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1.  Variational Implicit Solvation with Poisson–Boltzmann Theory 
We incorporate the Poisson–Boltzmann (PB) theory of electrostatics into our variational implicit-solvent model (VISM) for the solvation of charged molecules in an aqueous solvent. In order to numerically relax the VISM free-energy functional by our level-set method, we develop highly accurate methods for solving the dielectric PB equation and for computing the dielectric boundary force. We also apply our VISM-PB theory to analyze the solvent potentials of mean force and the effect of charges on the hydrophobic hydration for some selected molecular systems. These include some single ions, two charged particles, two charged plates, and the host–guest system Cucurbit[7]uril and Bicyclo[2.2.2]octane. Our computational results show that VISM with PB theory can capture well the sensitive response of capillary evaporation to the charge in hydrophobic confinement and the polymodal hydration behavior and can provide accurate estimates of binding affinity of the host–guest system. We finally discuss several issues for further improvement of VISM.
PMCID: PMC3985794  PMID: 24803864
2.  Structure, mechanism, and dynamics of UDP-galactopyranose mutase 
The flavoenzyme UDP-galactopyranose mutase (UGM) is a key enzyme in galactofuranose biosynthesis. The enzyme catalyzes the 6-to-5 ring contraction of UDP-galactopyranose to UDP-galactofuranose. Galactofuranose is absent in humans yet is an essential component of bacterial and fungal cell walls and a cell surface virulence factor in protozoan parasites. Thus, inhibition of galactofuranose biosynthesis is a valid strategy for developing new antimicrobials. UGM is an excellent target in this effort because the product of the UGM reaction represents the first appearance of galactofuranose in the biosynthetic pathway. The UGM reaction is redox neutral, which is atypical for flavoenzymes, motivating intense examination of the chemical mechanism and structural features that tune the flavin for its unique role in catalysis. These studies show that the flavin functions as nucleophile, forming a flavin-sugar adduct that facilitates galactose-ring opening and contraction. The 3-dimensional fold is novel and conserved among all UGMs, however the larger eukaryotic enzymes have additional secondary structure elements that lead to significant differences in quaternary structure, substrate conformation, and conformational flexibility. Here we present a comprehensive review of UGM three-dimensional structure, provide an update on recent developments in understanding the mechanism of the enzyme, and summarize computational studies of active site flexibility.
PMCID: PMC3946560  PMID: 24096172
flavin-dependent reaction; galactofuranose; non-redox reaction; neglected diseases; tuberculosis; redox-switch; conformational changes; protein dynamics
3.  The Marine Cyanobacterial Metabolite Gallinamide A is a Potent and Selective Inhibitor of Human Cathepsin L 
Journal of natural products  2013;77(1):92-99.
A number of marine natural products are potent inhibitors of proteases, an important drug target class in human diseases. Hence, marine cyanobacterial extracts were assessed for inhibitory activity to human cathepsin L. Herein, we have shown that gallinamide A potently and selectively inhibits the human cysteine protease, cathepsin L. With 30 min of preincubation, gallinamide A displayed an IC50 of 5.0 nM, and kinetic analysis demonstrated an inhibition constant of ki = 9000 ± 260 M−1 s−1. Preincubation-dilution and activity-probe experiments revealed an irreversible mode of inhibition, and comparative IC50 values display a 28- to 320- fold greater selectivity toward cathepsin L than closely related human cysteine cathepsins V or B. Molecular docking and molecular dynamics simulations were used to determine the pose of gallinamide in the active site of cathepsin L. These data resulted in the identification of a pose characterized by high stability, a consistent hydrogen bond network, and the reactive Michael acceptor enamide of gallinamide A positioned near the active site cysteine of the protease, leading to a proposed mechanism of covalent inhibition. These data reveal and characterize the novel activity of gallinamide A as a potent inhibitor of human cathepsin L.
