AMBER Software Research Articles

Applications of low-intensity pulsed ultrasound to increase monoclonal antibody production in CHO cells using shake flasks or wavebags

Many technologies, such as cell line screening and host cell engineering, culture media optimization and bioprocess optimization, have been proposed to increase monoclonal antibody (mAb) production in Chinese Hamster Ovary (CHO) cells. Unlike the existing biochemical approaches, we investigated stimulation using low-intensity pulsed ultrasound (LIPUS) as a purely physical approach, offering enhanced scalability, contamination control and cost-efficiency, while demonstrating significantly increased cell growth and antibody production. It was found that daily ultrasound treatments at 40 mW/cm2 for 5min during cell culture increased the production of human anti-IL-8 antibody by more than 30% using 10 or 30mL shake flasks. Further increasing the ultrasound dosage (either intensities or the treatment duration) did not appreciably increase cell growth or antibody production, however feeding the culture with additional highly-concentrated nutrients, glucose and amino acids (glutamine in this case), did further increase cell growth and antibody titer to 35%. Similar ultrasound treatments (40 mW/cm2, 5min per day) when scaled up to larger volume wavebags, resulted in a 25% increase in antibody production. Increased antibody production can be attributed to both elevated cell count and the ultrasound stimulation. Theoretical study of underlying mechanisms was performed through the simulations of molecular dynamics using the AMBER software package, with results showing that LIPUS increases cell permeability. The significance of this study is that LIPUS, as a physical-based stimulation approach, can be externally applied to the cell culture without worrying about contamination. By combining with the existing technologies in antibody production, LIPUS can achieve additional mAb yields. Because it can be easily integrated with existing cell culture apparatuses, the technology is expected to be more acceptable by the end users.

An investigation of the effects of hard and soft errors on graphics processing unit‐accelerated molecular dynamics simulations

SUMMARYMolecular dynamics (MD) simulations rely on the accurate evaluation and integration of Newton's equations of motion to propagate the positions of atoms in proteins during a simulation. As such, one can expect them to be sensitive to any form of numerical error that may occur during a simulation. Increasingly graphics processing units (GPUs) are being used to accelerate MD simulations. Current GPU architectures designed for high performance computing applications support error‐correcting codes (ECC) that detect and correct single bit‐flip soft error events in GPU memory; however, this error checking carries a penalty in terms of simulation speed. ECC is also a major distinguishing feature between high performance computing NVIDIA Tesla cards and the considerably more cost‐effective NVIDIA GeForce gaming cards. An argument often put forward for not using GeForce cards is that the results are unreliable because of the lack of ECC. In an initial attempt to quantify these concerns, an investigation of the reproducibility of GPU‐accelerated MD simulations using the AMBER software was conducted on the XSEDE supercomputer Keeneland, a cluster at Los Alamos National Laboratory, and a cluster at the San Diego Supercomputer Center. While the data collected are insufficient to make solid conclusions and more extensive testing is needed to provide quantitative statistics, the absence of ECC events and lack of any silent errors in all the simulations conducted to date suggest that these errors are exceedingly rare and as such the time and memory penalty of ECC may outweigh the utility of error checking functionality. However, a considerable amount of error originating from defective hardware was observed, which suggests that rigorous acceptance testing should be performed on new GPU‐based systems by repeatedly running reproducible yet realistic calculations.

계산화학적 방법을 통한 β-D-glucopyranose 구조 연구

본 연구에서는 <TEX>${\beta}$</TEX>-D-glucopyranose 분자의 hydroxymethyl group의 두 torsion angle의 변화에 따른 포텐셜 에너지의 변화를 진공 상태와 implicit water 상태에서 연구하였으며 이를 통해 Solvation Energy가 구조에 미치는 영향에 대해서 알아보았다. 계산에 사용한 프로그램은 AMBER package였으며, force field는 GLYCAM_06을 사용하였다. Solvation model은 Hawkins, Cramer, Truhlar 등이 제안한 generalized Born model을 사용하였다. 계산 결과, methyl hydroxyl group 내의 hydroxyl group이 고리구조의 hydroxyl group과 강한 수소결합이 가능한 영역에서 많은 변화가 일어났다. 이를 통해 solvation effect로 인해서 수소 결합의 중요성이 감소했다는 결론을 내렸다. In this study, we have investigated potential energy of <TEX>${\beta}$</TEX>-D-glucopyranose in vacuum and implicit water condition. By Comparing two conditions we find that how solvation energy influence <TEX>${\beta}$</TEX>-D-glucopyranose structure. We use AMBER package program and GLYCAM_06 force field. Solvation model was used for the generalized Born model with Hawkins, Cramer, Truhlar has been proposed. We conclude that difference of contour map of two conditions is caused by solvation effect by reducing hydrogen bonding interaction.

