Jian Jun Tan

Molecular dynamics simulations of the bacterial periplasmic heme binding proteins ShuT and PhuT.

ShuT and PhuT are two periplasmic heme binding proteins that shuttle heme between the outer and inner membranes of the Gram-negative bacteria. Periplasmic binding proteins (PBPs) generally exhibit considerable conformational changes during the ligand binding process, whereas ShuT and PhuT belong to a class of PBPs that do not show such behavior based on their apo and holo crystal structures. By employing a series of molecular dynamic simulations on the ShuT and the PhuT, the dynamics and functions of the two PBPs were investigated. Through monitoring the distance changes between the two conserved glutamates of ShuT and PhuT, it was found the two PBPs were more flexible than previously assumed, exhibiting obvious opening-closing motions which were more remarkable in the apo runs of ShuT. Based on the results of the domain motion analysis, large scale conformational transitions were found in all apo runs of ShuT and PhuT, hinting that the domain motions of the two PBPs may be intrinsic. On the basis of the results of the principle component analysis, distinct opening-closing and twisting motion tendencies were observed not only in the apo, but also in the holo simulations of the two PBPs. The Gaussian network model was applied in order to analyze the hinge bending regions. The most important bending regions of ShuT and PhuT are located around the midpoints of their respective connecting helixes. Finally, the flexibilities and the details of the simulations of ShuT and PhuT were discussed. Characterized by the remarkably large flexibilities, the loop constituted by Ala 169, Gly170 and Gly171 of ShuT and the beta-turn constituted by Ala176, Gly177 and Gly178 of PhuT may be important for the functions of the two PBPs. Furthermore, the Asn254 of ShuT and the Arg228 of PhuT may be indispensable for the binding or unbinding of heme, since it is involved in the important hydrogen bonding to the propionate side-chains of heme.

Study on the inhibitory mechanism and binding mode of the hydroxycoumarin compound NSC158393 to HIV-1 integrase by molecular modeling.

Human immunodeficiency virus type 1 integrase (IN) is an essential enzyme in the life cycle of this virus and also an important target for the study of anti‐HIV drugs. In this work, the binding modes of the wild type IN core domain and the two mutants, that is, W132G and C130S, with the 4‐hydroxycoumarin compound NSC158393 were evaluated by using the “relaxed complex” molecular docking approach combined with molecular dynamics (MD) simulations. Based on the monomer MD simulations, both of the two substitutions affect not only the stability of the 128–136 peptides, but also the flexibility of the functional 140s loop. In principle, NSC158393 binds the 128–136 peptides of IN; however, the specific binding modes for the three systems are various. According to the binding mode of NSC158393 with WT, NSC158393 can effectively interfere with the stability of the IN dimer by causing a steric hindrance around the monomer interface. Additionally, through the comparative analysis of the MD trajectories of the wild type IN and the IN‐NSC158393 complex, we found that NSC15893 may also exert its inhibitory function by diminishing the mobility of the function loop of IN. Three key binding residues, that is, W131, K136, and G134, were discovered by energy decomposition calculated with the Molecular Mechanics Generalized Born Surface Area method. Characterized by the largest binding affinity, W131 is likely to be indispensable for the ligand binding. All the above results are consistent with experiment data, providing us some helpful information for understanding the mechanism of the coumarin‐based inhibitors.

Allosteric transitions of the maltose transporter studied by an elastic network model

The maltose transporter from Escherichia coli is one of the ATP‐binding cassette (ABC) transporters that utilize the energy from ATP hydrolysis to translocate substrates across cellular membranes. Until 2011, three crystal structures have been determined for maltose transporter at different states in the process of transportation. Here, based on these crystal structures, the allosteric pathway from the resting state (inward‐facing) to the catalytic intermediate state (outward‐facing) is studied by applying an adaptive anisotropic network model. The results suggest that the allosteric transitions proceed in a coupled way. The closing of the nucleotide‐binding domains occurs first, and subsequently this conformational change is propagated to the transmembrane domains (TMD) via the EAA and EAS loops, and then to the maltose‐binding protein, which facilitates the translocation of the maltose. It is also found that there exist nonrigid‐body and asymmetric movements in the TMD. The cytoplasmic gate may only play the role of allosteric propagation during the transition from the pretranslocation to outward‐facing states. In addition, the results show that the movment of the helical subdomain towards the RecA‐like subdomain mainly occurs in the earlier stages of the transition. These results can provide some insights into the understanding of the mechanism of ABC transporters.