PMCID: PMC3932306  PMID: 24364476
4.  Discovery of Staphylococcus aureus Sortase A Inhibitors Using Virtual Screening and the Relaxed Complex Scheme 
Chemical biology & drug design  2013;82(4):10.1111/cbdd.12167.
Staphylococcus aureus is the leading cause of hospital-acquired infections in the United States. The emergence of multi-drug resistant strains of S. aureus has created an urgent need for new antibiotics. S. aureus uses the sortase A (SrtA) enzyme to display surface virulence factors suggesting that compounds that inhibit its activity will function as potent anti-infective agents. Here we report the identification of several inhibitors of SrtA using virtual screening methods that employ the relaxed complex scheme, an advanced computer-docking methodology that accounts for protein receptor flexibility. Experimental testing validates that several compounds identified in the screen inhibit the activity of SrtA. A lead compound based on the 2-phenyl-2,3-dihydro-1H-perimidine scaffold is particularly promising and its binding mechanism was further investigated using molecular dynamics simulations and by conducting preliminary structure activity relationship studies.
PMCID: PMC3841297  PMID: 23701677
Staphylococcus aureus; MRSA; sortase; SrtA; transpeptidation; Gram-positive; drug discovery; virtual screening; relaxed complex scheme; molecular dynamics; docking
5.  Thermodynamic integration to predict host-guest binding affinities 
An alchemical free energy method with explicit solvent molecular dynamics simulations was applied as part of the blind prediction contest SAMPL3 to calculate binding free energies for seven guests to an acyclic cucurbit-[n]uril host. The predictions included determination of protonation states for both host and guests, docking pose generation, and binding free energy calculations using thermodynamic integration. We found a root mean square error (RMSE) of 3.6 kcal mol−1 from the reference experimental results, with an R2 correlation of 0.51. The agreement with experiment for the largest contributor to this error, guest 6, is improved by 1.7 kcal mol−1 when a periodicity-induced free energy correction is applied. The corrections for the other ligands were significantly smaller, and altogether the RMSE was reduced by 0.4 kcal mol−1. We link properties of the host-guest systems during simulation to errors in the computed free energies. Overall, we show that charged host-guest systems studied here, initialized in unconfirmed docking poses, present a challenge to accurate alchemical simulation methods.
PMCID: PMC4113475  PMID: 22350568
Thermodynamic integration; Molecular dynamics; Docking; Host-guest; Blind prediction
6.  Molecular Dynamics Simulation Study of Conformational Changes of Transcription Factor TFIIS during RNA Polymerase II Transcriptional Arrest and Reactivation 
PLoS ONE  2014;9(5):e97975.
Transcription factor IIS (TFIIS) is a protein known for catalyzing the cleavage reaction of the 3′-end of backtracked RNA transcript, allowing RNA polymerase II (Pol II) to reactivate the transcription process from the arrested state. Recent structural studies have provided a molecular basis of protein-protein interaction between TFIIS and Pol II. However, the detailed dynamic conformational changes of TFIIS upon binding to Pol II and the related thermodynamic information are largely unknown. Here we use computational approaches to investigate the conformational space of TFIIS in the Pol II-bound and Pol II-free (unbound) states. Our results reveal two distinct conformations of TFIIS: the closed and the open forms. The closed form is dominant in the Pol II-free (unbound) state of TFIIS, whereas the open form is favorable in the Pol II-bound state. Furthermore, we discuss the free energy difference involved in the conformational changes between the two forms in the presence or absence of Pol II. Additionally, our analysis indicates that hydrophobic interactions and the protein-protein interactions between TFIIS and Pol II are crucial for inducing the conformational changes of TFIIS. Our results provide novel insights into the functional interplay between Pol II and TFIIS as well as mechanism of reactivation of Pol II transcription by TFIIS.