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald.

We present an implementation of explicit solvent all atom classical molecular dynamics (MD) within the AMBER program package that runs entirely on CUDA-enabled GPUs. First released publicly in April 2010 as part of version 11 of the AMBER MD package and further improved and optimized over the last two years, this implementation supports the three most widely used statistical mechanical ensembles (NVE, NVT, and NPT), uses particle mesh Ewald (PME) for the long-range electrostatics, and runs entirely on CUDA-enabled NVIDIA graphics processing units (GPUs), providing results that are statistically indistinguishable from the traditional CPU version of the software and with performance that exceeds that achievable by the CPU version of AMBER software running on all conventional CPU-based clusters and supercomputers. We briefly discuss three different precision models developed specifically for this work (SPDP, SPFP, and DPDP) and highlight the technical details of the approach as it extends beyond previously reported work [Götz et al., J. Chem. Theory Comput. 2012, DOI: 10.1021/ct200909j; Le Grand et al., Comp. Phys. Comm. 2013, DOI: 10.1016/j.cpc.2012.09.022].We highlight the substantial improvements in performance that are seen over traditional CPU-only machines and provide validation of our implementation and precision models. We also provide evidence supporting our decision to deprecate the previously described fully single precision (SPSP) model from the latest release of the AMBER software package.

PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data.

We describe PTRAJ and its successor CPPTRAJ, two complementary, portable, and freely available computer programs for the analysis and processing of time series of three-dimensional atomic positions (i.e., coordinate trajectories) and the data therein derived. Common tools include the ability to manipulate the data to convert among trajectory formats, process groups of trajectories generated with ensemble methods (e.g., replica exchange molecular dynamics), image with periodic boundary conditions, create average structures, strip subsets of the system, and perform calculations such as RMS fitting, measuring distances, B-factors, radii of gyration, radial distribution functions, and time correlations, among other actions and analyses. Both the PTRAJ and CPPTRAJ programs and source code are freely available under the GNU General Public License version 3 and are currently distributed within the AmberTools 12 suite of support programs that make up part of the Amber package of computer programs (see http://ambermd.org ). This overview describes the general design, features, and history of these two programs, as well as algorithmic improvements and new features available in CPPTRAJ.

Effects of generalized-Born implicit solvent models in NMR structure refinement

Rapid advances of computational power and method have made it practical to apply the time-consuming calculations with all-atom force fields and sophisticated potential energies into refining NMR structure. Added to the all-atom force field, generalized-Born implicit solvent model (GBIS) contributes substantially to improving the qualities of the resulting NMR structures. GBIS approximates the effects that explicit solvents bring about even with fairly reduced computational times. Although GBIS is employed in the final stage of NMR structure calculation with experimental restraints, the effects by GBIS on structures have been reported notable. However, the detailed effect is little studied in a quantitative way. In this study, we report GBIS refinements of ubiquitin and GB1 structures by six GBIS models of AMBER package with experimental distance and backbone torsion angle restraints. Of GBIS models tested, the calculations with igb

New linezolid-like 1,2,4-oxadiazoles active against Gram-positive multiresistant pathogens

The synthesis and the in vitro antibacterial activity of novel linezolid-like oxadiazoles are reported. Replacement of the linezolid morpholine C-ring with 1,2,4-oxadiazole results in an antibacterial activity against Staphylococcus aureus both methicillin-susceptible and methicillin-resistant comparable or even superior to that of linezolid. While acetamidomethyl or thioacetoamidomethyl moieties in the C(5) side-chain are required, fluorination of the phenyl B ring exhibits a slight effect on an antibacterial activity but its presence seems to reduce the compounds cytotoxicity. Molecular modeling performed using two different approaches – FLAP and Amber software – shows that in the binding pose of the newly synthesized compounds as compared with the crystallographic pose of linezolid, the 1,2,4-oxadiazole moiety seems to perfectly mimic the function of the morpholinic ring, since the H-bond interaction with U2585 is retained.

