A5058640779- Advanced Chemical Physics Studies
- Plant biochemistry and biosynthesis
- Mass Spectrometry Techniques and Applications
- Antimicrobial Peptides and Activities
- Machine Learning in Bioinformatics
- Laser-Matter Interactions and Applications
- Plant Gene Expression Analysis
- Atomic and Molecular Physics
- vaccines and immunoinformatics approaches
- Protein Structure and Dynamics
- GABA and Rice Research
- Spectroscopy and Quantum Chemical Studies
- Garlic and Onion Studies
- Biochemical and Structural Characterization
- Molecular Spectroscopy and Structure
- Microbial Metabolic Engineering and Bioproduction
- RNA and protein synthesis mechanisms
- Computational Drug Discovery Methods
- Analytical Chemistry and Chromatography
- Synthesis and biological activity
- Biological Activity of Diterpenoids and Biflavonoids
- Microfluidic and Capillary Electrophoresis Applications
- Crystallization and Solubility Studies
- Phytochemical compounds biological activities
- Photosynthetic Processes and Mechanisms
Chinese University of Hong Kong, Shenzhen
2020-2025
Chinese University of Hong Kong
2016-2020
University of Southampton
2019-2020
Heidelberg University
2009-2015
The University of Tokyo
2009
Merck & Co., Inc., Rahway, NJ, USA (United States)
1987
Abstract MicroRNAs (miRNAs) are noncoding RNAs with 18–26 nucleotides; they pair target mRNAs to regulate gene expression and produce significant changes in various physiological pathological processes. In recent years, the interaction between miRNAs their genes has become one of mainstream directions for drug development. As a large-scale biological database that mainly provides miRNA–target interactions (MTIs) verified by experiments, miRTarBase undergone five revisions enhancements. The...
The last 18 months, or more, have seen a profound shift in our global experience, with many of us navigating once-in-100-year pandemic. To date, COVID-19 remains life-threatening pandemic little to no targeted therapeutic recourse. discovery novel antiviral agents, such as vaccines and drugs, can provide solutions save human beings from severe infections; however, there is specifically effective treatment confirmed for now. Thus, great attention has been paid the use natural artificial...
The chemotaxis of CD4
Abstract The emergence and spread of antibiotic‐resistant bacteria pose a significant public health threat, necessitating the exploration alternative antibacterial strategies. Antibacterial peptide (ABP) is kind antimicrobial (AMP) that has potential ability to fight against infection, offering promising avenue for developing novel therapeutic interventions. This study introduces AMPActiPred, three‐stage computational framework designed identify ABPs, characterize their activity diverse...
Abstract Antiviral peptides (AVPs) have shown potential in inhibiting viral attachment, preventing fusion with host cells and disrupting replication due to their unique action mechanisms. They now become a broad-spectrum, promising antiviral therapy. However, identifying effective AVPs is traditionally slow costly. This study proposed new two-stage computational framework for AVP identification. The first stage identifies from wide range of peptides, the second recognizes targeting specific...
Hydroxycinnamoyl-CoA:shikimate hydroxycinnamoyltransferase (HCT) is an essential acyltransferase that mediates flux through plant phenylpropanoid metabolism by catalyzing a reaction between p-coumaroyl-CoA and shikimate, yet it also exhibits broad substrate permissiveness in vitro. How do enzymes like HCT avoid functional derailment cellular metabolites qualify as non-native substrates? Here, we combine X-ray crystallography molecular dynamics to reveal distinct dynamic modes of under native...
Radiation of the plant pyridoxal 5′-phosphate (PLP)-dependent aromatic l -amino acid decarboxylase (AAAD) family has yielded an array paralogous enzymes exhibiting divergent substrate preferences and catalytic mechanisms. Plant AAADs catalyze either decarboxylation or decarboxylation-dependent oxidative deamination acids to produce monoamines acetaldehydes, respectively. These compounds serve as key precursors for biosynthesis several important classes natural products, including indole...
Abstract Fungal infections have become a significant global health issue, affecting millions worldwide. Antifungal peptides (AFPs) emerged as promising alternative to conventional antifungal drugs due their low toxicity and propensity for inducing resistance. In this study, we developed deep learning‐based framework called DeepAFP efficiently identify AFPs. fully leverages mines composition information, evolutionary physicochemical properties of by employing combined kernels from multiple...
Cancer is one of the leading diseases threatening human life and health worldwide. Peptide-based therapies have attracted much attention in recent years. Therefore, precise prediction anticancer peptides (ACPs) crucial for discovering designing novel cancer treatments. In this study, we proposed a machine learning framework (GRDF) that incorporates deep graphical representation forest architecture identifying ACPs. Specifically, GRDF extracts features based on physicochemical properties...
Abstract C2′-halogenation has been recognized as an essential modification to enhance the drug-like properties of nucleotide analogs. The direct C2ʹ-halogenation 2′-deoxyadenosine-5′-monophosphate (dAMP) recently achieved using Fe(II)/α-ketoglutarate-dependent halogenase AdaV. However, limited substrate scope this enzyme hampers its broader applications. In study, we report two halogenases capable halogenating 2ʹ-deoxyguanosine monophosphate (dGMP), thereby expanding family halogenases....