PMCID: PMC4026522  PMID: 24842057
7.  Accelerated Molecular Dynamics Simulations with the AMOEBA Polarizable Force Field on Graphics Processing Units 
The accelerated molecular dynamics (aMD) method has recently been shown to enhance the sampling of biomolecules in molecular dynamics (MD) simulations, often by several orders of magnitude. Here, we describe an implementation of the aMD method for the OpenMM application layer that takes full advantage of graphics processing units (GPUs) computing. The aMD method is shown to work in combination with the AMOEBA polarizable force field (AMOEBA-aMD), allowing the simulation of long time-scale events with a polarizable force field. Benchmarks are provided to show that the AMOEBA-aMD method is efficiently implemented and produces accurate results in its standard parametrization. For the BPTI protein, we demonstrate that the protein structure described with AMOEBA remains stable even on the extended time scales accessed at high levels of accelerations. For the DNA repair metalloenzyme endonuclease IV, we show that the use of the AMOEBA force field is a significant improvement over fixed charged models for describing the enzyme active-site. The new AMOEBA-aMD method is publicly available ( and promises to be interesting for studying complex systems that can benefit from both the use of a polarizable force field and enhanced sampling.
PMCID: PMC3948463  PMID: 24634618
8.  Free energy landscape of G-protein coupled receptors, explored by accelerated molecular dynamics† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c3cp53962h Click here for additional data file.  
Physical Chemistry Chemical Physics  2014;16(14):6398-6406.
G-protein coupled receptors (GPCRs) mediate cellular responses to various hormones and neurotransmitters and are important targets for treating a wide spectrum of diseases.
G-protein coupled receptors (GPCRs) mediate cellular responses to various hormones and neurotransmitters and are important targets for treating a wide spectrum of diseases. They are known to adopt multiple conformational states (e.g., inactive, intermediate and active) during their modulation of various cell signaling pathways. Here, the free energy landscape of GPCRs is explored using accelerated molecular dynamics (aMD) simulations as demonstrated on the M2 muscarinic receptor, a key GPCR that regulates human heart rate and contractile forces of cardiomyocytes. Free energy profiles of important structural motifs that undergo conformational transitions upon GPCR activation and allosteric signaling are analyzed in detail, including the Arg3.50–Glu6.30 ionic lock, the Trp6.48 toggle switch and the hydrogen interactions between Tyr5.58–Tyr7.53.
PMCID: PMC3960983  PMID: 24445284
9.  AutoGrow 3.0: An Improved Algorithm for Chemically Tractable, Semi-Automated Protein Inhibitor Design 
Journal of molecular graphics & modelling  2013;44:10.1016/j.jmgm.2013.05.006.
We here present an improved version of AutoGrow (version 3.0), an evolutionary algorithm that works in conjunction with existing open-source software to automatically optimize candidate ligands for predicted binding affinity and other druglike properties. Though no substitute for the medicinal chemist, AutoGrow 3.0, unlike its predecessors, attempts to introduce some chemical intuition into the automated optimization process. AutoGrow 3.0 uses the rules of click chemistry to guide optimization, greatly enhancing synthesizability. Additionally, the program discards any growing ligand whose physical and chemical properties are not druglike. By carefully crafting chemically feasible druglike molecules, we hope that AutoGrow 3.0 will help supplement the chemist's efforts.
To demonstrate the utility of the program, we used AutoGrow 3.0 to generate predicted inhibitors of three important drug targets: T. brucei RNA editing ligase 1, peroxisome proliferator-activated receptor γ, and dihydrofolate reductase. In all cases, AutoGrow generated druglike molecules with high predicted binding affinities.
AutoGrow 3.0 is available free of charge ( under the terms of the GNU General Public License and has been tested on Linux and Mac OS X.
PMCID: PMC3842281  PMID: 23792207
drug design; click chemistry; autogrow; computational chemistry
10.  Utilizing a Dynamical Description of IspH to Aid in the Development of Novel Antimicrobial Drugs 
PLoS Computational Biology  2013;9(12):e1003395.