Exploring the Relationship between Sequences, Structures, Dynamical Behaviors and Functions of New Type Protein Drugs: DARPins

DARPins (designed ankyrin repeat proteins), new kinds of binding proteins, have the potential to overcome the defects of monoclonal antibodies, and hence may become the alternatives to antibodies and generate a novel therapeutic approach. DARPins can be selected to bind any given target proteins with high affinity and specificity. In the process of binding to target proteins, the reason why DARPins have high affinity to target proteins as well as the correlation among sequences, structures, dynamical behaviors and binding to target proteins are still unknown. This paper studied DARPins using the AMBER package with ff03 force field for molecular dynamics simulations, providing a theoretical basis for the research on a new type of protein drug. This shows that the DARPins have more dynamical behaviors regularity after binding to target proteins compared with non-binding DARPins, but the binding to target proteins does not always stabilize the structures of DARPins, and the changes in the regions of β-turn and loop are the most obvious. The changes in hydrogen bonds and hydrophobic interactions have close relationship with the changes in the stability and cross correlation of DARPins.

Multiscale modeling of solvation in chemical and biological nanosystems and in nanoporous materials

Statistical–mechanical, 3D-RISM-KH molecular theory of solvation (3D reference interaction site model with the Kovalenko–Hirata closure) is promising as an essential part of multiscale methodology for chemical and biomolecular nanosystems in solution. 3D-RISM-KH explains the molecular mechanisms of self-assembly and conformational stability of synthetic organic rosette nanotubes (RNTs), aggregation of prion proteins and β-sheet amyloid oligomers, protein-ligand binding, and function-related solvation properties of complexes as large as the Gloeobacter violaceus pentameric ligand-gated ion channel (GLIC) and GroEL/ES chaperone. Molecular mechanics/Poisson–Boltzmann (generalized Born) surface area [MM/PB(GB)SA] post-processing of molecular dynamics (MD) trajectories involving SA empirical nonpolar terms is replaced with MM/3D-RISM-KH statistical–mechanical evaluation of the solvation thermodynamics. 3D-RISM-KH has been coupled with multiple time-step (MTS) MD of the solute biomolecule driven by effective solvation forces, which are obtained analytically by converging the 3D-RISM-KH integral equations at outer time-steps and are calculated in between by using solvation force coordinate extrapolation (SFCE) in the subspace of previous solutions to 3D-RISM-KH. The procedure is stabilized by the optimized isokinetic Nosé–Hoover (OIN) chain thermostatting, which enables gigantic outer time-steps up to picoseconds to accurately calculate equilibrium properties. The multiscale OIN/SFCE/3D-RISM-KH algorithm is implemented in the Amber package and illustrated on a fully flexible model of alanine dipeptide in aqueous solution, exhibiting the computational rate of solvent sampling 20 times faster than standard MD with explicit solvent. Further substantial acceleration can be achieved with 3D-RISM-KH efficiently sampling essential events with rare statistics such as exchange and localization of solvent, ions, and ligands at binding sites and pockets of the biomolecule. 3D-RISM-KH was coupled with ab initio complete active space self-consistent field (CASSCF) and orbital-free embedding (OFE) Kohn–Sham (KS) density functional theory (DFT) quantum chemistry methods in an SCF description of electronic structure, optimized geometry, and chemical reactions in solution. The (OFE)KS-DFT/3D-RISM-KH multi-scale method is implemented in the Amsterdam Density Functional (ADF) package and extensively validated against experiment for solvation thermochemistry, photochemistry, conformational equilibria, and activation barriers of various nanosystems in solvents and ionic liquids (ILs). Finally, the replica RISM-KH-VM molecular theory for the solvation structure, thermodynamics, and electrochemistry of electrolyte solutions sorbed in nanoporous materials reveals the molecular mechanisms of sorption and supercapacitance in nanoporous carbon electrodes, which is drastically different from a planar electrical double layer.

Molecular Modeling Study on the Three-dimensional Structure of the Luciferase Protein inVibrio-qinghaiensissp.-Q67

