keyword
https://read.qxmd.com/read/38503396/unlocking-bacterial-defense-exploring-the-potent-inhibition-of-nora-efflux-pump-by-coumarin-derivatives-in-staphylococcus-aureus
#21
JOURNAL ARTICLE
Ana Luíza A R Martin, Raimundo Luiz Silva Pereira, Janaína Esmeraldo Rocha, Pablo A M Farias, Thiago S Freitas, Francisco Rodrigo de Lemos Caldas, Fernando G Figueredo, Nadghia Figueiredo Leite Sampaio, Cícera Datiane de Morais Oliveira-Tintino, Saulo Relison Tintino, Gabriel Costa A da Hora, Maria Carolina Pacheco Lima, Irwin Rose A de Menezes, Diogo T Carvalho, Henrique D M Coutinho, Marta M F Fonteles
The occurrence of bacterial resistance has been increasing, compromising the treatment of various infections. The high virulence of Staphylococcus aureus allows for the maintenance of the infectious process, causing many deaths and hospitalizations. The MepA and NorA efflux pumps are transporter proteins responsible for expelling antimicrobial agents such as fluoroquinolones from the bacterial cell. Coumarins are phenolic compounds that have been studied for their diverse biological actions, including against bacteria...
March 20, 2024: Microbial Pathogenesis
https://read.qxmd.com/read/38503157/c-met-pathway-in-human-malignancies-and-its-targeting-by-natural-compounds-for-cancer-therapy
#22
REVIEW
Chakrabhavi Dhananjaya Mohan, Muthu K Shanmugam, Siddegowda Gopalapura Shivanne Gowda, Arunachalam Chinnathambi, Kanchugarakoppal S Rangappa, Gautam Sethi
BACKGROUND: c-MET is a receptor tyrosine kinase which is classically activated by HGF to activate its downstream signaling cascades such as MAPK, PI3K/Akt/mTOR, and STAT3. The c-MET modulates cell proliferation, epithelial-mesenchymal transition (EMT), immune response, morphogenesis, apoptosis, and angiogenesis. The c-MET has been shown to serve a prominent role in embryogenesis and early development. The c-MET pathway is deregulated in a broad range of malignancies, due to overexpression of ligands or receptors, genomic amplification, and MET mutations...
January 18, 2024: Phytomedicine
https://read.qxmd.com/read/38502854/mechanism-of-salidroside-regulating-autophagy-based-on-network-pharmacology-and-molecular-docking
#23
JOURNAL ARTICLE
Yihong Chai, Feng Chen, Hongxing Li, Xiaohong Sun, Panpan Yang, YaMing Xi
Salidroside is a natural product of phenols with a wide range of pharmacological functions, but whether it plays a role in regulating autophagy is unclear. We systematically investigated the regulatory effect and molecular mechanism of salidroside on autophagy through network pharmacology, which provided a theoretical basis for subsequent experimental research. First, the target genes of salidroside were obtained using the Chinese Medicine System Pharmacology Database and Analysis Platform, and the target genes were converted into standardized gene names using the Uniprot website...
March 15, 2024: Anti-cancer Drugs
https://read.qxmd.com/read/38502551/impact-of-halogen-bonds-on-protein-peptide-binding-and-protein-structural-stability-revealed-by-computational-approaches
#24
JOURNAL ARTICLE
Jintian Li, Liping Zhou, Zijian Han, Leyun Wu, Jianfang Zhang, Weiliang Zhu, Zhijian Xu
Halogen bonds (XBs) are essential noncovalent interactions in molecular recognition and drug design. Current studies on XBs in drug design mainly focus on the interactions between halogenated ligands and target proteins, lacking a systematic study of naturally existing and artificially prepared halogenated residue XBs (hr_XBs) and their characteristics. Here, we conducted a computational study on the potential hr_XBs in proteins/peptides using database searching, quantum mechanics calculations, and molecular dynamics simulations...