The nonmevalonate pathway is responsible for isoprenoid production in microbes, including H. pylori, M. tuberculosis and P. falciparum, but is nonexistent in humans, thus providing a desirable route for antibacterial and antimalarial drug discovery. We coordinate a structural study of IspH, a [4Fe-4S] protein responsible for converting HMBPP to IPP and DMAPP in the ultimate step in the nonmevalonate pathway. By performing accelerated molecular dynamics simulations on both substrate-free and HMBPP-bound [Fe4S4]2+ IspH, we elucidate how substrate binding alters the dynamics of the protein. Using principal component analysis, we note that while substrate-free IspH samples various open and closed conformations, the closed conformation observed experimentally for HMBPP-bound IspH is inaccessible in the absence of HMBPP. In contrast, simulations with HMBPP bound are restricted from accessing the open states sampled by the substrate-free simulations. Further investigation of the substrate-free simulations reveals large fluctuations in the HMBPP binding pocket, as well as allosteric pocket openings – both of which are achieved through the hinge motions of the individual domains in IspH. Coupling these findings with solvent mapping and various structural analyses reveals alternative druggable sites that may be exploited in future drug design efforts.
Author Summary
Drug resistance has recently entered into media conversations through the lens of MRSA (methicillin-resistant Staphylococcus aureus) infections, but conventional therapies are also failing to address resistance in cases of malaria and other bacterial infections, such as tuberculosis. To address these problems, we must develop new antibacterial and antimalarial medications. Our research focuses on understanding the structure and dynamics of IspH, an enzyme whose function is necessary for the survival of most bacteria and malaria-causing protozoans. Using computer simulations, we track how the structure of IspH changes in the presence and absence of its natural substrate. By inspecting the pockets that form in the normal motions of IspH, we propose a couple new routes by which new molecules may be developed to disrupt the function of IspH. It is our hope that these structural studies may be precursors to the development of novel therapies that may add to our current arsenal against bacterial and malarial infections.
PMCID: PMC3868525  PMID: 24367248
11.  Multi-core CPU or GPU-accelerated Multiscale Modeling for Biomolecular Complexes 
Molecular based mathematical biology  2013;1:10.2478/mlbmb-2013-0009.
Multi-scale modeling plays an important role in understanding the structure and biological functionalities of large biomolecular complexes. In this paper, we present an efficient computational framework to construct multi-scale models from atomic resolution data in the Protein Data Bank (PDB), which is accelerated by multi-core CPU and programmable Graphics Processing Units (GPU). A multi-level summation of Gaus-sian kernel functions is employed to generate implicit models for biomolecules. The coefficients in the summation are designed as functions of the structure indices, which specify the structures at a certain level and enable a local resolution control on the biomolecular surface. A method called neighboring search is adopted to locate the grid points close to the expected biomolecular surface, and reduce the number of grids to be analyzed. For a specific grid point, a KD-tree or bounding volume hierarchy is applied to search for the atoms contributing to its density computation, and faraway atoms are ignored due to the decay of Gaussian kernel functions. In addition to density map construction, three modes are also employed and compared during mesh generation and quality improvement to generate high quality tetrahedral meshes: CPU sequential, multi-core CPU parallel and GPU parallel. We have applied our algorithm to several large proteins and obtained good results.
PMCID: PMC3858848  PMID: 24352481
efficient computation; multi-scale modeling; biomolecular complex * mesh generation; multi-core CPU; GPU
12.  Farnesyl diphosphate synthase inhibitors from in silico screening 
Chemical biology & drug design  2013;81(6):742-748.
The relaxed complex scheme is an in silico drug screening method that accounts for receptor flexibility by using molecular dynamics simulations. Here, we used this approach combined with similarity searches and experimental inhibition assays to identify several low micro-molar, non-bisphosphonate inhibitors, bisamidines, of farnesyl diphosphate synthase (FPPS), an enzyme targeted by some anti-cancer and anti-microbial agents and for the treatment of bone resorption diseases. This novel class of FPPS inhibitors have more drug-like properties than existing bisphosphonate inhibitors, making them interesting pharmaceutical leads.