Bioluminescence technique derived from the luciferase-based catalization reactions has been widely used in chemistry, biological assay and environmental science. The three-dimensional crystal structures of luciferase proteins in some firefly and luminescent bacteria were elucidated. Vibrio qinghaiensis sp.-Q67 (Q67), one of freshwater luminescent bacteria which was extracted from Gymnocypris przewalskii in Qinghai lake, has been used in biological assay and toxicity evaluation of many chemicals. However, the crystal structure of the luciferase (the most important catalyzer to bioluminescent) in Q67 is still not established, which hinders the process of the study on the molecular mechanism of toxicities of chemicals to Q67. In this study, the three dimensional structure of bacterial luciferase in Q67 was constructed by using the heterodimeric homol- ogy modeling combined with the molecular dynamics simulation which were performed with explicit TIP3P water. The simulation system was equilibrated at 4 ns, and was prolonged for another 4 ns for extracting the equilibrium trajectories at the 8th ns. The stability of the system was monitored through the convergences of energy, temperature, and global root mean square deviation (RMSD). The ptraj modules in the AMBER software were used to analyze hydrogen bond occupancy be- tween α and β subunit. And then, the molecular mechanics generalized born surface area method was applied to identify critical amino acids of the α and β subunits that interact with each other during the native heterotetrameric structure forma- tion. It was shown that the luciferase in Q67 is a heterdimer including two polypeptide subunits (α and β) and the stabilization of this heterodimer was mainly determined by the van der waals force. The specificity of association is realized by hydrogen bonds formed between subunits. However, the electrostatic interaction from the net charge on α and β subunit is unfavorable to the stability of the dimer. The active sites of flavin mononucleotide binding to the luciferase in Q67 are located in the ac- tive pocket of α subunit. The β subunit is helpful to keep the structural stability of the active sites on the α subunit. Keywords heterodimer; luciferase; homology modeling; freshwater luminescent bacteria; molecular dynamics

Resolving the Negative Potential Side (n-side) Water-accessible Proton Pathway of F-type ATP Synthase by Molecular Dynamics Simulations

The rotation of F(1)F(o)-ATP synthase is powered by the proton motive force across the energy-transducing membrane. The protein complex functions like a turbine; the proton flow drives the rotation of the c-ring of the transmembrane F(o) domain, which is coupled to the ATP-producing F(1) domain. The hairpin-structured c-protomers transport the protons by reversible protonation/deprotonation of a conserved Asp/Glu at the outer transmembrane helix (TMH). An open question is the proton transfer pathway through the membrane at atomic resolution. The protons are thought to be transferred via two half-channels to and from the conserved cAsp/Glu in the middle of the membrane. By molecular dynamics simulations of c-ring structures in a lipid bilayer, we mapped a water channel as one of the half-channels. We also analyzed the suppressor mutant cP24D/E61G in which the functional carboxylate is shifted to the inner TMH of the c-protomers. Current models concentrating on the "locked" and "open" conformations of the conserved carboxylate side chain are unable to explain the molecular function of this mutant. Our molecular dynamics simulations revealed an extended water channel with additional water molecules bridging the distance of the outer to the inner TMH. We suggest that the geometry of the water channel is an important feature for the molecular function of the membrane part of F(1)F(o)-ATP synthase. The inclination of the proton pathway isolates the two half-channels and may contribute to a favorable clockwise rotation in ATP synthesis mode.

A tutorial for molecular dynamics simulations using Amber package

In this paper we present a tutorial for performing molecular dynamics calculations utilizing Amber package. Through it we explain the function of each step in a theoretical work of MD, thus enabling the application of acquired knowledge to other systems without many difficulties. For this tutorial, we simulated by MD and analyzed various geometrical and structual parameters for doxycycline, a potent antimicrobial agent.

An overview of the Amber biomolecular simulation package

AbstractMolecular dynamics (MD) allows the study of biological and chemical systems at the atomistic level on timescales from femtoseconds to milliseconds. It complements experiment while also offering a way to follow processes difficult to discern with experimental techniques. Numerous software packages exist for conducting MD simulations of which one of the widest used is termed Amber. Here, we outline the most recent developments, since version 9 was released in April 2006, of the Amber and AmberTools MD software packages, referred to here as simply the Amber package. The latest release represents six years of continued development, since version 9, by multiple research groups and the culmination of over 33 years of work beginning with the first version in 1979. The latest release of the Amber package, version 12 released in April 2012, includes a substantial number of important developments in both the scientific and computer science arenas. We present here a condensed vision of what Amber currently supports and where things are likely to head over the coming years. Figure 1 shows the performance in ns/day of the Amber package version 12 on a single‐core AMD FX‐8120 8‐Core 3.6GHz CPU, the Cray XT5 system, and a single GPU GTX680. © 2012 John Wiley &amp; Sons, Ltd.This article is categorized under: Software &gt; Molecular Modeling

Routine Access to Millisecond Time Scale Events with Accelerated Molecular Dynamics

In this work, we critically assess the ability of the all-atom enhanced sampling method accelerated molecular dynamics (aMD) to investigate conformational changes in proteins that typically occur on the millisecond time scale. We combine aMD with the inherent power of graphics processor units (GPUs) and apply the implementation to the bovine pancreatic trypsin inhibitor (BPTI). A 500 ns aMD simulation is compared to a previous millisecond unbiased brute force MD simulation carried out on BPTI, showing that the same conformational space is sampled by both approaches. To our knowledge, this represents the first implementation of aMD on GPUs and also the longest aMD simulation of a biomolecule run to date. Our implementation is available to the community in the latest release of the Amber software suite (v12), providing routine access to millisecond events sampled from dynamics simulations using off the shelf hardware.

