Article
Multidisciplinary Sciences
Vikram Khipple Mulligan, Sean Workman, Tianjun Sun, Stephen Rettie, Xinting Li, Liam J. Worrall, Timothy W. Craven, Dustin T. King, Parisa Hosseinzadeh, Andrew M. Watkins, P. Douglas Renfrew, Sharon Guffy, Jason W. Labonte, Rocco Moretti, Richard Bonneau, Natalie C. J. Strynadka, David Baker
Summary: This study presents a structure-guided computational method for designing peptide macrocycles using a mixture of L- and D-amino acids to inhibit therapeutic targets. The experimental results show that this method can effectively predict peptide binding propensity and inhibitory activity, as demonstrated in the interaction with NDM-1.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Han Gao, Jia-Qi Li, Peng-Wei Kang, Jia-Zhu Chigan, Huan Wang, Lu Liu, Yin-Sui Xu, Le Zhai, Ke-Wu Yang
Summary: This study constructed and characterized an effective M beta L inhibitor, which showed preferential inhibition against NDM-1, potential antibacterial activities, and synergistic effects with meropenem. The research provided a new framework for the development of NDM-1 inhibitors.
BIOORGANIC CHEMISTRY
(2021)
Article
Chemistry, Medicinal
Liqiang Hu, Huixin Yang, Tao Yu, Fangfang Chen, Runqiu Liu, Shuyuan Xue, Shuangzhan Zhang, Wuyu Mao, Changge Ji, Hao Wang, Hexin Xie
Summary: This study demonstrates the effectiveness of stereochemically altered cephalosporins as potent inhibitors against NDM-1, a major cause of antibiotic resistance. The findings provide a new approach to combat antibiotic resistance.
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Le Zhai, Yue Jiang, Yang Shi, Miao Lv, Ya-Li Pu, Hua-Lei Cheng, Jia-Yu Zhu, Ke-Wu Yang
Summary: The irregular use of antibiotics has led to the development of antibiotic-resistant bacteria, specifically metallo-beta-lactamases. This study identified eight compounds that have strong inhibitory effects on NDM-1, with one compound being the most effective inhibitor. The presence of a hydroxyl group in the compounds was found to improve their inhibitory activity. Additionally, these compounds demonstrated antibacterial effects on NDM-1-producing bacteria and showed low cytotoxicity in cell experiments.
BIOORGANIC CHEMISTRY
(2022)
Article
Chemistry, Medicinal
Zainab Bibi, Irfa Asghar, Naeem Mahmood Ashraf, Iftikhar Zeb, Umer Rashid, Arslan Hamid, Maria Kanwal Ali, Ashraf Atef Hatamleh, Munirah Abdullah Al-Dosary, Raza Ahmad, Muhammad Ali
Summary: This study utilized virtual screening and molecular dynamics simulations to explore phytochemicals as inhibitors of New Delhi Metallo-beta-lactamase (NDM-1). Three potential inhibitors were identified based on their docking scores, RMSD values, and other critical parameters. These findings could contribute to addressing antibiotic resistance.
Article
Immunology
Jacqueline Findlay, Laurent Poirel, Julie Kessler, Andreas Kronenberg, Patrice Nordmann
Summary: The study in Switzerland found that NDM-positive CPE, primarily consisting of Klebsiella pneumoniae and Escherichia coli, were prevalent, with NDM-1 and NDM-5 variants being the most common. Some isolates also co-produced a second carbapenemase and a 16S rRNA methylase. Successful plasmids and global lineages were identified as major factors contributing to the increasing prevalence of NDMs in Switzerland.
EMERGING INFECTIOUS DISEASES
(2021)
Article
Chemistry, Multidisciplinary
Radhika Mehta, Dann D. Rivera, David J. Reilley, Dominique Tan, Pei W. Thomas, Abigail Hinojosa, Alesha C. Stewart, Zishuo Cheng, Caitlyn A. Thomas, Michael W. Crowder, Anastassia N. Alexandrova, Walter Fast, Emily L. Que
Summary: The development of a fluorescent probe that reports on the metalation state of NDM within Escherichia coli provides a novel tool to study metal ion sequestration in host-pathogen interactions. The probe selectively coordinates the dizinc metal cluster of NDM and offers a way to monitor the enzyme's response to metal ions.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Microbiology
Xiaoxia Gu, Mengzhu Zheng, Lixia Chen, Hua Li
Summary: This article summarizes NDM-1 inhibitors developed since 2018, classifies these compounds by chemical scaffolds, and points out inconsistencies and notable problems in these studies, which are expected to benefit future research.
