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Uncovering Molecular Bases Underlying Bone Morphogenetic Protein Receptor Inhibitor Selectivity.

Alsamarah A, LaCuran AE, Oelschlaeger P, Hao J, Luo Y - PLoS ONE (2015)

Bottom Line: Hence, small molecules targeting BMP type I receptors (BMPRI) to interrupt BMP signaling are believed to be an effective approach to treat these diseases.We found that, while the rigid docking method used here gave nearly identical binding affinity scores among the three kinases; free energy perturbation coupled with Hamiltonian replica-exchange molecular dynamics (FEP/H-REMD) simulations reproduced the absolute binding free energies in excellent agreement with experimental data.Our results provide critical information for designing exclusively selective BMP inhibitors for the development of effective pharmacotherapy for diseases caused by aberrant BMP signaling.

View Article: PubMed Central - PubMed

Affiliation: Department of Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, Pomona, California, United States of America.

ABSTRACT
Abnormal alteration of bone morphogenetic protein (BMP) signaling is implicated in many types of diseases including cancer and heterotopic ossifications. Hence, small molecules targeting BMP type I receptors (BMPRI) to interrupt BMP signaling are believed to be an effective approach to treat these diseases. However, lack of understanding of the molecular determinants responsible for the binding selectivity of current BMP inhibitors has been a big hindrance to the development of BMP inhibitors for clinical use. To address this issue, we carried out in silico experiments to test whether computational methods can reproduce and explain the high selectivity of a small molecule BMP inhibitor DMH1 on BMPRI kinase ALK2 vs. the closely related TGF-β type I receptor kinase ALK5 and vascular endothelial growth factor receptor type 2 (VEGFR2) tyrosine kinase. We found that, while the rigid docking method used here gave nearly identical binding affinity scores among the three kinases; free energy perturbation coupled with Hamiltonian replica-exchange molecular dynamics (FEP/H-REMD) simulations reproduced the absolute binding free energies in excellent agreement with experimental data. Furthermore, the binding poses identified by FEP/H-REMD led to a quantitative analysis of physical/chemical determinants governing DMH1 selectivity. The current work illustrates that small changes in the binding site residue type (e.g. pre-hinge region in ALK2 vs. ALK5) or side chain orientation (e.g. Tyr219 in caALK2 vs. wtALK2), as well as a subtle structural modification on the ligand (e.g. DMH1 vs. LDN193189) will cause distinct binding profiles and selectivity among BMP inhibitors. Therefore, the current computational approach represents a new way of investigating BMP inhibitors. Our results provide critical information for designing exclusively selective BMP inhibitors for the development of effective pharmacotherapy for diseases caused by aberrant BMP signaling.

No MeSH data available.


Related in: MedlinePlus

Binding conformations of DMH1 in ALK2 (top) and ALK5 (bottom) from molecular dynamics simulations.The conserved triad of amino acids consists of the gatekeeper and two pre-hinge residues shown in VDW mode. The rest of the protein is shown in surface mode.
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pone.0132221.g006: Binding conformations of DMH1 in ALK2 (top) and ALK5 (bottom) from molecular dynamics simulations.The conserved triad of amino acids consists of the gatekeeper and two pre-hinge residues shown in VDW mode. The rest of the protein is shown in surface mode.

Mentions: As previously described, the docking pose of DMH1 in ALK2 shares similar features with the ALK2-LDN193189 complex crystal structure, in which the pyrazolo[1,5-a]pyrimidine moiety of DMH1 faces the hinge region and forms a direct hydrogen bond with His286 in ALK2 (Fig 6A). This hydrogen bond is also seen in other crystal structures of BMPRI kinases, ALK6 (PDB ID: 3MDY) and ALK1 (PDB ID: 3MY0), in complex with LDN193189. However this favorable electrostatic interaction is absent between DMH1 and ALK5 (Fig 3). In search of a possible explanation, we compared the sequence conservation among three families of kinases (Table 2). We found that BMPRI kinases (ALK1, 2, 3 and 6) share a conserved amino acid triad Leu281, Ile282 and Thr283 (ALK2 numbering) adjacent to the ATP binding site, which we denote the “pre-hinge” region. Thr283 is known as the “gatekeeper” as it blocks access of ligands to a hydrophobic pocket next to the site of ATP binding [26]. In TGF-β kinases (ALK4, ALK5, ALK7), this pre-hinge triad consists instead of a conserved sequence Leu278, Val279 and Ser280 (ALK5 numbering) [14, 19, 59]. In our simulation, this less bulky pre-hinge triad in ALK5 allows the DMH1 quinoline ring to reach deeper within this hydrophobic region (Fig 6B). This binding pose shift results in the loss of two major favorable electrostatic interactions between DMH1 and His283 and Lys232 in ALK5. Noticeably, ALK4, which has the same pre-hinge triad as ALK5, also does not bind DMH1. On the other hand, crystal structures of ALK5 with the potent ALK5 inhibitors SB431542 (PDB ID 3TZM), GW855857 (PDB ID 3HMM), compound 19 (PDB ID 2WOU), and indolinone (PDB ID 2X7O) [26, 60–62] indicate that their binding is associated with two hydrogen bonds, one of which must be with the hinge region His283. Therefore, our model can explain why DMH1 is not a potent inhibitor of ALK5.


