S288T mutation altering MmpL3 periplasmic domain channel and H-bond network: a novel dual drug resistance mechanism.

CONTEXT: Mycobacterial membrane proteins Large 3 (MmpL3) is responsible for the transport of mycobacterial acids out of cell membrane to form cell wall, which is essential for the survival of Mycobacterium tuberculosis (Mtb) and has become a potent anti-tuberculosis target. SQ109 is an ethambutol (EMB) analogue, as a novel anti-tuberculosis drug, can effectively inhibit MmpL3, and has completed phase 2b-3 clinical trials. Drug resistance has always been the bottleneck problem in clinical treatment of tuberculosis. The S288T mutant of MmpL3 shows significant resistance to the inhibitor SQ109, while the specific action mechanism remains unclear. The results show that MmpL3 S288T mutation causes local conformational change with little effect on the global structure. With MmpL3 bound by SQ109 inhibitor, the distance between D710 and R715 increases resulting in H-bond destruction, but their interactions and proton transfer function are still restored. In addition, the rotation of Y44 in the S288T mutant leads to an obvious bend in the periplasmic domain channel and an increased number of contact residues, reducing substrate transport efficiency. This work not only provides a possible dual drug resistance mechanism of MmpL3 S288T mutant but also aids the development of novel anti-tuberculosis inhibitors. METHODS: In this work, molecular dynamics (MD) and quantum mechanics (QM) simulations both were performed to compare inhibitor (i.e., SQ109) recognition, motion characteristics, and H-bond energy change of MmpL3 after S288T mutation. In addition, the WT_SQ109 complex structure was obtained by molecular docking program (Autodock 4.2); Molecular Mechanics/ Poisson Boltzmann Surface Area (MM-PBSA) and Solvated Interaction Energy (SIE) methods were used to calculate the binding free energies (∆Gbind); Geometric criteria were used to analyze the changes of hydrogen bond networks.

Molecular recognition of ITIM/ITSM domains with SHP2 and their allosteric effect.

Src homology 2-domain-containing tyrosine phosphatase 2 (SHP2) is a non-receptor protein tyrosine phosphatase that is widely expressed in a variety of cells and regulates the immune response of T cells through the PD-1 pathway. However, the activation mechanism and allosteric effects of SHP2 remain unclear, hindering the development of small molecule inhibitors. For the first time, in this study, the complex structure formed by the intact PD-1 tail and SHP2 was modeled. The molecular recognition and conformational changes of inactive/active SHP2 versus ITIM/ITSM were compared based on prolonged MD simulations. The relative flexibility of the two SH2 domains during MD simulations contributes to the recruitment of ITIM/ITSM and supports the subsequent conformational change of SHP2. The binding free energy calculation shows that inactive SHP2 has a higher affinity for ITIM/ITSM than active SHP2, mainly because the former's N-SH2 refers to the α-state. In addition, a significant decrease in the contribution to the binding energy of certain residues (e.g., R32, S34, K35, T42, and K55) of conformationally transformed SHP2 contributes to the above result. These detailed changes during conformational transition will provide theoretical guidance for the molecular design of subsequent novel anticancer drugs.

Research Progress on hCNT3 Structure/Function and Nucleoside Anticancer Drugs.