March 19, 2024: Journal of Medicinal Chemistry
https://read.qxmd.com/read/38500508/identifying-potential-monkeypox-virus-inhibitors-an-in-silico-study-targeting-the-a42r-protein
#25
JOURNAL ARTICLE
Carolyn N Ashley, Emmanuel Broni, Chanyah M Wood, Tunmise Okuneye, Mary-Pearl T Ojukwu, Qunfeng Dong, Carla Gallagher, Whelton A Miller
Monkeypox (now Mpox), a zoonotic disease caused by the monkeypox virus (MPXV) is an emerging threat to global health. In the time span of only six months, from May to October 2022, the number of MPXV cases breached 80,000 and many of the outbreaks occurred in locations that had never previously reported MPXV. Currently there are no FDA-approved MPXV-specific vaccines or treatments, therefore, finding drugs to combat MPXV is of utmost importance. The A42R profilin-like protein of the MPXV is involved in cell development and motility making it a critical drug target...
2024: Frontiers in Cellular and Infection Microbiology
https://read.qxmd.com/read/38496952/unveiling-the-antiviral-capabilities-of-targeting-human-dihydroorotate-dehydrogenase-against-sars-cov-2
#26
JOURNAL ARTICLE
Aline D Purificação, Sabrina Silva-Mendonça, Luiza V Cruz, Carolina Q Sacramento, Jairo R Temerozo, Natalia Fintelman-Rodrigues, Caroline Souza de Freitas, Bruna Fleck Godoi, Miguel Menezes Vaidergorn, Juliana Almeida Leite, Luis Carlos Salazar Alvarez, Murillo V Freitas, Meryck F B Silvac, Bianca A Martin, Renata F V Lopez, Bruno J Neves, Fabio T M Costa, Thiago M L Souza, Flavio da Silva Emery, Carolina Horta Andrade, M Cristina Nonato
The urgent need for effective treatments against emerging viral diseases, driven by drug-resistant strains and new viral variants, remains critical. We focus on inhibiting the human dihydroorotate dehydrogenase ( Hs DHODH), one of the main enzymes responsible for pyrimidine nucleotide synthesis. This strategy could impede viral replication without provoking resistance. We evaluated naphthoquinone fragments, discovering potent Hs DHODH inhibition with IC50 ranging from 48 to 684 nM, and promising in vitro anti-SARS-CoV-2 activity with EC50 ranging from 1...
March 12, 2024: ACS Omega
https://read.qxmd.com/read/38496882/clinical-efficacy-and-potential-mechanism-of-ginseng-polysaccharides-in-the-treatment-of-non-small-cell-lung-cancer-based-on-meta-analysis-associated-with-network-pharmacology
#27
JOURNAL ARTICLE
Qi Zhao, Le Bai, Dongwei Zhu, Tingyuan Li, Jie Xu, Yong Xu, Xianmei Zhou
BACKGROUND: The ginseng polysaccharide injection is a well-known traditional Chinese medicine often employed as a supplementary treatment for cancer. This treatment can not only alleviate the adverse effects caused by tumor radiotherapy and chemotherapy but also enhance the immune system of individuals diagnosed with lung cancer. It is important to acknowledge the efficacy of ginseng polysaccharide injection in the treatment of non-small cell lung cancer (NSCLC). However, these small-sample studies may have certain biases, and the underlying mechanisms of ginseng polysaccharides therapy for NSCLC are still unclear...
March 30, 2024: Heliyon
https://read.qxmd.com/read/38496694/survivin-in-lung-cancer-a-potential-target-for-therapy-and-prevention-a-narrative-review
#28
REVIEW
Akhil Goud Pachimatla, Robert Fenstermaker, Michael Ciesielski, Sai Yendamuri
BACKGROUND AND OBJECTIVE: A versatile biomarker, survivin, is highly expressed in proliferating cells of multiple cancers in humans and animals. It is an apoptosis-regulating protein, engaging in a cascade of reactions that involve several other genes and protein interactions. Currently, researchers are investigating its therapeutic potential due to the evidence linking its overexpression to advanced-stage lung cancer. This review is centered around examining survivin-related molecular mechanisms and its therapeutic role specifically in lung cancer...
