Ab initio prediction of protein-ligand binding structures by replica-exchange umbrella sampling simulations

We have developed a prediction method for the binding structures of ligands with proteins. Our method consists of three steps. First, replica-exchange umbrella sampling simulations are performed along the distance between a putative binding site of a protein and a ligand as the reaction coordinate. Second, we obtain the potential of mean force (PMF) of the unbiased system using the weighted histogram analysis method and determine the distance that corresponds to the global minimum of PMF. Third, structures that have this global-minimum distance and energy values around the average potential energy are collected and analyzed using the principal component analysis. We predict the binding structure as the global-minimum free energy state on the free energy landscapes along the two major principal component axes. As test cases, we applied our method to five protein-ligand complex systems. Starting from the configuration in which the protein and the ligand are far away from each other in each system, our method predicted the ligand binding structures in excellent agreement with the experimental data from Protein Data Bank.     

Two‐dimensional replica‐exchange method for predicting protein–ligand binding structures

We have developed a two‐dimensional replica‐exchange method for the prediction of protein–ligand binding structures. The first dimension is the umbrella sampling along the reaction coordinate, which is the distance between a protein binding pocket and a ligand. The second dimension is the solute tempering, in which the interaction between a ligand and a protein and water is weakened. The second dimension is introduced to make a ligand follow the umbrella potential more easily and enhance the binding events, which should improve the sampling efficiency. As test cases, we applied our method to two protein‐ligand complex systems (MDM2 and HSP 90‐alpha). Starting from the configuration in which the protein and the ligand are far away from each other in each system, our method predicted the ligand binding structures in excellent agreement with the experimental data from Protein Data Bank much faster with the improved sampling efficiency than the replica‐exchange umbrella sampling method that we have previously developed. © 2013 Wiley Periodicals, Inc.     

Transformation between α‐helix and β‐sheet structures of one and two polyglutamine peptides in explicit water molecules by replica‐exchange molecular dynamics simulations

Aggregation of polyglutamine peptides with β‐sheet structures is related to some important neurodegenerative diseases such as Huntington's disease. However, it is not clear how polyglutamine peptides form the β‐sheets and aggregate. To understand this problem, we performed all‐atom replica‐exchange molecular dynamics simulations of one and two polyglutamine peptides with 10 glutamine residues in explicit water molecules. Our results show that two polyglutamine peptides mainly formed helix or coil structures when they are separated, as in the system with one‐polyglutamine peptide. As the interpeptide distance decreases, the intrapeptide β‐sheet structure sometimes appear as an intermediate state, and finally the interpeptide β‐sheets are formed. We also find that the polyglutamine dimer tends to form the antiparallel β‐sheet conformations rather than the parallel β‐sheet, which is consistent with previous experiments and a coarse‐grained molecular dynamics simulation. © 2014 Wiley Periodicals, Inc.     

Ergodicity and model quality in template‐restrained canonical and temperature/Hamiltonian replica exchange coarse‐grained molecular dynamics simulations of proteins

Molecular simulations restrained to single or multiple templates are commonly used in protein‐structure modeling. However, the restraints introduce additional barriers, thus impairing the ergodicity of simulations, which can affect the quality of the resulting models. In this work, the effect of restraint types and simulation schemes on ergodicity and model quality was investigated by performing template‐restrained canonical molecular dynamics (MD), multiplexed replica‐exchange molecular dynamics, and Hamiltonian replica exchange molecular dynamics (HREMD) simulations with the coarse‐grained UNRES force field on nine selected proteins, with pseudo‐harmonic log‐Gaussian (unbounded) or Lorentzian (bounded) restraint functions. The best ergodicity was exhibited by HREMD. It has been found that non‐ergodicity does not affect model quality if good templates are used to generate restraints. However, when poor‐quality restraints not covering the entire protein are used, the improved ergodicity of HREMD can lead to significantly improved protein models. © 2017 Wiley Periodicals, Inc.     