MICROBIOLOGICAL RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Jia-Zhu Chigan, Zhenxin Hu, Lu Liu, Yin-Sui Xu, Huan-Huan Ding, Ke-Wu Yang
Summary: The superbug infection caused by metallo-beta-lactamases (M beta Ls) has become an urgent health threat. In this study, compounds were synthesized and tested for their inhibitory effect on M beta L NDM-1. Among them, 1e and 1f showed the strongest inhibition, with an IC50 value of 0.02 mu M against NDM-1. This study provides potential lead compounds for further development of clinically useful inhibitors targeting NDM-1.
BIOORGANIC CHEMISTRY
(2022)
Article
Chemistry, Analytical
Hongyu Gan, Yaowen Liang, Yun Tang, Manna Huang, Yiqian Wan
Summary: A practical electrochemical method was established to determine the inhibitory activity of New Delhi metallo-beta-lactamase-1 (NDM-1) inhibitors, using a bare pencil graphite electrode (PGE) as the working electrode and imipenem as the substrate. The results were consistent with those from the UV-vis high-throughput assay method.
MICROCHEMICAL JOURNAL
(2023)
Article
Biotechnology & Applied Microbiology
Ying Ge, Peng-Wei Kang, Jia-Qi Li, Han Gao, Le Zhai, Le-Yun Sun, Cheng Chen, Ke-Wu Yang
Summary: The study demonstrated that thiosemicarbazones are valuable scaffolds for developing inhibitors of NDM-1 and drug-resistant bacteria carrying NDM-1, and they also exhibit synergistic antimicrobial effects with other antibiotics, showing strong activity against bacteria harboring NDM-1.
JOURNAL OF ANTIBIOTICS
(2021)
Article
Biochemistry & Molecular Biology
Jia-Qi Li, Le-Yun Sun, Zhihui Jiang, Cheng Chen, Han Gao, Jia-Zhu Chigan, Huan-Huan Ding, Ke-Wu Yang
Summary: A new scaffold was constructed for inhibiting NDM-1, showing promising results in combating bacterial infections and providing important insights for the development of anti-NDM-1 drugs.
BIOORGANIC CHEMISTRY
(2021)
Article
Chemistry, Multidisciplinary
Wen Bin Jin, Chen Xu, Xiao Lin Qi, Ping Zeng, Wei Gao, Ki Hon Lai, Jiachi Chiou, Edward W. C. Chan, Yun-Chung Leung, Tak Hang Chan, Kwok-Yin Wong, Sheng Chen, Kin-Fai Chan
Summary: Efficient construction of a series of trans-1,3,4-trisubstituted pyrrolidines via boric acid-catalyzed 1,3-dipolar cycloaddition for biological evaluation against NDM-1 positive carbapenem-resistant Enterobacteriaceae. Compound 10e showed low cytotoxicity, moderate NDM-1 enzyme inhibition, and potent synergistic activity against clinically isolated NDM-1 positive CRE, suggesting it as a promising starting point for carbapenem antibiotic adjuvants.
NEW JOURNAL OF CHEMISTRY
(2021)
Article
Chemistry, Medicinal
Kalyan C. Nagulapalli Venkata, Morgan Ellebrecht, Siddharth K. Tripathi
Summary: Antimicrobial stewardship is crucial in treating bacterial infections; NDM-1 is an enzyme that enables bacterial resistance; extensive research has been invested in search of NDM-1 inhibitors.
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2021)
Article
Multidisciplinary Sciences
Azhar Salari-jazi, Karim Mahnam, Parisa Sadeghi, Mohamad Sadegh Damavandi, Jamshid Faghri
Summary: The study conducted multi-step virtual screening in the NPASS database to identify potential metallo-beta -lactamase inhibitors. The efficacy of these compounds was evaluated through molecular docking and molecular dynamics simulations, while protein sequence alignment and pharmacophore modeling revealed conserved residues.
SCIENTIFIC REPORTS
(2021)
Review
Chemistry, Physical
Hua Guo, Wenyu Hu, Duowen Yang, Dan Wan, Hao Xu, Wei Yan, Xiaoliang Jin
Summary: Electrochemical characterization is crucial for understanding the degradation and properties of electrodes. In the field of anodic oxidation (AO) for wastewater treatment, electrochemical characterization mainly focuses on qualitative comparison of catalytic activity and electrode stability. However, the influence of reaction environment and the need for horizontal comparison should be considered. Common electrochemical indexes obtained from cyclic voltammetry, linear sweep voltammetry, electrochemical impedance spectroscopy, and other methods should be carefully tested according to the requirements of AO. Monitoring and predicting system performance can be achieved by observing the variation of these indexes before and after the degradation process.