Membrane protein human concentrative nucleoside transporter 3 (hCNT3) can not only transport extracellular nucleosides into the cell but also transport various nucleoside-derived anticancer drugs to the focus of infection for therapeutic effects. Typical nucleoside anticancer drugs, including fludarabine, cladabine, decitabine, and clofarabine, are recognized by hCNT3 and then delivered to the lesion site for their therapeutic effects. hCNT3 is highly conserved during the evolution from lower to higher vertebrates, which contains scaffold and transport domains in structure and delivers substrates by coupling with Na+ and H+ ions in function. In the process of substrate delivery, the transport domain rises from the lower side of transmembrane 9 (TM9) in the inward conformation to the upper side of the outward conformation, accompanied by the collaborative motion of TM7b/ TM4b and hairpin 1b (HP1b)/ HP2b. With the report of a series of three-dimensional structures of homologous CNTs, the structural characteristics and biological functions of hCNT3 have attracted increasing attention from pharmacists and biologists. Our research group has also recently designed an anticancer lead compound with high hCNT3 transport potential based on the structure of 5-fluorouracil. In this work, the sequence evolution, conservation, molecular structure, cationic chelation, substrate recognition, elevator motion pattern and nucleoside derivative drugs of hCNT3 were reviewed, and the differences in hCNT3 transport mode and nucleoside anticancer drug modification were summarized, aiming to provide theoretical guidance for the subsequent molecular design of novel anticancer drugs targeting hCNT3.

Ethanol Oxidation via 12-Electron Pathway on Spiky Au@AuPd Nanoparticles Assisted by Near-Infrared Light.

In this work, ethanol oxidation reaction (EOR) via 12-electron (C1-12e) pathway on spiky Au@AuPd nanoparticles (NPs) with ultrathin AuPd alloy shells is achieved in alkaline media with the assistance of the near-infrared (NIR) light. It is found that OH radicals can be produced from the OHads species adsorbed on the surfaces of Pd atoms led by surface plasmon resonance (SPR) effect of spiky Au@AuPd NPs under the irradiation of NIR light. Moreover, OH radicals play the key role for the achievement of EOR proceeded by the desirable C1-12e pathway because OH radicals can directly break the C-C bonds of ethanol. Accordingly, the electrocatalytic performance of spiky Au@AuPd NPs toward EOR under NIR light is greatly improved. For instance, their mass activity can be up to 33.2 A mgpd -1 in the 0.5 m KOH solution containing 0.5 m ethanol, which is about 158 times higher than that of commercial Pd/C catalysts (0.21 A mgpd -1 ) and is better than those of the state-of-the-art Pd-based catalysts reported in literature thus far, to the best of our knowledge. Moreover, their highest mass activity can be further improved to 118.3 A mgpd -1 in the 1.5 m KOH solution containing 1.25 m ethanol.

The enhancement in the performance of ultra-small core-shell Au@AuPt nanoparticles toward HER and ORR by surface engineering.

In this work, ultra-small core-shell (USCS) Au38.4@Au4.1Pt57.5 nanoparticles (NPs) with an optimal Pt-to-Au ratio were successfully prepared by the optimal etching treatment of USCS Au@AuPt NPs by Fe(III) ions to remove some exposed Au atoms on their outermost surfaces. The as-prepared USCS Au38.4@Au4.1Pt57.5 NPs with Fe(III)-etching treatment for 2 h loaded on carbon black as catalysts (USCS2h Au38.4@Au4.1Pt57.5-NP/C catalysts) exhibit superior electrocatalytic activity and durability for both the hydrogen evolution reaction (HER) and oxygen reduction reaction (ORR) in acidic media. For instance, the overpotential of USCS2h Au38.4@Au4.1Pt57.5-NP/C catalysts toward the HER is 13 mV at a current density of -10 mA cm-2 (η10 = 13 mV), which is much better than that of commercial Pt/C catalysts (η10 = 31 mV). Moreover, their mass activity (63.8 A mgPt-1) is about 16.4 times larger than that of commercial Pt/C catalysts (3.9 A mgPt-1). In addition, they also present better long-term stability. Furthermore, they also show an improved activity toward the ORR in terms of the half-wave potential (E1/2) (0.89 V vs. RHE), which is more positive by about 38 mV than commercial Pt/C catalysts (0.852 V). In addition, they also show a higher kinetic current density (14.22 mA cm-2 at 0.85 V) and better long-term durability. This etching-treatment strategy can be extended to further improve the catalytic performance of ultra-small Au-based bimetallic or multi-metallic NPs by surface engineering.