PMCID: PMC3671582  PMID: 23421555
13.  Population Based Reweighting of Scaled Molecular Dynamics 
The Journal of Physical Chemistry. B  2013;117(42):12759-12768.
Molecular dynamics simulation using enhanced sampling methods is one of the powerful computational tools used to explore protein conformations and free energy landscapes. Enhanced sampling methods often employ either an increase in temperature or a flattening of the potential energy surface to rapidly sample phase space, and a corresponding reweighting algorithm is used to recover the Boltzmann statistics. However, potential energies of complex biomolecules usually involve large fluctuations on a magnitude of hundreds of kcal/mol despite minimal structural changes during simulation. This leads to noisy reweighting statistics and complicates the obtainment of accurate final results. To overcome this common issue in enhanced conformational sampling, we propose a scaled molecular dynamics method, which modifies the biomolecular potential energy surface and employs a reweighting scheme based on configurational populations. Statistical mechanical theory is applied to derive the reweighting formula, and the canonical ensemble of simulated structures is recovered accordingly. Test simulations on alanine dipeptide and the fast folding polypeptide Chignolin exhibit sufficiently enhanced conformational sampling and accurate recovery of free energy surfaces and thermodynamic properties. The results are comparable to long conventional molecular dynamics simulations and exhibit better recovery of canonical statistics over methods which employ a potential energy term in reweighting.
PMCID: PMC3808002  PMID: 23721224
14.  Correlated Motions and Residual Frustration in Thrombin 
The Journal of Physical Chemistry. B  2013;117(42):12857-12863.
Thrombin is the central protease in the cascade of blood coagulation proteases. The structure of thrombin consists of a double β-barrel core surrounded by connecting loops and helices. Compared to chymotrypsin, thrombin has more extended loops that are thought to have arisen from insertions in the serine protease that evolved to impart greater specificity. Previous experiments showed thermodynamic coupling between ligand binding at the active site and distal exosites. We present a combined approach of molecular dynamics (MD), accelerated molecular dynamics (AMD), and analysis of the residual local frustration of apo-thrombin and active-site-bound (PPACK-thrombin). Community analysis of the MD ensembles identified changes upon active site occupation in groups of residues linked through correlated motions and physical contacts. AMD simulations, calibrated on measured residual dipolar couplings, reveal that upon active site ligation, correlated loop motions are quenched, but new ones connecting the active site with distal sites where allosteric regulators bind emerge. Residual local frustration analysis reveals a striking correlation between frustrated contacts and regions undergoing slow time scale dynamics. The results elucidate a motional network that probably evolved through retention of frustrated contacts to provide facile conversion between ensembles of states.
PMCID: PMC3808083  PMID: 23621631
15.  Variational Implicit-Solvent Modeling of Host–Guest Binding: A Case Study on Cucurbit[7]uril| 
The synthetic host cucurbit[7]uril (CB[7]) binds aromatic guests or metal complexes with ultrahigh affinity compared with that typically displayed in protein–ligand binding. Due to its small size, CB[7] serves as an ideal receptor–ligand system for developing computational methods for molecular recognition. Here, we apply the recently developed variational implicit-solvent model (VISM), numerically evaluated by the level-set method, to study hydration effects in the high-affinity binding of the B2 bicyclo[2.2.2]octane derivative to CB[7]. For the unbound host, we find that the host cavity favors the hydrated state over the dry state due to electrostatic effects. For the guest binding, we find reasonable agreement to experimental binding affinities. Dissection of the individual VISM free-energy contributions shows that the major driving forces are water-mediated hydrophobic interactions and the intrinsic (vacuum) host–guest van der Waals interactions. These findings are in line with recent experiments and molecular dynamics simulations with explicit solvent. It is expected that the level-set VISM, with further refinement on the electrostatic descriptions, can efficiently predict molecular binding and recognition in a wide range of future applications.