Modeling the Yew Tree Tubulin and a Comparison of its Interaction with Paclitaxel to Human Tubulin

To explore possible ways in which yew tree tubulin is naturally resistant to paclitaxel. While the yew produces a potent cytotoxin, paclitaxel, it is immune to paclitaxel's cytotoxic action. Tubulin sequence data for plant species were obtained from Alberta 1000 Plants Initiative. Sequences were assembled with Trinity de novo assembly program and tubulin identified. Homology modeling using MODELLER software was done to generate structures for yew tubulin. Molecular dynamics simulations and molecular mechanics Poisson-Boltzmann calculations were performed with the Amber package to determine binding affinity of paclitaxel to yew tubulin. ClustalW2 program and PHYLIP package were used to perform phylogenetic analysis on plant tubulin sequences. We specifically analyzed several important regions in tubulin structure: the high-affinity paclitaxel binding site, as well as the intermediate binding site and microtubule nanopores. Our analysis indicates that the high-affinity binding site contains several substitutions compared to human tubulin, all of which reduce the binding energy of paclitaxel. The yew has achieved a significant reduction of paclitaxel's affinity for its tubulin by utilizing several specific residue changes in the binding pocket for paclitaxel.

Application of Adaptive QM/MM Methods to Molecular Dynamics Simulations of Aqueous Systems.

The difference-based adaptive solvation quantum mechanics/molecular mechanics (adQM/MM) method (J. Chem. Theory Comput.2009, 5, 2212) as implemented in the Amber software was applied to the study of several chemical processes in solution. The adQM/MM method is based on an efficient selection scheme that enables quantum-mechanical treatment of the active region of a molecular system in solution taking explicitly into account diffusion of solvent molecules between the QM and the MM regions. Specifically, adQM/MM molecular dynamics simulations are carried out to characterize (1) the free energy profiles of halide exchange SN2 reactions in water, (2) the hydration structure of the Cl(-) ion, and (3) the solvation structure of the zwitterionic form of glycine in water. A comparison is made with the results obtained using standard MM and QM/MM methods as well as with the available fully QM and experimental data. In all cases, it is shown that the adaptive QM/MM simulations provide a physically realistic description of the system of interest.

Molecular theory of solvation for supramolecules and soft matter structures: application to ligand binding, ion channels, and oligomeric polyelectrolyte gelators

We combine the statistical–mechanical 1D/3D-RISM-KH molecular theory of solvation with DFT electronic structure calculations and MD and coarse-grained DPD simulations, and apply them to study association phenomena in synthetic organic soft matter and biomolecular systems. This combined approach from electronic to molecular structure and coarse-graining allows us to address complex processes occurring in solution on very long timescales, such as protein–ligand binding, distributions of electrolyte solution species in ion channels, and oligomeric polyelectrolyte gelation. The statistics of rare events involving supramolecular solute and solvent is accounted for analytically within the 3D-RISM-KH molecular theory of solvation. The hybrid MD/3D-RISM-KH method for molecular dynamics of the biomolecule in the potential of mean force obtained with the molecular theory of solvation has been implemented in the Amber package. The 3D molecular theory of solvation also replaces MM/GB(PB)SA post-processing using empirical treatment of non-polar contributions with MM/3D-RISM-KH evaluation of the solvation thermodynamics. The 3D-RISM-KH theory accurately yields the solvation structure for biomolecular systems as large as the GroEL chaperonin complex, GLIC ion channel, and 3D maps of ligand binding affinity of antiprion compound to mouse PrPC prion protein at once without phenomenological approximations. We apply the DFT/1D-3D-RISM-KH/DPD multiscale approach to investigate the structural and dynamical properties and gelation ability of oligomeric polyelectrolyte gelators, towards understanding of the gelation mechanism.

