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Role of Molecular Interactions and Protein Rearrangement in the Dissociation Kinetics of p38? MAP Kinase Type-I/II/III Inhibitors.

ABSTRACT: Understanding the governing factors of fast or slow inhibitor binding/unbinding assists in developing drugs with preferred kinetic properties. For inhibitors with the same binding affinity targeting different binding sites of the same protein, the kinetic behavior can profoundly differ. In this study, we investigated unbinding kinetics and mechanisms of fast (type-I) and slow (type-II/III) binders of p38? mitogen-activated protein kinase, where the crystal structures showed that type-I and type-II/III inhibitors bind to pockets with different conformations of the Asp-Phe-Gly (DFG) motif. The work used methods that combine conventional molecular dynamics (MD), accelerated molecular dynamics (AMD) simulations, and the newly developed pathway search guided by internal motions (PSIM) method to find dissociation pathways. The study focuses on revealing key interactions and molecular rearrangements that hinder ligand dissociation by using umbrella sampling and post-MD processing to examine changes in free energy during ligand unbinding. As anticipated, the initial dissociation steps all require breaking interactions that appeared in crystal structures of the bound complexes. Interestingly, for type-I inhibitors such as SB2, p38? keeps barrier-free conformational fluctuation in the ligand-bound complex and during ligand dissociation. In contrast, with a type-II/III inhibitor such as BIRB796, with the rearrangements of p38? in its bound state, ligand unbinding features energetically unfavorable protein-ligand concerted movement. Our results also show that the type-II/III inhibitors preferred dissociation pathways through the allosteric channel, which is consistent with an existing publication. The study suggests that the level of required protein rearrangement is one major determining factor of drug binding kinetics in p38? systems, providing useful information for development of inhibitors.

SUBMITTER: You W

PROVIDER: S-EPMC5975198 | biostudies-literature | 2018 May

REPOSITORIES: biostudies-literature

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Role of Molecular Interactions and Protein Rearrangement in the Dissociation Kinetics of p38α MAP Kinase Type-I/II/III Inhibitors.

You Wanli W Chang Chia-En A CA

Journal of chemical information and modeling 20180416 5

Understanding the governing factors of fast or slow inhibitor binding/unbinding assists in developing drugs with preferred kinetic properties. For inhibitors with the same binding affinity targeting different binding sites of the same protein, the kinetic behavior can profoundly differ. In this study, we investigated unbinding kinetics and mechanisms of fast (type-I) and slow (type-II/III) binders of p38α mitogen-activated protein kinase, where the crystal structures showed that type-I and type- ...[more]

PMID: 29620886

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Project description:The protonation constants () of 3,6,9,15-tetraazabicyclo[9.3.1]pentadeca-1(15),11,13-triene-3,6,9-triacetic acid (PCTA) and stability constants of complexes formed between this pyridine-containing macrocycle and several different metal ions have been determined in 1.0 M KCl at 25 degrees C and compared to previous literature values. The first protonation constant was found to be 0.5-0.6 log units higher than the value reported previously, and a total of five protonation steps were detected (log = 11.36, 7.35, 3.83, 2.12, and 1.29). The stability constants of complexes formed between PCTA and Mg2+, Ca2+, Cu2+, and Zn2+ were also somewhat higher than those previously reported, but this difference could be largely attributed to the higher first protonation constant of the ligand. Stability constants of complexes formed between PCTA and the Ln3+ series of ions and Y3+ were determined by using an "out-of-cell" potentiometric method. These values ranged from log K = 18.15 for Ce(PCTA) to log K = 20.63 for Yb(PCTA), increasing along the Ln series in proportion to decreasing Ln3+ cation size. The rates of complex formation for Ce(PCTA), Eu(PCTA), Y(PCTA), and Yb(PCTA) were followed by conventional UV-vis spectroscopy in the pH range 3.5-4.4. First-order rate constants (saturation kinetics) obtained for different ligand-to-metal ion ratios were consistent with the rapid formation of a diprotonated intermediate, Ln(H(2)PCTA)(2+). The stabilities of the intermediates as determined from the kinetic data were 2.81, 3.12, 2.97, and 2.69 log K units for Ce(H(2)PCTA), Eu(H(2)PCTA), Y(H(2)PCTA), and Yb(H(2)PCTA), respectively. Rearrangement of these intermediates to the fully chelated complexes was the rate-determining step, and the rate constant (k(r)) for this process was found to be inversely proportional to the proton concentration. The formation rates (k(OH)) increased with a decrease in the lanthanide ion size [9.68 x 10(7), 1.74 x 10(8), 1.13 x 10(8), and 1.11 x 10(9) M(-1) s(-1) for Ce(PCTA), Eu(PCTA), Y(PCTA), and Yb(PCTA), respectively]. These data indicate that the Ln(PCTA) complexes exhibit the fastest formation rates among all lanthanide macrocyclic ligand complexes studied to date. The acid-catalyzed dissociation rates (k1) varied with the cation from 9.61 x 10(-4), 5.08 x 10(-4), 1.07 x 10(-3), and 2.80 x 10(-4) M(-1) s(-1) for Ce(PCTA), Eu(PCTA), Y(PCTA), and Yb(PCTA), respectively.