February 29, 2024: Translational Lung Cancer Research
https://read.qxmd.com/read/38494273/evolution-of-methods-to-detect-paraneoplastic-antibodies
#29
REVIEW
Patrick Waters, John R Mills, Hannah Fox
An adaptive immune response in less than 1% of people who develop cancer produces antibodies against neuronal proteins. These antibodies can be associated with paraneoplastic syndromes, and their accurate detection should instigate a search for a specific cancer. Over the years, multiple systems, from indirect immunofluorescence to live cell-based assays, have been developed to identify these antibodies. As the specific antigens were identified, high throughput, multi-antigen substrates such as line blots and ELISAs were developed for clinical laboratories...
2024: Handbook of Clinical Neurology
https://read.qxmd.com/read/38493447/clinical-practice-guidelines-for-molecular-tumor-marker-2nd-edition-review-part-2
#30
JOURNAL ARTICLE
Yoshinori Kikuchi, Hideaki Shimada, Fumiyuki Yamasaki, Taku Yamashita, Koji Araki, Kohei Horimoto, Satoshi Yajima, Masakazu Yashiro, Keigo Yokoi, Haruhiko Cho, Takuya Ehira, Kazunari Nakahara, Hiroshi Yasuda, Kazutoshi Isobe, Tetsu Hayashida, Shingo Hatakeyama, Koichiro Akakura, Daisuke Aoki, Hiroyuki Nomura, Yuji Tada, Yuki Yoshimatsu, Hayato Miyachi, Chiaki Takebayashi, Ichiro Hanamura, Hiroyuki Takahashi
In recent years, rapid advancement in gene/protein analysis technology has resulted in target molecule identification that may be useful in cancer treatment. Therefore, "Clinical Practice Guidelines for Molecular Tumor Marker, Second Edition" was published in Japan in September 2021. These guidelines were established to align the clinical usefulness of external diagnostic products with the evaluation criteria of the Pharmaceuticals and Medical Devices Agency. The guidelines were scoped for each tumor, and a clinical questionnaire was developed based on a serious clinical problem...
March 17, 2024: International Journal of Clinical Oncology
https://read.qxmd.com/read/38493179/identification-and-validation-of-irf6-related-to-ovarian-cancer-and-biological-function-and-prognostic-value
#31
JOURNAL ARTICLE
Shihao Hong, Ni Fu, Shanliang Sang, Xudong Ma, Fangying Sun, Xiao Zhang
BACKGROUND: Ovarian cancer (OC) is a severe gynecological malignancy with significant diagnostic and therapeutic challenges. The discovery of reliable cancer biomarkers can be used to adjust diagnosis and improve patient care. However, serous OC lacks effective biomarkers. We aimed to identify novel biomarkers for OC and their pathogenic causes. METHODS: The present study used the differentially expressed genes (DEGs) obtained from the "Limma" package and WGCNA modules for intersection analysis to obtain DEGs in OC...
March 16, 2024: Journal of Ovarian Research
https://read.qxmd.com/read/38491812/protein-phosphatase-2a-modulation-and-connection-with-mirnas-and-natural-products
#32
JOURNAL ARTICLE
Ya-Ting Chuang, Ching-Yu Yen, Jen-Yang Tang, Fang-Rong Chang, Yi-Hong Tsai, Kuo-Chuan Wu, Tsu-Ming Chien, Hsueh-Wei Chang
Protein phosphatase 2A (PP2A), a heterotrimeric holoenzyme (scaffolding, catalytic, and regulatory subunits), regulates dephosphorylation for more than half of serine/threonine phosphosites and exhibits diverse cellular functions. Although several studies on natural products and miRNAs have emphasized their impacts on PP2A regulation, their connections lack systemic organization. Moreover, only part of the PP2A family has been investigated. This review focuses on the PP2A-modulating effects of natural products and miRNAs' interactions with potential PP2A targets in cancer and non-cancer cells...