CURRENT OPINION IN ELECTROCHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Baochao Zhang, Shuhan Luo, Shanshan Wu, Jingjing Li, Fangting He, Ruocheng Luo, Yating Wu, Meiling Pan, Li Yong, Xiaofang Pei
Summary: The fatty acid compositions of three major types of Zanthoxylum bungeanum seed oil (ZSO) were compared, and Zanthoxylum bungeanum maximum seed oil (ZBSO) had the highest content of unsaturated fatty acids. All tested ZSOs exhibited anti-inflammatory and anti-osteoclastogenesis activities, and their anti-osteoclastogenesis effects may be related to the suppression of the NF-kappa B pathway.
CHEMISTRY & BIODIVERSITY
(2023)
Article
Chemistry, Physical
Dandan Lu, Rodrigo Urzua-Leiva, Otoniel Denis-Alpizar, Hua Guo
Summary: The hyperthermal dynamics and kinetics of the title reaction, which plays an important role in hypersonic chemistry for atmospheric entry vehicles, are investigated using quasi-classical trajectory methods on a recently developed ground electronic state potential energy surface. The dynamics calculations indicated that the reaction follows a complex-forming mechanism, despite its large endoergicity. The calculated differential cross section is forward-backward symmetric, consistent with a long-lived reaction intermediate supported by the NCN potential well . The lifetime of the reaction complex is sufficiently long that the vibrational distribution of the CN product can be predicted by the phase space theory. The calculated vibrational state specific and thermal rate coefficients follow the Arrhenius behavior, and the agreement with existing low-temperature experimental thermal rate coefficients is satisfactory. Extrapolations to high temperatures relev a n t to hypersonic conditions are provided.
JOURNAL OF PHYSICAL CHEMISTRY A
(2023)
Article
Chemistry, Physical
Dandan Lu, Hua Guo
Summary: The dynamics and kinetics of nonadiabatic excitation of C(3P) to C(1D) induced by hyperthermal collisions with N2 molecules were investigated using quantum mechanical and two semiclassical nonadiabatic methods. The interaction potential energy surfaces and spin-orbit coupling were represented by a diabatic potential energy matrix, which facilitated the spin-forbidden process. Quantum dynamics calculations showed small transition probabilities due to weak spin-orbit coupling, with the most favored spin-flip transition near the threshold. The results also revealed strong oscillations and vibrational state-specified rate coefficients, with the N2 collision partner increasing the excitation rate at low temperatures but reversing the trend at high temperatures. The semiclassical methods qualitatively reproduced the quantum rate coefficients.
JOURNAL OF PHYSICAL CHEMISTRY A
(2023)
Article
Chemistry, Physical
Brendan C. Sweeny, Bryan A. Long, Dominique Maffucci, Junxiang Zuo, Hua Guo, Albert A. Viggiano, Shaun G. Ard, Nicholas S. Shuman
Summary: The kinetics of the reaction between Zr+ and CH4 were investigated over a range of temperatures and pressures using a selected-ion flow tube apparatus. The measured rate constants were found to be small, indicating that the reaction is not very efficient. Two products, ZrCH4+ and ZrCH2+, were observed. A statistical modeling approach was used to fit the experimental data and revealed important information about the reaction mechanism and energetics. The results showed that the formation of the bimolecular product is favored over competing processes, and the energy of the products and reaction depend on various factors.
JOURNAL OF PHYSICAL CHEMISTRY A
(2023)
Article
Chemistry, Physical
James F. E. Croft, Pablo G. Jambrina, F. Javier Aoiz, Hua Guo, N. Balakrishnan
Summary: This study focuses on the collisions of two D2 molecules prepared in the v = 2 vibrational level and j = 2 rotational level. Quantum calculations were performed to identify key resonance features that contribute to the angular distribution in the experimental results.
JOURNAL OF PHYSICAL CHEMISTRY A
(2023)
Article
Chemistry, Physical
Liang Zhang, Junxiang Zuo, Yury V. V. Suleimanov, Hua Guo
Summary: A ring polymer molecular dynamics (RPMD) method is proposed for calculating the dissociative chemisorption rate coefficient on surfaces. The RPMD rate theory considers quantum effects such as zero-point energy and tunneling, while using classical trajectories for simulation. The method is applied to H-2 dissociative chemisorption and shows deviations from Arrhenius behavior at low temperatures due to tunneling. On Pt(111), where dissociation has a barrierless pathway, the RPMD rate coefficient agrees with the experimentally derived thermal sticking coefficient within a factor of 2 over a wide temperature range. Significant quantum effects are also observed.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Chemistry, Multidisciplinary
Fenfei Wei, Sen Lin, Hua Guo
Summary: This paper presents a theoretical investigation of methane dissociation on a Pt(110)-(2 x 1) surface using a machine-learned potential energy surface. The simulations show good agreement with experimental results at high incidence energies and provide an explanation for negative activation at low incidence energies.