PMCID: PMC3770055  PMID: 24039554
16.  Simulations of Biased Agonists in the β2 Adrenergic Receptor with Accelerated Molecular Dynamics 
Biochemistry  2013;52(33):5593-5603.
The biased agonism of the G protein-coupled receptors (GPCRs), where in addition to a traditional G protein-signaling pathway a GPCR promotes intracellular signals though β-arrestin, is a novel paradigm in pharmacology. Biochemical and biophysical studies have suggested that a GPCR forms a distinct ensemble of conformations signaling through the G protein and β-arrestin. Here we report on the dynamics of the β2 adrenergic receptor bound to the β-arrestin and G protein-biased agonists and the empty receptor to further characterize the receptor conformational changes caused by biased agonists. We use conventional and accelerated molecular dynamics (aMD) simulations to explore the conformational transitions of the GPCR from the active state to the inactive state. We found that aMD simulations enable monitoring of the transition within the nanosecond time scale while capturing the known microscopic characteristics of the inactive states, such as the ionic lock, the inward position of F6.44, and water clusters. Distinct conformational states are shown to be stabilized by each biased agonist. In particular, in simulations of the receptor with the β-arrestin-biased agonist N-cyclopentylbutanepherine, we observe a different pattern of motions in helix 7 when compared to simulations with the G protein-biased agonist salbutamol that involves perturbations of the network of interactions within the NPxxY motif. Understanding the network of interactions induced by biased ligands and the subsequent receptor conformational shifts will lead to development of more efficient drugs.
PMCID: PMC3763781  PMID: 23879802
17.  Iterative Molecular Dynamics—Rosetta Protein Structure Refinement Protocol to Improve Model Quality 
Rosetta is one of the prime tools for high resolution protein structure refinement. While its scoring function can distinguish native-like from non-native-like conformations in many cases, the method is limited by conformational sampling for larger proteins, that is, leaving a local energy minimum in which the search algorithm may get stuck. Here, we test the hypothesis that iteration of Rosetta with an orthogonal sampling and scoring strategy might facilitate exploration of conformational space. Specifically, we run short molecular dynamics (MD) simulations on models created by de novo folding of large proteins into cryoEM density maps to enable sampling of conformational space not directly accessible to Rosetta and thus provide an escape route from the conformational traps. We present a combined MD–Rosetta protein structure refinement protocol that can overcome some of these sampling limitations. Two of four benchmark proteins showed incremental improvement through all three rounds of the iterative refinement protocol. Molecular dynamics is most efficient in applying subtle but important rearrangements within secondary structure elements and is thus highly complementary to the Rosetta refinement, which focuses on side chains and loop regions.
PMCID: PMC3744128  PMID: 23956701
18.  Comparing Neural-Network Scoring Functions and the State of the Art: Applications to Common Library Screening 
We compare established docking programs, AutoDock Vina and Schrödinger’s Glide, to the recently published NNScore scoring functions. As expected, the best protocol to use in a virtual-screening project is highly dependent on the target receptor being studied. However, the mean screening performance obtained when candidate ligands are docked with Vina and rescored with NNScore 1.0 is not statistically different than the mean performance obtained when docking and scoring with Glide. We further demonstrate that the Vina and NNScore docking scores both correlate with chemical properties like small-molecule size and polarizability. Compensating for these potential biases leads to improvements in virtual screen performance. Composite NNScore-based scoring functions suited to a specific receptor further improve performance. We are hopeful that the current study will prove useful for those interested in computer-aided drug design.