Project description:The thermodynamic, kinetic, and structural properties of Ln3+ complexes with the bifunctional DO3A-ACE4- ligand and its amide derivative DO3A-BACE4- (modelling the case where DO3A-ACE4- ligand binds to vector molecules) have been studied in order to confirm the usefulness of the corresponding Gd3+ complexes as relaxation labels of targeted MRI contrast agents. The stability constants of the Mg2+ and Ca2+ complexes of DO3A-ACE4- and DO3A-BACE4- complexes are lower than for DOTA4- and DO3A3-, while the Zn2+ and Cu2+ complexes have similar and higher stability than for DOTA4- and DO3A3- complexes. The stability constants of the Ln(DO3A-BACE)- complexes increase from Ce3+ to Gd3+ but remain practically constant for the late Ln3+ ions (represented by Yb3+). The stability constants of the Ln(DO3A-ACE)4- and Ln(DO3A-BACE)4- complexes are several orders of magnitude lower than those of the corresponding DOTA4- and DO3A3- complexes. The formation rate of Eu(DO3A-ACE)- is one order of magnitude slower than for Eu(DOTA)-, due to the presence of the protonated amine group, which destabilizes the protonated intermediate complex. This protonated group causes the Ln(DO3A-ACE)- complexes to dissociate several orders of magnitude faster than Ln(DOTA)- and its absence in the Ln(DO3A-BACE)- complexes results in inertness similar to Ln(DOTA)- (as judged by the rate constants of acid assisted dissociation). The 1H NMR spectra of the diamagnetic Y(DO3A-ACE)- and Y(DO3A-BACE)- reflect the slow dynamics at low temperatures of the intramolecular isomerization process between the SA pair of enantiomers, R-Λ(λλλλ) and S-Δ(δδδδ). The conformation of the Cα-substituted pendant arm is different in the two complexes, where the bulky substituent is further away from the macrocyclic ring in Y(DO3A-BACE)- than the amino group in Y(DO3A-ACE)- to minimize steric hindrance. The temperature dependence of the spectra reflects slower ring motions than pendant arms rearrangements in both complexes. Although losing some thermodynamic stability relative to Gd(DOTA)-, Gd(DO3A-BACE)- is still quite inert, indicating the usefulness of the bifunctional DO3A-ACE4- in the design of GBCAs and Ln3+-based tags for protein structural NMR analysis.

Dataset Information

Role of Molecular Interactions and Protein Rearrangement in the Dissociation Kinetics of p38? MAP Kinase Type-I/II/III Inhibitors.

Publications

Role of Molecular Interactions and Protein Rearrangement in the Dissociation Kinetics of p38α MAP Kinase Type-I/II/III Inhibitors.

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