Article
Chemistry, Physical
Hongwei Song, Hua Guo
Summary: This Perspective focuses on the dynamics of gas-phase bimolecular reactions with submerged barriers, which are prevalent in combustion, atmospheric chemistry, astrochemistry, and plasma chemistry. The temperature dependence of the rate coefficients for such reactions is often non-Arrhenius and complex, and the corresponding dynamics may also be quite different from those with significant barriers or those completely dominated by capture. Recent experimental and theoretical studies have revealed interesting dynamical behaviors, particularly at relatively low temperatures or collision energies, enriching our understanding of these unusual reactions.
ACS PHYSICAL CHEMISTRY AU
(2023)
Correction
Chemistry, Physical
Humberto da Silva, Qian Yao, Masato Morita, Brian K. Kendrick, Hua Guo, Naduvalath Balakrishnan
Summary: This article corrects the errors in the investigation of the Li + CaF reaction under cold conditions and provides accurate results and explanations.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Computer Science, Information Systems
Lin Zhang, Qianqian Lu, Shanshan Wu
Summary: The Internet of Things (IoT) helps establish massive viewpoints and complicated yet functional operational systems, which can strengthen the entire supply chain. However, integration of human resource management (HRM) and supply chain management (SCM) has been severely delayed due to a larger integration gap and fuzziness. This study proposes a fuzzy-based HRM-SCM strategy and emphasizes the educational requirement as the most influential HRM element. The study also suggests using IoT for supply chain analytics and Butter Ant Optimization (BAO) for improving SCM performance. The proposed IoT+FL+BAO approach significantly improves supply chain performance, efficiency, employee satisfaction, decision-making scale, prediction rate, and F1-score.
INTERNET OF THINGS
(2023)
Article
Chemistry, Physical
Dandan Lu, Breno R. L. Galvao, Antonio J. C. Varandas, Hua Guo
Summary: The dynamics and kinetics of spin-forbidden transitions between N(D-2) and N(S-4) mediated by collisions with N-2 molecules were investigated using quantum wave packet (WP) method and semi-classical coherent switches with decay of mixing (CSDM) method. These transitions compete with exchange reaction channels on both doublet and quartet potential energy surfaces. The WP and CSDM quenching rate coefficients were in reasonable agreement with each other, reproducing previous theoretical results. For the excitation process, the agreement between the two approaches depended on the treatment of zero-point energy (ZPE) in the product, as the high endoergicity of this process led to severe violation of vibrational ZPE. The Gaussian-binning (GB) method improved the agreement with the quantum result. The excitation rate coefficients were two orders of magnitude smaller than those of the adiabatic exchange reaction, indicating inefficient intersystem crossing due to weak spin-orbit coupling between the two spin manifolds of the N-3 system.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Reed Nieman, Michael Sands, Yingqi Wang, Timothy K. Minton, Erin E. Mussoni, Jeffrey Engerer, Hua Guo
Summary: In order to investigate the gas-surface chemistry on the thermal protection system of a hypersonic vehicle, extensive periodic density functional theory (DFT) calculations are conducted to study the interaction between atomic oxygen/nitrogen and highly oriented pyrolytic graphite (HOPG) surfaces. The calculated reaction energies and barriers provide important information for adsorption, desorption, diffusion, recombination, and other reactions. The results are compared with a finite-rate model and suggest that some model parameters may need further refinement. These calculations contribute to the development of a predictive kinetic model for the complex reaction network under hypersonic flight conditions.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Humberto da Silva Jr, Qian Yao, Masato Morita, Brian K. Kendrick, Hua Guo, Naduvalath Balakrishnan
Summary: This paper reports the ab initio electronic structure and full-dimensional quantum dynamical calculations of the Li + CaF -> LiF + Ca chemical reaction. The results show that the Li + CaF reaction populates several low-lying vibrational levels and many rotational levels of the product LiF molecule, and the reaction is inefficient in the 1-100 mK regime, allowing sympathetic cooling of CaF by collisions with cold Li atoms.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Yingqi Wang, Hua Guo
Summary: A recent study using scanning tunneling microscopy showed that N2 dissociation on Ru(0001) generates N atoms with high exoergicity, which can migrate away from the impact site. In this work, theoretical investigation based on a high-dimensional potential energy surface and neural network representation was conducted to study the dynamics of these hot nitrogen atoms. Simulation results revealed that typically only one N atom undergoes significant migration while the other remains near the impact site. The average final separation between the two N atoms is much smaller than the experimental report, mainly attributed to high diffusion barrier and fast energy dissipation to surface phonons.
JOURNAL OF PHYSICAL CHEMISTRY C
(2023)