PMCID: PMC3735370  PMID: 23734946
19.  iAPBS: a programming interface to Adaptive Poisson-Boltzmann Solver (APBS) 
The Adaptive Poisson-Boltzmann Solver (APBS) is a state-of-the-art suite for performing Poisson-Boltzmann electrostatic calculations on biomolecules. The iAPBS package provides a modular programmatic interface to the APBS library of electrostatic calculation routines. The iAPBS interface library can be linked with a FORTRAN or C/C++ program thus making all of the APBS functionality available from within the application. Several application modules for popular molecular dynamics simulation packages – Amber, NAMD and CHARMM are distributed with iAPBS allowing users of these packages to perform implicit solvent electrostatic calculations with APBS.
PMCID: PMC3419494  PMID: 22905037
20.  Insertion of the Ca2+-Independent Phospholipase A2 into a Phospholipid Bilayer via Coarse-Grained and Atomistic Molecular Dynamics Simulations 
PLoS Computational Biology  2013;9(7):e1003156.
Group VI Ca2+-independent phospholipase A2 (iPLA2) is a water-soluble enzyme that is active when associated with phospholipid membranes. Despite its clear pharmaceutical relevance, no X-ray or NMR structural information is currently available for the iPLA2 or its membrane complex. In this paper, we combine homology modeling with coarse-grained (CG) and all-atom (AA) molecular dynamics (MD) simulations to build structural models of iPLA2 in association with a phospholipid bilayer. CG-MD simulations of the membrane insertion process were employed to provide a starting point for an atomistic description. Six AA-MD simulations were then conducted for 60 ns, starting from different initial CG structures, to refine the membrane complex. The resulting structures are shown to be consistent with each other and with deuterium exchange mass spectrometry (DXMS) experiments, suggesting that our approach is suitable for the modeling of iPLA2 at the membrane surface. The models show that an anchoring region (residues 710–724) forms an amphipathic helix that is stabilized by the membrane. In future studies, the proposed iPLA2 models should provide a structural basis for understanding the mechanisms of lipid extraction and drug-inhibition. In addition, the dual-resolution approach discussed here should provide the means for the future exploration of the impact of lipid diversity and sequence mutations on the activity of iPLA2 and related enzymes.
Author Summary
The Ca2+-independent phospholipase A2 (iPLA2) enzyme is a potential target for the development of medicinal agents against heart and neurological diseases, multiple sclerosis, arthritis, and cancer. However, no structural information is currently available for the iPLA2. The binding of the enzyme to human membranes is driven by favorable electrostatic and non-polar interactions, but the detailed influence of these factors is not well understood. In this paper, we have combined coarse-grained and all-atom simulations of a homology model of the iPLA2. The coarse-grained description allows highly efficient simulations of the protein insertion into a lipid bilayer, while the all-atom simulations are used to refine the structures of the protein–membrane complexes. Finally, the resulting structures are validated experimentally with deuterium exchange experiments. In future works, this approach could be used to build models of other PLA2s. The iPLA2 models presented here open the door to the computational design of new inhibitors with improved potency and selectivity.
PMCID: PMC3723492  PMID: 23935474
21.  Accounting for receptor flexibility and enhanced sampling methods in computer aided drug design 
Chemical biology & drug design  2013;81(1):10.1111/cbdd.12051.
Protein flexibility plays a major role in biomolecular recognition. In many cases it is not obvious how molecular structure will change upon association with other molecules. In proteins these changes can be major, with large deviations in overall backbone structure, or they can be more subtle as in a side chain rotation. Either way the algorithms that predict the favorability of biomolecular association require relatively accurate predictions of the bound structure to give an accurate assessment of the energy involved in association. Here we review a number of techniques that have been proposed to accommodate receptor flexibility in the simulation of small molecules binding to protein receptors. We investigate modifications to standard rigid receptor docking algorithms, and also explore enhanced sampling techniques, and the combination of free energy calculations and enhanced sampling techniques. The understanding and allowance for receptor flexibility are helping to make computer simulations of ligand protein binding more accurate. These developments may help improve the efficiency of drug discovery and development. Efficiency will be essential as we begin to see personalized medicine tailored to individual patients, which means specific drugs are needed for each patient’s genetic makeup.
