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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.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.

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

Left: Superposition of wtALK2 (cyan) and caALK2 (orange) backbone in cartoon. P-loop Tyr219 is shown in sticks with overlapped snapshots from the last 2 ns of simulation. DMH1 atoms are shown as small spheres. Right: RMSF of the P-loop in the unbound (apo) and DMH1 bound states. Statistical difference is represented by an * above the bound conformation; * = P < 0.05.
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pone.0132221.g005: Left: Superposition of wtALK2 (cyan) and caALK2 (orange) backbone in cartoon. P-loop Tyr219 is shown in sticks with overlapped snapshots from the last 2 ns of simulation. DMH1 atoms are shown as small spheres. Right: RMSF of the P-loop in the unbound (apo) and DMH1 bound states. Statistical difference is represented by an * above the bound conformation; * = P < 0.05.

Mentions: During our investigation of ALK2, we first used the caALK2 crystal structure (PDB ID 3Q4U). Although the docking score (estimated binding free energy) of DMH1 agrees well with the experimental value of -9.6 kcal/mol, the FEP/H-REMD calculated binding free energy is -6.2 kcal/mol (Table 1). When we used the wtALK2 crystal structure (PDB ID 3H9R), the binding free energy is -8.5 kcal/mol. Interestingly, the binding poses of DMH1 in wtALK2 and caALK2 are nearly identical. The averaged van der Waals interactions between the binding site and DMH1 also show a similar pattern, except that a favorable P-loop (also termed phosphate-binding loop) Tyr219 peak in wtALK2 is completely missing in caALK2 (Fig 4). Dynamic trajectories showed Tyr219 in wtALK2 always pointing inwards (Tyr219-in), forming favorable hydrophobic contacts with the quinoline moiety of DMH1 and a water-mediated hydrogen bond with N4 on the pyrimidine moiety 25% of simulation time (Fig 4). In contrast, Tyr219 in caALK2 is pointing outwards away from the ligand throughout the simulation (Fig 5 left). In addition, the root mean square fluctuation (RMSF) of the P-loop indicated that its fluctuation did not change upon DMH1 binding to wtALK2; whereas, DMH1 binding to caALK2 increased RMSF (Fig 5 right). Thus, the differences in both the interaction energy and the P-loop fluctuation confirm that the favorable interaction between DMH1 and Tyr219 can only be established when Tyr219 is pointing inward as in the wtALK2.


Uncovering Molecular Bases Underlying Bone Morphogenetic Protein Receptor Inhibitor Selectivity.

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

Left: Superposition of wtALK2 (cyan) and caALK2 (orange) backbone in cartoon. P-loop Tyr219 is shown in sticks with overlapped snapshots from the last 2 ns of simulation. DMH1 atoms are shown as small spheres. Right: RMSF of the P-loop in the unbound (apo) and DMH1 bound states. Statistical difference is represented by an * above the bound conformation; * = P < 0.05.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4489870&req=5

pone.0132221.g005: Left: Superposition of wtALK2 (cyan) and caALK2 (orange) backbone in cartoon. P-loop Tyr219 is shown in sticks with overlapped snapshots from the last 2 ns of simulation. DMH1 atoms are shown as small spheres. Right: RMSF of the P-loop in the unbound (apo) and DMH1 bound states. Statistical difference is represented by an * above the bound conformation; * = P < 0.05.
Mentions: During our investigation of ALK2, we first used the caALK2 crystal structure (PDB ID 3Q4U). Although the docking score (estimated binding free energy) of DMH1 agrees well with the experimental value of -9.6 kcal/mol, the FEP/H-REMD calculated binding free energy is -6.2 kcal/mol (Table 1). When we used the wtALK2 crystal structure (PDB ID 3H9R), the binding free energy is -8.5 kcal/mol. Interestingly, the binding poses of DMH1 in wtALK2 and caALK2 are nearly identical. The averaged van der Waals interactions between the binding site and DMH1 also show a similar pattern, except that a favorable P-loop (also termed phosphate-binding loop) Tyr219 peak in wtALK2 is completely missing in caALK2 (Fig 4). Dynamic trajectories showed Tyr219 in wtALK2 always pointing inwards (Tyr219-in), forming favorable hydrophobic contacts with the quinoline moiety of DMH1 and a water-mediated hydrogen bond with N4 on the pyrimidine moiety 25% of simulation time (Fig 4). In contrast, Tyr219 in caALK2 is pointing outwards away from the ligand throughout the simulation (Fig 5 left). In addition, the root mean square fluctuation (RMSF) of the P-loop indicated that its fluctuation did not change upon DMH1 binding to wtALK2; whereas, DMH1 binding to caALK2 increased RMSF (Fig 5 right). Thus, the differences in both the interaction energy and the P-loop fluctuation confirm that the favorable interaction between DMH1 and Tyr219 can only be established when Tyr219 is pointing inward as in the wtALK2.

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.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.

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