Insight into the Inhibitory Mechanism and Binding Mode Between D77 and HIV-1 Integrase by Molecular Modeling Methods

Abstract Integrase is an essential enzyme in the life cycle of Human immunodeficiency virus type 1 (HIV-1) and also an important target for designing integrase inhibitors. In this paper, the binding modes between the wild type integrase core domain (ICD) and the W131A mutant ICD with the benzoic acid derivative—D77 were investigated using the molecular docking combined with molecular dynamics (MD) simulations. The result of MD simulations showed that the W131A substitution affected the flexibility of the region 150–167 in both the monomer A and B of the mutant type ICD. In principle, D77 interacted with the residues around the Lens Epithelium-Derived Growth Factor (LEDGF/p75) binding site which is nearby the HIV-1 integrase dimer interface. However, the specific binding modes for D77-wild type integrase and D77-mutant integrase systems are various. According to the binding mode of D77 with the wild type ICD, D77 can effectively intervene with the binding of LEDGF/p75 to integrase due to a steric hindrance effect around the LEDGF/p75 binding site. In addition, we found that D77 might also affect its inhibitory action by reducing the flexibility of the region 150–167 of integrase. Through energy decomposition calculated with the Molecular Mechanics Generalized Born Surface Area approach to estimate the binding affinity, it seems likely that W131 and E170 are indispensable for the ligand binding, as characterized by the largest binding affinity. All the above results are consistent with the experimental data, providing us with some helpful information not only for the understanding of the mechanism of this kind of inhibitor but also for the rational drug design.

Allosteric transitions of ATP-binding cassette transporter MsbA studied by the adaptive anisotropic network model

The transporter MsbA is a kind of multidrug resistance ATP‐binding cassette transporter that can transport lipid A, lipopolysaccharides, and some amphipathic drugs from the cytoplasmic to the periplasmic side of the inner membrane. In this work, we explored the allosteric pathway of MsbA from the inward‐ to outward‐facing states during the substrate transport process with the adaptive anisotropic network model. The results suggest that the allosteric transitions proceed in a coupled way. The large‐scale closing motions of the nucleotide‐binding domains occur first, accompanied with a twisting motion at the same time, which becomes more obvious in middle and later stages, especially for the later. This twisting motion plays an important role for the rearrangement of transmembrane helices and the opening of transmembrane domains on the periplasmic side that mainly take place in middle and later stages respectively. The topological structure plays an important role in the motion correlations above. The conformational changes of nucleotide‐binding domains are propagated to the transmembrane domains via the intracellular helices IH1 and IH2. Additionally, the movement of the transmembrane domains proceeds in a nonrigid body, and the two monomers move in a symmetrical way, which is consistent with the symmetrical structure of MsbA. These results are helpful for understanding the transport mechanism of the ATP‐binding cassette exporters. Proteins 2015; 83:1643–1653.

Studies on binding free energies and the binding mode by docking and MM-PBSA in gp41-ligand complex

Despite the synthetic peptides inhibit HIV-1 entry, its application may be limited due to the high cost of the peptide production and lack of its oral availability. Thus, it is necessary to identify the small molecule inhibitors reacting with the same or overlapping target sites on gp41 recognizing the antiviral peptides. In this paper, a small inhibitor (TP1) is docked into the hydrophobic grooves of gp41 by using Autodock software, resulting in five alternative energetically favorable models. The molecular mechanics-Poisson Boltzmann surface area (MM-PBSA) method is applied to calculate the binding free energies. The data from other studies were used to define our preferred models. We found that only one binding mode is supported by the experimental evidence. The model could be used to design more effective HIV-1 inhibitors targeted to the HIV-1 gp41 core structure.