PMCID: PMC3540989  PMID: 23253130
Computer aided drug design; structure based drug design; receptor flexibility; ensemble docking; relaxed complex scheme; molecular dynamics; accelerated molecular dynamics; free energy calculation
23.  The Molecular Dynamics of Trypanosoma brucei UDP-Galactose 4′-Epimerase: A Drug Target for African Sleeping Sickness 
Chemical biology & drug design  2012;80(2):173-181.
During the past century, several epidemics of human African trypanosomiasis, a deadly disease caused by the protist Trypanosoma brucei, have afflicted sub-Saharan Africa. Over 10,000 new victims are reported each year, with hundreds of thousands more at risk. As current drug treatments are either highly toxic or ineffective, novel trypanocides are urgently needed. The T. brucei galactose-synthesis pathway is one potential therapeutic target. Though galactose is essential for T. brucei survival, the parasite lacks the transporters required to intake galactose from the environment. UDP-galactose 4′-epimerase (TbGalE) is responsible for the epimerization of UDP-glucose to UDP-galactose and so is of great interest to medicinal chemists. Using molecular dynamics simulations, we investigate the atomistic motions of TbGalE in both the apo and holo states. The sampled conformations and protein dynamics depend not only on the presence of a UDP-sugar ligand, but also on the chirality of the UDP-sugar C4 atom. This dependence provides important insights into TbGalE function and may help guide future computer-aided drug-discovery efforts targeting this protein.
PMCID: PMC3399956  PMID: 22487100
TbGalE; Trypanosoma brucei; UDP-Galactose-4’-Epimerase; African Sleeping Sickness; Molecular Dynamics; Protein Structure
24.  A Nonlinear Elasticity Model of Macromolecular Conformational Change Induced by Electrostatic Forces 
In this paper we propose a nonlinear elasticity model of macromolecular conformational change (deformation) induced by electrostatic forces generated by an implicit solvation model. The Poisson-Boltzmann equation for the electrostatic potential is analyzed in a domain varying with the elastic deformation of molecules, and a new continuous model of the electrostatic forces is developed to ensure solvability of the nonlinear elasticity equations. We derive the estimates of electrostatic forces corresponding to four types of perturbations to an electrostatic potential field, and establish the existance of an equilibrium configuration using a fixed-point argument, under the assumption that the change in the ionic strength and charges due to the additional molecules causing the deformation are sufficiently small. The results are valid for elastic models with arbitrarily complex dielectric interfaces and cavities, and can be generalized to large elastic deformation caused by high ionic strength, large charges, and strong external fields by using continuation methods.
PMCID: PMC2423821  PMID: 19461946
Macromolecular Conformational Change; Nonlinear Elasticity; Continuum Modeling; Poisson-Boltzmann equation; Electrostatic Force; Coupled System; Fixed Point
25.  Novel cruzain inhibitors for the treatment of Chagas’ disease 
Chemical biology & drug design  2012;80(3):398-405.
The protozoan parasite Trypanosoma cruzi, the etiological agent of Chagas’ disease, affects millions of individuals and continues to be an important global health concern. The poor efficacy and unfavorable side effects of current treatments necessitate novel therapeutics. Cruzain, the major cysteine protease of T. cruzi, is one potential novel target. Recent advances in a class of vinyl-sulfone inhibitors are encouraging; however, as most potential therapeutics fail in clinical trials and both disease progression and resistance call for combination therapy with several drugs, the identification of additional classes of inhibitory molecules is essential. Using an exhaustive virtual-screening and experimental-validation approach, we identify several additional small-molecule cruzain inhibitors. Further optimization of these chemical scaffolds could lead to the development of novel drugs useful in the treatment of Chagas’ disease.
PMCID: PMC3503458  PMID: 22613098
cruzain; cruzipain; Chagas’ disease; Trypanosoma cruzi; computer-aided drug discovery; cysteine protease inhibitor

Results 1-25 (179)