Investigating the Dynamic Binding Behavior of PMX53 Cooperating with Allosteric Antagonist NDT9513727 to C5a Anaphylatoxin Chemotactic Receptor 1 through Gaussian Accelerated Molecular Dynamics and Free-Energy Perturbation Simulations

Abstract

C5a anaphylatoxin chemotactic receptor 1 (C5aR1) is an important target in anti-inflammatory therapeutics. The cyclic peptide antagonist PMX53 binds to the orthosteric site located in the extracellular vestibule of C5aR1, and the non-peptide antagonist NDT9513727 binds to the allosteric site formed by the middle region of TM3 (trans-membrane helix), TM4, and TM5. We catch a sight of the variational binding mode of PMX53 during the Gaussian accelerated molecular dynamic (GaMD) simulations. In the binary complex of C5aR1 and PMX53, the PMX53 takes a dynamic binding mechanism during the simulation. Namely, the side chain of Arg6 of PMX53 extends to TM6-TM7 (pose 1) or swings to TM5 (pose 2), forming a salt bridge with Glu199. Meanwhile, in the ternary complex of C5aR1 with PMX53 and NDT9513727, the side chain of Arg6 of PMX53 swings to TM5 (pose 2) from extending to TM6–TM7 (pose 1) at the beginning of the GaMD simulation. In subsequent simulation, PMX53 stabilizes in the pose 2 binding mode by forming a stable salt bridge with Glu199. The free-energy perturbation (FEP) calculations demonstrate that pose 1 (ΔG binding = −10.94 kcal/mol) is more stable in the binary complex and pose 2 (ΔG binding = −7.91 kcal/mol) is unstable because of highly dynamic TM5. NDT9513727 interacts directly with TM4 and TM5 and stabilizes the hydrophobic stack between the extracellular sides of the two helices. Therefore, pose 2 (ΔG binding = −16.27 kcal/mol) is notably stable than pose 1 (ΔG binding = −9.78 kcal/mol) in the ternary complex. The identification of a novel binding mode of PMX53 and the detailed structural information of PMX53 interacting with a receptor obtained by GaMD simulations will be helpful in designing potent antagonists of C5aR1.

Deep Learning Dynamic Allostery of G-Protein-Coupled Receptors

“…They reduced fluctuations of the intracellular domains of TM3, TM4, and TM5 ( Figure 2C-2E ), as well as ICL2 in β 2 AR ( Figure 2C ). This was consistent with recent finding that the NDT9513727 NAM stabilized TM5 through the hydrophobic stacking between TM4 and TM5 72 . Binding of NNC0640 to GLP1R and MK-0893 to GLR stabilized the lipid-facing pocket on the intracellular domains of TM7 and TM6, respectively ( Figure 2H, 2J and Supplementary Figure 4H, 4J ).…”

“…Avacopan-binding to the C5AR1 confined the TM4 and TM5 extracellular domains from two conformational states to only state “S1”, where the TM4 and TM5 extracellular ends adopted the more closed conformation to stabilize NAM binding ( Figures 4E and 2E ). The hydrophobic stacking found between TM4 and TM5 extracellular ends was again in good agreement with previous finding by Xiaoli et al 72 . Binding of MK-0893 to the GLR confined the conformational space from three states (“S1”-S3”) to only state “S1”, in which the middle of TM5 and TM6 as well as TM6 and TM7 extracellular ends adopted the more closed conformations ( Figure 4J ).…”

Deep Learning Dynamic Allostery of G-Protein-Coupled Receptors

“…2C). This was consistent with recent nding that the NDT9513727 NAM stabilized TM5 through the hydrophobic stacking between TM4 and TM5 72 . Binding of NNC0640 to GLP1R and MK-0893 to GLR stabilized the lipid-facing pocket on the intracellular domains of TM7 and TM6, respectively (Fig.…”

“…4E and 2E). The hydrophobic stacking found between TM4 and TM5 extracellular ends was again in good agreement with previous nding by Xiaoli et al 72 . Binding of MK-0893 to the GLR con ned the conformational space from three states ("S1"-S3") to only state "S1", in which the middle of TM5 and TM6 as well as TM6 and TM7 extracellular ends adopted the more closed conformations (Fig.…”

Recent Advances in Alchemical Binding Free Energy Calculations for Drug Discovery

“…FEP calculations not only allow for pose validation but can also provide mechanistic insight into conditional binding events. Xiaoli et al 26 reported FEP calculations for the cyclic peptide antagonist PMX53 binding to C5a anaphylatoxin chemotactic receptor 1 (C5aR1). Depending on whether the allosteric nonpeptide antagonist NTD9513727 was bound to C5aR1, binding of PMX53 to the binary or the ternary complex was favored by FEP providing energetic insights to the allosteric mechanism of NTD9513727.…”