March 16, 2024: Environmental Toxicology
https://read.qxmd.com/read/38491685/truncated-stochastically-switching-processes
#33
JOURNAL ARTICLE
Paul C Bressloff
There are a large variety of hybrid stochastic systems that couple a continuous process with some form of stochastic switching mechanism. In many cases the system switches between different discrete internal states according to a finite-state Markov chain, and the continuous dynamics depends on the current internal state. The resulting hybrid stochastic differential equation (hSDE) could describe the evolution of a neuron's membrane potential, the concentration of proteins synthesized by a gene network, or the position of an active particle...
February 2024: Physical Review. E
https://read.qxmd.com/read/38491400/on-the-use-of-tandem-mass-spectra-acquired-from-samples-of-evolutionarily-distant-organisms-to-validate-methods-for-false-discovery-rate-estimation
#34
JOURNAL ARTICLE
Dominik Madej, Henry Lam
Estimating the false discovery rate (FDR) of peptide identifications is a key step in proteomics data analysis, and many methods have been proposed for this purpose. Recently, an entrapment-inspired protocol to validate methods for FDR estimation appeared in articles showcasing new spectral library search tools. That validation approach involves generating incorrect spectral matches by searching spectra from evolutionarily distant organisms (entrapment queries) against the original target search space. Although this approach may appear similar to the solutions using entrapment databases, it represents a distinct conceptual framework whose correctness has not been verified yet...
March 15, 2024: Proteomics
https://read.qxmd.com/read/38491261/virtuouspocketome-a-computational-tool-for-screening-protein-ligand-complexes-to-identify-similar-binding-sites
#35
JOURNAL ARTICLE
Lorenzo Pallante, Marco Cannariato, Lampros Androutsos, Eric A Zizzi, Agorakis Bompotas, Xhesika Hada, Gianvito Grasso, Athanasios Kalogeras, Seferina Mavroudi, Giacomo Di Benedetto, Konstantinos Theofilatos, Marco A Deriu
Protein residues within binding pockets play a critical role in determining the range of ligands that can interact with a protein, influencing its structure and function. Identifying structural similarities in proteins offers valuable insights into their function and activation mechanisms, aiding in predicting protein-ligand interactions, anticipating off-target effects, and facilitating the development of therapeutic agents. Numerous computational methods assessing global or local similarity in protein cavities have emerged, but their utilization is impeded by complexity, impractical automation for amino acid pattern searches, and an inability to evaluate the dynamics of scrutinized protein-ligand systems...
March 15, 2024: Scientific Reports
https://read.qxmd.com/read/38490980/immunopeptidomics-based-identification-of-naturally-presented-non-canonical-circrna-derived-peptides
#36
JOURNAL ARTICLE
Humberto J Ferreira, Brian J Stevenson, HuiSong Pak, Fengchao Yu, Jessica Almeida Oliveira, Florian Huber, Marie Taillandier-Coindard, Justine Michaux, Emma Ricart-Altimiras, Anne I Kraemer, Lana E Kandalaft, Daniel E Speiser, Alexey I Nesvizhskii, Markus Müller, Michal Bassani-Sternberg
Circular RNAs (circRNAs) are covalently closed non-coding RNAs lacking the 5' cap and the poly-A tail. Nevertheless, it has been demonstrated that certain circRNAs can undergo active translation. Therefore, aberrantly expressed circRNAs in human cancers could be an unexplored source of tumor-specific antigens, potentially mediating anti-tumor T cell responses. This study presents an immunopeptidomics workflow with a specific focus on generating a circRNA-specific protein fasta reference. The main goal of this workflow is to streamline the process of identifying and validating human leukocyte antigen (HLA) bound peptides potentially originating from circRNAs...
