SLIDE 1 Advanced Techniques: Applications
Pablo Campomanes | CECAM QM/MM School Hybrid Quantum Mechanics / Molecular Mechanics (QM/MM) Approaches to Biochemistry and Beyond
SLIDE 2 In which scenarios QM/MM is useful? When this method is the best/unique option?
QM part: ü DFT ü e- play key role MM part: ü Classical force field ü Environmental effects
SLIDE 3
Main limitations of QM/MM? How to overcome them? The sampling bottleneck Fast oscillations around each minimun Slow jumping over the barrier
SLIDE 4
Beyond standard QM/MM techniques q Blue Moon Ensemble (Thermodynamic Integration) q Metadynamics Main limitations of QM/MM? How to overcome them?
Accelerated Schemes
SLIDE 5
Chemical Reactivity: Binding of Ru- based drugs to the Nucleosome Core Particle
SLIDE 6 Ru-based drugs: Chemical structure and properties
[(η6-pcymene)Ru(1,3,5-triaza-7-phosphaadamantane)Cl2] [(η6-pcymene)Ru(ethylenediamine)Cl]PF6
Activated through hydrolysis inside cells (low [Cl-]) Present low toxicity and high selectivity
Different intracellular targets
Both can bind to naked DNA and isolated proteins Inactive against primary tumors Active against metastases Cytotoxic anti-primary tumor activity Inactive against metastases
SLIDE 7
Selective Binding of Ru(II) drugs (histone .vs. DNA)
SLIDE 8
Ru(II) metallo-drugs Binding: Reaction Coordinate
SLIDE 9
Ru(II) metallo-drugs Binding: Reaction Coordinate
SLIDE 10
Main keywords to include in CP2K input file
&FORCE_EVAL &SUBSYS &COLVAR !COLVAR 1 &DISTANCE ATOMS 217 258 &END DISTANCE &END COLVAR &MOTION &CONSTRAINT &COLLECTIVE COLVAR 1 INTERMOLECULAR TRUE TARGET [angstrom] 3.4 &END COLLECTIVE &LAGRANGE MULTIPLIERS ON &END LAGRANGE MULTIPLIERS &END CONSTRAINT
SLIDE 11
Ru(II) metallo-drugs Binding: Reaction Mechanism
SLIDE 12
Ru-arene metallo-drugs Binding: PMF profiles from TI
SLIDE 13 RAED-C binding: Critical structures & Free energies
Nature Comm., 5, 3462 (2014)
SLIDE 14 RAPTA-C binding: Critical structures & Free energies
Nature Comm., 5, 3462 (2014)
SLIDE 15 Ru-based drugs: Chemical structure and properties
[(η6-pcymene)Ru(1,3,5-triaza-7-phosphaadamantane)Cl2] [(η6-pcymene)Ru(ethylenediamine)Cl]PF6
Different intracellular targets
Accessible histone sites on the surface of the nucleosome, steric constraints in the double helix pose an obstacle towards accommodating two bulky ligands in the case of RAPTA-C
YES
Development of new Ru drugs with “ad hoc” cytotoxic properties, via ligand-based modulation of DNA versus protein binding
SLIDE 16
Enzymatic reactivity Catalases .vs. Peroxidases
SLIDE 17
Mode of action of catalases .vs. peroxidases
Protective role: catalyze peroxidic bond heterolytic cleavage in H2O2 ü Avoid accumulation of ROS ü Regulate ROS in signaling pathways
SLIDE 18
Catalases .vs. peroxidases - Previous studies
Cpd I reduction is rate-determining step
SLIDE 19 Catalases .vs. peroxidases – Active site differences
peroxidases catalases
Knowledge of mechanism of Cpd I reduction by H2O2 in catalases “QASR” Rational engineering of peroxidases with higher activity vs. H2O2 disproportionation
SLIDE 20 His42 Pro139 Arg38 His170
BLYP/TZV2P GTH pseudopotentials 320 Ry cutoff BO dynamics NVT ensemble 0.5 fs timestep AMBER ff. for MM part
QM/MM MD simulations (CP2K)
Quartet spin state
SLIDE 21
- Identification of a small number of CVs able to
describe the activated process of interest (reduced dimensionality)
- The dynamics in the CV space is driven by the
addition of a history-dependent potential term constructed by the addition of gaussians centered along the trajectory
Metadynamics: accelerating rare events
Rare events: Events that happen on a very long time scale
Special techniques must be used
SLIDE 22 ΔsCV1 = 0.05 ΔsCV2 = 0.08 W = 0.6 kcal/mol tMTD = 15 fs
Collective Variables
CV1: CN from O(peroxide) to H(peroxide) CV2: CN from O(oxoferryl) to H(peroxide)+H(wat)
- J. Am. Chem. Soc., 137, 11170 (2015)
(O2 formation) (H2O2 formation)
SLIDE 23
Main keywords to include in CP2K input file
&FORCE_EVAL &SUBSYS &COLVAR !COLVAR 1 &COORDINATION ATOMS_FROM 40 41 ATOMS_TO 42 43 R0 [angstrom] 1.00 NN 12 ND 15 &END COORDINATION &END COLVAR &COLVAR !COLVAR 2 &COORDINATION ATOMS_FROM 46 ATOMS_TO 42 43 86 87 R0 [angstrom] 1.80 NN 3 ND 6 &END COORDINATION &END COLVAR
SLIDE 24 Main keywords to include in CP2K input file
&MOTION &FREE ENERGY METHOD METADYN &METADYN DO_HILLS NT_HILLS 30 WW 0.001 &METAVAR COLVAR 1 WIDTH 0.05 &END METAVAR &METAVAR COLVAR 2 WIDTH 0.08 &END METAVAR &END METADYN &END FREE ENERGY
ΔsCV1 = 0.05 ΔsCV2 = 0.08 W = 0.6 kcal/mol tMTD = 15 fs
SLIDE 25
Mechanism for Cpd I reduction in peroxidases
SLIDE 26
Free Energy Profile for Cpd I reduction in HRP
2H2O2 à 2H2O + O2
SLIDE 27 Free Energy Profile for Cpd I reduction in HRP
ΔG≠ = 18.7 kcal mol-1 ΔG≠ = 11.5 kcal mol-1
SLIDE 28
Spin density reorganization along pathways
&FORCE_EVAL &DFT &PRINT &E_DENSITY_CUBE FILENAME spinden.cube &END E_DENSITY_CUBE &END PRINT &END DFT
SLIDE 29 Mechanism of Cpd I reduction by H2O2 in catalases
- M. Alfonso-Prieto; X. Biarnés; P. Vidossich; C. Rovira; J. Am. Chem. Soc. 2009, 131, 11751.
Pathway A: His-mediated mechanism
SLIDE 30 Mechanism of Cpd I reduction by H2O2 in catalases
- M. Alfonso-Prieto; X. Biarnés; P. Vidossich; C. Rovira; J. Am. Chem. Soc. 2009, 131, 11751.
Pathway B: direct mechanism Competitive routes (ΔG ~ 13 kcal mol-1)
SLIDE 31 Comparison of rate-determining step: HPC .vs. HRP
1. Larger size of active site cavity in HRP
(evolved to catalyze oxidation of bulkier substrates)
ü Weaker interactions between HOO• and distal site residues 2. Existence of “wet” active site in HRP .vs. “dry” active site in HPC ü Water-mediated H-bond network is disrupted -> energetic cost for reorienting HOO• at TS increases Helicobacter pylori catalase Horseradish peroxidase
- J. Am. Chem. Soc., 137, 11170 (2015)