Molecular Mechanics Investigation of an Adenine–Adenine Non-Canonical Pair Conformational Change

Conformational changes are important in RNA for binding and catalysis and understanding these changes is important for understanding how RNA functions. Computational techniques using all-atom molecular models can be used to characterize conformational changes in RNA. These techniques are applied to an RNA conformational change involving a single base pair within a nine base pair RNA duplex. The Adenine-Adenine (AA) non-canonical pair in the sequence 5'GGUGAAGGCU3' paired with 3'PCCGAAGCCG5', where P is Purine, undergoes conformational exchange between two conformations on the timescale of tens of microseconds, as demonstrated in a previous NMR solution structure [Chen, G., et al., Biochemistry, 2006. 45: 6889-903]. The more populated, major, conformation was estimated to be 0.5 to 1.3 kcal/mol more stable at 30 °C than the less populated, minor, conformation. Both conformations are trans-Hoogsteen/sugar edge pairs, where the interacting edges on the adenines change with the conformational change. Targeted Molecular Dynamics (TMD) and Nudged Elastic Band (NEB) were used to model the pathway between the major and minor conformations using the AMBER software package. The adenines were predicted to change conformation via intermediates in which they are stacked as opposed to hydrogen-bonded. The predicted pathways can be described by an improper dihedral angle reaction coordinate. Umbrella sampling along the reaction coordinate was performed to model the free energy profile for the conformational change using a total of 1800 ns of sampling. Although the barrier height between the major and minor conformations was reasonable, the free energy difference between the major and minor conformations was the opposite of that expected based on the NMR experiments. Variations in the force field applied did not improve the misrepresentation of the free energies of the major and minor conformations. As an alternative, the Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) approximation was applied to predict free energy differences between the two conformations using a total of 800 ns of sampling. MM-PBSA also incorrectly predicted the major conformation to be higher in free energy than the minor conformation.

Multiscale methods for nanochemistry and biophysics in solution

Statistical–mechanical, 3D-RISM-KH molecular theory of solvation is an integral equation theory of molecular liquids capable of describing, from the first principles, solvation structure and thermodynamics in complex nanoscale systems. The 3D-RISM-KH theory accurately yields the solvation structure for biomolecular systems as large as chaperonins and ion channels. It predicts 3D maps of ligand binding affinity at once without using empirical scoring functions, and has significant potential for computer-aided drug design. Recently, the 3D-RISM-KH theory was coupled with MD simulations by contracting solvent degrees of freedom to treat solvated biomolecules, and the MD/3D-RISM-KH multiscale method was implemented in the Amber molecular dynamics package [T. Luchko et al., 2010, [ 29]]. The MD/3D-RISM-KH method allows one to study biomolecular processes on extremely long timescales, as the statistics of rare solvent and ligand events is accounted for analytically. We further replaced the MM/GB(PB)SA post-processing which evaluates the free energy by empirical treatment of non-polar solvation effects with the MM/3D-RISM-KH method which employs 3D-RISM-KH to evaluate the solvation thermodynamics. In this paper, we briefly review the 3D-RISM-KH theory as well as the MD/3D-RISM-KH multiscale method implemented in the Amber package. We illustrate the MM/3D-RISM-KH method on binding of thiamine (vitamin of group B) to extracytoplasmic thiamine-binding lipoprotein MG289, and on the microscopic solvation properties of the bacterial Gloeobacter violaceus pentameric ligand-gated ion channel (GLIC) homologue.

Free Energy Calculations and Binding Analysis of Two Potential Anti- Influenza Drugs with Polymerase Basic Protein-2 (PB2)

Influenza viruses cause a significant level of morbidity and mortality in the population every year. Their resistance to current anti-influenza drugs increases the difficulty of flu treatment. Thus, development of new anti-influenza drugs is necessary in regards of prevent the tragedy of influenza pandemic. The Polymerase basic protein 2 (PB2) subunit of influenza virus RNA polymerase is one of potential targets for new drugs because the binding of PB2 with the 5' cap of the host pre-mRNAs is the initial step of the virus' protein synthesis. In this study, we compared the binding potency of PB2 cap binding domain with two small molecules, i.e., RO and PPT28, with that of PB2 with cap analog m7GTP. The calculated binding energies showed that RO and PPT28 had higher binding affinity with PB2. Further interaction analysis showed that the important parts for binding were the five- and six-member heterocyclic rings (the 6/5-member rings) of small molecules, as well as the hydrophobic parts of RO and PPT28 which had good interactions with the hydrophobic residues in the binding cavity. Thus, RO and PPT28 are two potential anti-influenza drugs targeted PB2, which may inhibit the growth of influenza virus by competitively binding with the cap structure binding domain of PB2.