Efficient estimation of binding free energies between peptides and an MHC class II molecule using coarse‐grained molecular dynamics simulations with a weighted histogram analysis method

We estimate the binding free energy between peptides and an MHC class II molecule using molecular dynamics (MD) simulations with the weighted histogram analysis method (WHAM). We show that, owing to its more thorough sampling in the available computational time, the binding free energy obtained by pulling the whole peptide using a coarse‐grained (CG) force field (MARTINI) is less prone to significant error induced by inadequate‐sampling than using an atomistic force field (AMBER). We further demonstrate that using CG MD to pull 3–4 residue peptide segments while leaving the remaining peptide segments in the binding groove and adding up the binding free energies of all peptide segments gives robust binding free energy estimations, which are in good agreement with the experimentally measured binding affinities for the peptide sequences studied. Our approach thus provides a promising and computationally efficient way to rapidly and reliably estimate the binding free energy between an arbitrary peptide and an MHC class II molecule. © 2017 Wiley Periodicals, Inc.     

A new soft‐core potential function for molecular dynamics applied to the prediction of protein loop conformations

We have developed a new soft‐core potential function for the conformational search of complex systems with molecular dynamics. The potential function was designed to maintain the main equilibrium properties of the original force field, which means that the soft‐core potential gives physically realistic performance also without additional restraints, different from most of the previous soft‐core potential functions. The performance of the method was demonstrated by applying it to the problem of finding native conformations for protein loops. Short loops from neocarzinostatin and parvalbumin were used as the first test cases. The use of the new soft‐core potential function was shown to improve significantly the performance of molecular dynamics in the search of the native conformation of protein loops. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 388–397, 2000     

Synthesis,crystal structure and activity evaluation of novel 3,4‐dihydro‐1‐benzoxepin‐5(2H)‐one derivatives as protein–tyrosine kinase (PTK) inhibitors

Four new 3,4‐dihydro‐1‐benzoxepin‐5(2H )‐one derivatives, namely (E )‐4‐(5‐bromo‐2‐hydroxybenzylidene)‐6,8‐dimethoxy‐3,4‐dihydrobenzo[b ]oxepin‐5(2H )‐one, ( 7 ), (E )‐4‐[(E )‐3‐(5‐bromo‐2‐hydroxyphenyl)allylidene]‐6,8‐dimethoxy‐3,4‐dihydrobenzo[b ]oxepin‐5(2H )‐one, ( 8 ), (E )‐4‐(5‐bromo‐2‐hydroxybenzylidene)‐6‐hydroxy‐8‐methoxy‐3,4‐dihydrobenzo[b ]oxepin‐5(2H )‐one, C₁₈H₁₅BrO₅, ( 9 ), and (E )‐4‐[(E )‐3‐(5‐bromo‐2‐hydroxyphenyl)allylidene]‐6‐hydroxy‐8‐methoxy‐3,4‐dihydrobenzo[b ]oxepin‐5(2H )‐one, ( 10 ), have been synthesized and characterized by FT–IR, NMR and MS. The structure of ( 9 ) was confirmed by single‐crystal X‐ray diffraction. Crystal structure analysis shows that molecules of ( 9 ) are connected into a one‐dimensional chain in the [010] direction through classical hydrogen bonds and these chains are further extended into a three‐dimensional network via C—H…O interactions. The inhibitory activities of these compounds against protein–tyrosine kinases (PTKs) show that 6‐hydroxy‐substituted compounds ( 9 ) and ( 10 ) are more effective for inhibiting ErbB1 and ErbB2 than are 6‐methoxy‐substituted compounds ( 7 ) and ( 8 ). This may be because ( 9 ) and ( 10 ) could effectively bind to the active pockets of the protein through intermolecular interactions.     

Poly(L‐lysine) and clay nanocomposite with desired matrix secondary structure: Effects of polypeptide molecular weight

Nanocomposites (NC) were formed using cationic poly(L ‐lysine) (PLL), a semicrystalline polypeptide, that was reinforced by sodium montmorillonite (MMT) clay via solution intercalation technique. By varying solution conditions such as pH, temperature, and polypeptide concentration in the presence of clay platelets, the secondary structure of PLL was controllably altered into α‐helical, β‐sheet, and random coil. The high molecular weight polypeptide shows a strong propensity to fold into the β‐sheet structure when cast as films, irrespective of the initial secondary structure in solution. Nanocomposite local morphology confirms intercalated MMT platelets with PLL over a wide range of compositions. © 2006 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 45: 239–252, 2007.     