Computer-Aided Design, Synthesis, and Biological Activity Evaluation of Potent Fusion Inhibitors Targeting HIV-1 gp41

This discovered and optimized several novel HIV-1 fusion inhibitors and further evaluated the inhibitory activities of these compounds in vitro. Here, we have reported the computer-aided design, synthesis, and biological evaluation of a series of small molecule fusion inhibitors targeting HIV-1 gp41. Based on the structure of inhibitor (NB2), we carried out de novo design and screened out a series of novel structure molecules by using Leapfrog and Autodock programs. Our structure-based modification obtained a potent fusion inhibitor (IC₅₀ = 41.1 µg/mL). Several novel compounds were discovered as fusion inhibitors, which suggested that our design methodology is reliable, paving the way for de novo design of novel small-molecule HIV inhibitors targeting gp41.

A combinatorial scoring function for protein–RNA docking

Protein–RNA docking is still an open question. One of the main challenges is to develop an effective scoring function that can discriminate near‐native structures from the incorrect ones. To solve the problem, we have constructed a knowledge‐based residue‐nucleotide pairwise potential with secondary structure information considered for nonribosomal protein–RNA docking. Here we developed a weighted combined scoring function RpveScore that consists of the pairwise potential and six physics‐based energy terms. The weights were optimized using the multiple linear regression method by fitting the scoring function to L_rmsd for the bound docking decoys from Benchmark II. The scoring functions were tested on 35 unbound docking cases. The results show that the scoring function RpveScore including all terms performs best. Also RpveScore was compared with the statistical mechanics‐based method derived potential ITScore‐PR, and the united atom‐based statistical potentials QUASI‐RNP and DARS‐RNP. The success rate of RpveScore is 71.6% for the top 1000 structures and the number of cases where a near‐native structure is ranked in top 30 is 25 out of 35 cases. For 32 systems (91.4%), RpveScore can find the binding mode in top 5 that has no lower than 50% native interface residues on protein and nucleotides on RNA. Additionally, it was found that the long‐range electrostatic attractive energy plays an important role in distinguishing near‐native structures from the incorrect ones. This work can be helpful for the development of protein–RNA docking methods and for the understanding of protein–RNA interactions. RpveScore program is available to the public at http://life.bjut.edu.cn/kxyj/kycg/2017116/14845362285362368_1.html Proteins 2017; 85:741–752.

Prediction of the binding model of HIV-1 gp41 with small molecule inhibitors

Despite the synthetic peptides inhibit HIV-1 entry; its application of this peptide therapy may be limited due to the high cost of the peptide production and lack of its oral availability. Thus, it is necessary to identify the small molecule inhibitors reacting with the same or overlapping target sites on gp41 recognizing the antiviral peptides. In this work, a small inhibitor (TP1) is docked into the hydrophobic grooves of gp41 by using AutoDock software, resulting in five alternative energetically favorable models. The data from other studies were used to define our preferred models. We found that only one binding mode is supported by the experimental evidence. The model could be used to design more effective HIV-1 inhibitors targeted to the HIV-I gp41 core structure

Study on the binding mode of the integrase with DNA via steered molecular dynamics simulation.

Human immunodeficiency virus type 1 (HIV-1) integrase (IN) is an essential enzyme in the lifecycle of this virus and also an important target for the study of anti-HIV drugs. In the current work, a model for the active site of IN and viral DNA was built by combining experimental data with the results of steered molecular dynamics simulation. The model was then taken into a series automatic molecular docking calculations with two groups of inhibitors. According to the results of molecular docking, the inhibitors of the second group share a similar binding model with those of the first group, though they have no common scaffold. The newly built model of the IN-DNA complex is helpful for our subsequent research on the design of IN inhibitors.