 faced towards ECL2 and made a short-lived contact with the Cys188 backbone carbonyl oxygen. (B) 50 ns: Arg6 underwent a large shift involving re-location and formation of an electrostatic interaction with Asp282, accompanied by movement of the top region of TM2 to shorten the distance to TM7. (C) 80 ns: similar protein-ligand interactions as at 50 ns, reflecting stable and long-lasting interactions between 3D53 and C5aR. Hydrogen bonds are depicted as dotted lines. (D) Distance measurements between stated residues and TM helices throughout MD simulations. (E) Root mean square fluctuation (RMSF) of C5aR residue sidechains throughout MD simulations.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4837355&req=5

f6: Representation of C5aR-3D53 interactions at multiple time points in MD simulations.C5aR-3D53 complex at (A) 10 ns: Arg6 of 3D53 faced towards ECL2 and made a short-lived contact with the Cys188 backbone carbonyl oxygen. (B) 50 ns: Arg6 underwent a large shift involving re-location and formation of an electrostatic interaction with Asp282, accompanied by movement of the top region of TM2 to shorten the distance to TM7. (C) 80 ns: similar protein-ligand interactions as at 50 ns, reflecting stable and long-lasting interactions between 3D53 and C5aR. Hydrogen bonds are depicted as dotted lines. (D) Distance measurements between stated residues and TM helices throughout MD simulations. (E) Root mean square fluctuation (RMSF) of C5aR residue sidechains throughout MD simulations.
Mentions: To investigate a possible mechanism accounting for the long residence time of 3D53 on the receptor C5aR, molecular dynamics (MD) simulations were performed for the C5aR-3D53 complex derived from a homology model of C5aR built from an antagonist-CXCR4 crystal structure21 (PDB code: 3ODU). After 0–10 ns simulation (Fig. 6A), Arg6 of 3D53 faced extracellular loop 2 (ECL2) of C5aR making a short-lived contact with the Cys188 backbone carbonyl oxygen. After 15 ns, Arg6 moved closer to transmembrane helix TM7 and began to form hydrogen bonds with Asp282 (Fig. 6B). This interaction remarkably closed the distance between the sidechains of these residues from 15 Å to 2 Å (Fig. 6B,D). During intermediate MD simulations, Arg6 of 3D53 sandwiched between TM2 and TM7 (TM2-TM7dist 13 Å to 6.5 Å, Fig. 6D), forming stable hydrogen bonds with the backbone oxygen of Ile91 and the sidechain of Asp282 (Fig. 6C). This led to a stable salt-bridge throughout the later 85 ns and constituted the most stable protein-ligand contact observed (Supplementary Fig. 1). Previous results supported an interaction between Arg6 of 3D53 and Asp282, since Asp282Ala mutation caused a 10-fold loss in affinity of 3D5322. In MD simulations, Arg175 and Glu199 also maintained hydrogen bond contact (Fig. 6B,C), suggesting stabilization of an inactive C5aR conformation. Trp5 of 3D53 was found to switch between aromatic pi-interactions and a H-bond interaction with Tyr290, the distance between the NH from the indole ring and the hydroxyl group of Tyr290 being monitored in Fig. 6D.

Bottom Line: The unusually long residence time of 3D53 on its receptor was mechanistically probed by molecular dynamics simulations, which revealed long-lasting interactions that trap the antagonist within the receptor.Despite negligible oral bioavailability, 3D53 was much more orally efficacious than W54011 or JJ47 in preventing repeated agonist insults to induce rat paw oedema over 24 h.Thus, residence time on a receptor can trump drug-likeness in determining efficacy, even oral efficacy, of pharmacological agents.

View Article: PubMed Central - PubMed

Affiliation: Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia.

ABSTRACT
Drug discovery and translation are normally based on optimizing efficacy by increasing receptor affinity, functional potency, drug-likeness (rule-of-five compliance) and oral bioavailability. Here we demonstrate that residence time of a compound on its receptor has an overriding influence on efficacy, exemplified for antagonists of inflammatory protein complement C5a that activates immune cells and promotes disease. Three equipotent antagonists (3D53, W54011, JJ47) of inflammatory responses to C5a (3 nM) were compared for drug-likeness, receptor affinity and antagonist potency in human macrophages, and anti-inflammatory efficacy in rats. Only the least drug-like antagonist (3D53) maintained potency in cells against higher C5a concentrations and had a much longer duration of action (t1/2 ~ 20 h) than W54011 or JJ47 (t1/2 ~ 1 -3 h) in inhibiting macrophage responses. The unusually long residence time of 3D53 on its receptor was mechanistically probed by molecular dynamics simulations, which revealed long-lasting interactions that trap the antagonist within the receptor. Despite negligible oral bioavailability, 3D53 was much more orally efficacious than W54011 or JJ47 in preventing repeated agonist insults to induce rat paw oedema over 24 h. Thus, residence time on a receptor can trump drug-likeness in determining efficacy, even oral efficacy, of pharmacological agents.

No MeSH data available.


Related in: MedlinePlus