Synthesis and characterization of novel chelated dimethylamino lithium arylamide dimers: molecular structure of [1‐LiNPhCHPhCH2‐2‐NMe2C6H4]2

The reaction of 1‐NHPhCHPh‐2‐NMe₂C₆H₄ ( 1 ) and 1‐NHPhCHPhCH₂‐2‐NMe₂C₆H₄ ( 2 ) with n‐BuLi in diethyl ether gave the solvent‐free chelated dimethylamino lithium amides [1‐LiNPhCHPh‐2‐NMe₂C₆H₄]₂ ( 3 ) and [1‐LiNPhCHPhCH₂‐2‐NMe₂C₆H₄]₂ ( 4 ). The lithium amides 3 and 4 were characterized by ¹H, ⁷Li, and ¹³C NMR spectroscopy. A crystal structure determination was carried out on 4 , which is the first example of a structurally characterized solvent‐free dimeric chelated dimethylamino lithium arylamide with three‐coordinate lithium centers that contains a seven‐membered chelate ring. Copyright © 2003 John Wiley & Sons, Ltd.     

Placevent: An algorithm for prediction of explicit solvent atom distribution—Application to HIV‐1 protease and F‐ATP synthase

We have created a simple algorithm for automatically predicting the explicit solvent atom distribution of biomolecules. The explicit distribution is coerced from the three‐dimensional (3D) continuous distribution resulting from a 3D reference interaction site model (3D‐RISM) calculation. This procedure predicts optimal location of solvent molecules and ions given a rigid biomolecular structure and the solvent composition. We show examples of predicting water molecules near the KNI‐272 bound form of HIV‐1 protease and predicting both sodium ions and water molecules near the rotor ring of F‐adenosine triphosphate (ATP) synthase. Our results give excellent agreement with experimental structure with an average prediction error of 0.39–0.65 Å. Further, unlike experimental methods, this method does not suffer from the partial occupancy limit. Our method can be performed directly on 3D‐RISM output within minutes. It is extremely useful for examining multiple specific solvent–solute interactions, as a convenient method for generating initial solvent structures for molecular dynamics calculations, and may assist in refinement of experimental structures. © 2012 Wiley Periodicals, Inc.     

Complete experimental and theoretical proton and carbon nuclear magnetic resonance spectral assignments,molecular structure and conformational study of 1‐cyclohexylpiperazine and 1‐(4‐pyridyl)piperazine

The possible stable forms and molecular structures of 1‐cyclohexylpiperazine (1‐chpp) and 1‐(4‐pyridyl)piperazine (1‐4pypp) molecules have been studied experimentally and theoretically using nuclear magnetic resonance(NMR) spectroscopy. ¹³C, ¹⁵N cross‐polarization magic‐angle spinning NMR and liquid phase¹H, ¹³C, DEPT, COSY, HETCOR and INADEQUATE NMR spectra of 1‐chpp (C₁₀H₂₀N₂) and 1‐4pypp (C₉H₁₃N₂) have been reported. Solvent effects on nuclear magnetic shielding tensors have been investigated using CDCl₃, CD₃ OD, dimethylsulfoxide (DMSO)‐d₆, (CD₃)₂CO, D₂O and CD₂Cl₂. ¹H and ¹³C NMR chemical shifts have been calculated for the most stable two conformers, equatorial–equatorial (e–e) and axial–equatorial (a–e) forms of 1‐chpp and 1‐4pypp using B3LYP/6‐311++G(d,p)//6‐31G(d) level of theory. Results from experimental and theoretical data showed that the molecular geometry and the mole fractions of stable conformers of both molecules are solvent dependent. Copyright © 2009 John Wiley & Sons, Ltd.