Uncovering Molecular Bases Underlying Bone Morphogenetic Protein Receptor Inhibitor Selectivity.

Alsamarah A, LaCuran AE, Oelschlaeger P, Hao J, Luo Y - PLoS ONE (2015)

Binding conformations of DMH1 in ALK2 (top) and ALK5 (bottom) from molecular dynamics simulations.The conserved triad of amino acids consists of the gatekeeper and two pre-hinge residues shown in VDW mode. The rest of the protein is shown in surface mode.
© Copyright Policy
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4489870&req=5

pone.0132221.g006: Binding conformations of DMH1 in ALK2 (top) and ALK5 (bottom) from molecular dynamics simulations.The conserved triad of amino acids consists of the gatekeeper and two pre-hinge residues shown in VDW mode. The rest of the protein is shown in surface mode.
Mentions: As previously described, the docking pose of DMH1 in ALK2 shares similar features with the ALK2-LDN193189 complex crystal structure, in which the pyrazolo[1,5-a]pyrimidine moiety of DMH1 faces the hinge region and forms a direct hydrogen bond with His286 in ALK2 (Fig 6A). This hydrogen bond is also seen in other crystal structures of BMPRI kinases, ALK6 (PDB ID: 3MDY) and ALK1 (PDB ID: 3MY0), in complex with LDN193189. However this favorable electrostatic interaction is absent between DMH1 and ALK5 (Fig 3). In search of a possible explanation, we compared the sequence conservation among three families of kinases (Table 2). We found that BMPRI kinases (ALK1, 2, 3 and 6) share a conserved amino acid triad Leu281, Ile282 and Thr283 (ALK2 numbering) adjacent to the ATP binding site, which we denote the “pre-hinge” region. Thr283 is known as the “gatekeeper” as it blocks access of ligands to a hydrophobic pocket next to the site of ATP binding [26]. In TGF-β kinases (ALK4, ALK5, ALK7), this pre-hinge triad consists instead of a conserved sequence Leu278, Val279 and Ser280 (ALK5 numbering) [14, 19, 59]. In our simulation, this less bulky pre-hinge triad in ALK5 allows the DMH1 quinoline ring to reach deeper within this hydrophobic region (Fig 6B). This binding pose shift results in the loss of two major favorable electrostatic interactions between DMH1 and His283 and Lys232 in ALK5. Noticeably, ALK4, which has the same pre-hinge triad as ALK5, also does not bind DMH1. On the other hand, crystal structures of ALK5 with the potent ALK5 inhibitors SB431542 (PDB ID 3TZM), GW855857 (PDB ID 3HMM), compound 19 (PDB ID 2WOU), and indolinone (PDB ID 2X7O) [26, 60–62] indicate that their binding is associated with two hydrogen bonds, one of which must be with the hinge region His283. Therefore, our model can explain why DMH1 is not a potent inhibitor of ALK5.

Bottom Line: Hence, small molecules targeting BMP type I receptors (BMPRI) to interrupt BMP signaling are believed to be an effective approach to treat these diseases.We found that, while the rigid docking method used here gave nearly identical binding affinity scores among the three kinases; free energy perturbation coupled with Hamiltonian replica-exchange molecular dynamics (FEP/H-REMD) simulations reproduced the absolute binding free energies in excellent agreement with experimental data.Our results provide critical information for designing exclusively selective BMP inhibitors for the development of effective pharmacotherapy for diseases caused by aberrant BMP signaling.

View Article: PubMed Central - PubMed

Affiliation: Department of Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, Pomona, California, United States of America.

ABSTRACT
Abnormal alteration of bone morphogenetic protein (BMP) signaling is implicated in many types of diseases including cancer and heterotopic ossifications. Hence, small molecules targeting BMP type I receptors (BMPRI) to interrupt BMP signaling are believed to be an effective approach to treat these diseases. However, lack of understanding of the molecular determinants responsible for the binding selectivity of current BMP inhibitors has been a big hindrance to the development of BMP inhibitors for clinical use. To address this issue, we carried out in silico experiments to test whether computational methods can reproduce and explain the high selectivity of a small molecule BMP inhibitor DMH1 on BMPRI kinase ALK2 vs. the closely related TGF-β type I receptor kinase ALK5 and vascular endothelial growth factor receptor type 2 (VEGFR2) tyrosine kinase. We found that, while the rigid docking method used here gave nearly identical binding affinity scores among the three kinases; free energy perturbation coupled with Hamiltonian replica-exchange molecular dynamics (FEP/H-REMD) simulations reproduced the absolute binding free energies in excellent agreement with experimental data. Furthermore, the binding poses identified by FEP/H-REMD led to a quantitative analysis of physical/chemical determinants governing DMH1 selectivity. The current work illustrates that small changes in the binding site residue type (e.g. pre-hinge region in ALK2 vs. ALK5) or side chain orientation (e.g. Tyr219 in caALK2 vs. wtALK2), as well as a subtle structural modification on the ligand (e.g. DMH1 vs. LDN193189) will cause distinct binding profiles and selectivity among BMP inhibitors. Therefore, the current computational approach represents a new way of investigating BMP inhibitors. Our results provide critical information for designing exclusively selective BMP inhibitors for the development of effective pharmacotherapy for diseases caused by aberrant BMP signaling.

No MeSH data available.


Related in: MedlinePlus