March 15, 2024: Nature Communications
https://read.qxmd.com/read/38490030/role-of-micrornas-as-post-transcription-regulators-of-matrix-metalloproteinases-and-their-association-in-tuberculous-meningitis
#37
JOURNAL ARTICLE
Apoorva Aggarwal, Neeraj Singla, Monidipa Konar, Maninder Kaur, Kusum Sharma, Kajal Jain, Manish Modi, Sadhna Sharma
Matrix metalloproteinases (MMPs) have a role in driving neuroinflammation in infectious as well as non-infectious diseases; however, recent reports have potentiated the role of microRNAs in regulating MMPs at post-transcriptional levels, leading to dysregulation of crucial MMP functions like tissue remodelling, blood brain barrier integrity, etc. In present study, microRNAs regulating MMPs (MMP2 and MMP3) were selected from database search followed by literature support. Expression of these microRNAs i.e., hsa-miR-495-3p, hsa-miR-132-3p and hsa-miR-21-5p was assessed by RT-PCR and the protein levels of MMPs were assessed by ELISA in the cerebrospinal fluid (CSF) of tuberculous meningitis (TBM) patients, healthy controls (HC) and non-infectious neuroinflammatory disease (NID) patients...
March 5, 2024: Tuberculosis
https://read.qxmd.com/read/38489730/identification-and-prognostic-analysis-of-candidate-biomarkers-for-lung-metastasis-in-colorectal-cancer
#38
JOURNAL ARTICLE
Yuxing Liu, Chenming Liu, Dong Huang, Chenyang Ge, Lin Chen, Jianfei Fu, Jinlin Du
Colorectal cancer (CRC) is one of the most prevalent types of malignant tumors. It's vital to explore new biomarkers and potential therapeutic targets in CRC lung metastasis through adopting integrated bioinformatics tools. Multiple cohort datasets and databases were integrated to clarify and verify potential key candidate biomarkers and signal transduction pathways in CRC lung metastasis. DAVID, STRING, UALCAN, GEPIA, TIMER, cBioPortal, THE HUMAN PROTEIN ATLAS, GSEA 4.3.2, FUNRICH 3.1.3, and R 4.2.3 were utilized in this study...
March 15, 2024: Medicine (Baltimore)
https://read.qxmd.com/read/38489696/network-pharmacology-and-molecular-docking-to-explore-the-mechanism-of-a-clinical-proved-recipe-for-external-use-of-clearing-heat-and-removing-dampness-in-the-treatment-of-immune-related-cutaneous-adverse-events
#39
JOURNAL ARTICLE
Shuyi Chen, Rui Yu, Fangmin Zhao, Lin Sun, Yudan Yin, Gaochenxi Zhang, Qunwei Chen, Qijin Shu
Immune-related cutaneous adverse events (ircAEs) will undermine the patients' quality of lives, and interrupt the antitumor therapy. A clinical proved recipe for external use of clearing heat and removing dampness (Qing-Re-Li-Shi Formula, hereinafter referred to as "QRLSF") is beneficial to the treatment of ircAEs in clinical practice. Our study will elucidate the mechanism of QRLSF against ircAEs based on network pharmacology and molecular docking. The active components and corresponding targets of QRLSF were collected through traditional Chinese medicine systems pharmacology database...
March 15, 2024: Medicine (Baltimore)
https://read.qxmd.com/read/38486999/ehmt2-promotes-tumorigenesis-in-gnaq-11-mutant-uveal-melanoma-via-arhgap29-mediated-rhoa-pathway
#40
JOURNAL ARTICLE
Yongyun Li, Tianyu Zhu, Jie Yang, Qianqian Zhang, Shiqiong Xu, Shengfang Ge, Renbing Jia, Jianming Zhang, Xianqun Fan
Constitutive activation of GNAQ/11 is the initiative oncogenic event in uveal melanoma (UM). Direct targeting GNAQ/11 has yet to be proven feasible as they are vital for a plethora of cellular functions. In search of genetic vulnerability for UM, we found that inhibition of euchromatic histone lysine methyltransferase 2 (EHMT2) expression or activity significantly reduced the proliferation and migration capacity of cancer cells. Notably, elevated expression of EHMT2 had been validated in UM samples. Furthermore, Kaplan-Meier survival analysis indicated high EHMT2 protein level was related to poor recurrence-free survival and a more advanced T stage...
March 2024: Acta Pharmaceutica Sinica. B
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