A beta-lactone isolated from Fusarium sp. has been shown to be a potent specific inhibitor of the enzyme 3-hydroxy-3-methylglutaryl coenzyme (HMG-CoA) synthase [(S)-3-hydroxy-3-methylglutaryl-CoA acetoacetyl-CoA-lyase (CoA-acetylating), EC, 4.1.3.5] rat liver. The structure this beta-lactone, termed L-659,699, is (E,E)-11-[3-(hydroxy-methyl)-4-oxo-2-oxytanyl]-3,5,7-trimethyl-2,4 - undecadienenoic acid. partially purified preparation cytoplasmic HMG-CoA liver was inhibited by L-659,699 with...
The resonant Auger process is studied in intense x-ray laser fields. It shown that the dressing of initial and decaying states by field leads to coupled complex potential surfaces which, even for diatomic molecules, possess intersections at which nonadiabatic couplings are singular. HCl as an explicit showcase example. exact results differ qualitatively from those without rotations. A wealth phenomena expected decay processes
We investigate the ionization of HeNe from below He $1s3p$ excitation to threshold. observe ${\mathrm{HeNe}}^{+}$ ions with an enhancement by more than a factor 60 when side couples resonantly radiation field. These are experimental proof two-center resonant photoionization mechanism predicted Najjari et al. [Phys. Rev. Lett. 105, 153002 (2010)]. Furthermore, our data provide electronic and vibrational state resolved decay widths interatomic Coulombic in dimers. find that lifetime strongly...
Steroid hormones are essential in stress response, immune system regulation, and reproduction mammals. Steroids with 3-oxo-Δ4 structure, such as testosterone or progesterone, catalyzed by steroid 5α-reductases (SRD5As) to generate their corresponding 3-oxo-5α steroids, which for multiple physiological pathological processes. SRD5A2 is already a target of clinically relevant drugs. However, the detailed mechanism SRD5A-mediated reduction remains elusive. Here we report crystal structure...
Inflammation is a biological response to harmful stimuli, aiding in the maintenance of tissue homeostasis. However, excessive or persistent inflammation can precipitate myriad pathological conditions. Although current treatments such as NSAIDs, corticosteroids, and immunosuppressants are effective, they have side effects resistance issues. In this backdrop, anti-inflammatory peptides (AIPs) emerged promising therapeutic approach against inflammation. Leveraging machine learning methods, we...
Substrate permissiveness has long been regarded as the raw materials for evolution of new enzymatic functions. In land plants, hydroxycinnamoyltransferase (HCT) is an essential enzyme phenylpropanoid metabolism. Although enzymes are normally associated with high substrate specificity, HCT can utilize a variety non-native substrates. To examine structural and dynamic basis in this enzyme, we report crystal structure from Selaginella moellendorffii molecular dynamics (MD) simulations performed...
One of the major challenges in cancer therapy lies limited targeting specificity exhibited by existing anti-cancer drugs. Tumor-homing peptides (THPs) have emerged as a promising solution to this issue, due their capability specifically bind and accumulate tumor tissues while minimally impacting healthy tissues. THPs are short oligopeptides that offer superior biological safety profile, with minimal antigenicity, faster incorporation rates into target cells/tissues. However, identifying...
Abstract Cancer is a severe illness that significantly threatens human life and health. Anticancer peptides (ACPs) represent promising therapeutic strategy for combating cancer. In silico methods enable rapid accurate identification of ACPs without extensive material resources. This study proposes two-stage computational framework called ACP-CapsPred, which can accurately identify characterize their functional activities across different cancer types. ACP-CapsPred integrates protein language...
We propose an estimator that allows us to calculate the value of a simple system’s partition function using finite sampling. The core idea is neglect contribution from high energy microstates, which are difficult be sampled properly, and then volume correction term compensate for this. As proof concept, applied several model systems, ranging harmonic oscillator Lennard-Jones fluid with hundreds particles. Our results agree well numerically exact solutions or reference data, demonstrating...
Drug-induced liver injury (DILI) is a major challenge in drug development, often leading to clinical trial failures and market withdrawals due toxicity. This study presents StackDILI, computational framework designed accelerate toxicity assessment by predicting DILI risk. StackDILI integrates multiple molecular descriptors extract structural physicochemical features, including the constitution, pharmacophore, MACCS, E-state descriptors. Additionally, genetic algorithm employed for feature...
The dynamics of the resonant Auger (RA) process core-excited C${}^{*}$O(1$s$${}^{\ensuremath{-}1}{\ensuremath{\pi}}^{*},{v}_{r}=0$) molecule in an intense x-ray laser field is studied theoretically. theoretical approach includes analog conical intersections complex potential energy surfaces ground and ``dressed'' states due to pulses, taking into account decay resonance direct photoionization state, both populating same final ionic coherently, as well state itself. light-induced nonadiabatic...