Review
Biochemical Research Methods
Apurva Badkas, Sebastien De Landtsheer, Thomas Sauter
Summary: Drug repositioning has gained significant attention in the past decade. Computational approaches, particularly network-based methods, have played a crucial role in uncovering unintuitive functional relationships and identifying repositioning candidates in drug-disease and other networks. Various structural network measures contribute to these efforts and hold potential for wider applications, especially in the field of drug repositioning.
BRIEFINGS IN BIOINFORMATICS
(2021)
Review
Pharmacology & Pharmacy
Jun-Lin Yu, Qing-Qing Dai, Guo-Bo Li
Summary: Drug repositioning is an attractive strategy for discovering new therapeutic uses for approved or investigational drugs. Deep learning has gained attention for its potential in target prediction and drug repositioning, improving efficiency and success rates.
DRUG DISCOVERY TODAY
(2022)
Article
Biochemical Research Methods
Jingbo Yang, Denan Zhang, Lei Liu, Guoqi Li, Yiyang Cai, Yan Zhang, Hongbo Jin, Xiujie Chen
Summary: This article integrated the features of chemical-genomics and pharmaco-genomics to establish a drug-substructure-indication network for predicting therapeutic effects, demonstrating high accuracy and reliability.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Hossein Lanjanian, Shadi Hosseini, Zahra Narimani, Sogol Meknatkhah, Gholam Hossein Riazi
Summary: The study aimed to develop a pipeline to identify potential protein-protein interaction inhibitors by screening phytochemicals from Middle Eastern antiviral herbs. A series of simulations were performed to determine candidate molecules for inhibiting PPIs involved in COVID-19.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Review
Oncology
Binsheng He, Fangxing Hou, Changjing Ren, Pingping Bing, Xiangzuo Xiao
Summary: Drug repositioning, the practice of using existing drugs for new disease indications, has become popular due to the high cost and failure rate of developing new drugs. With the aid of high-throughput sequencing techniques, efficient methods have been proposed and applied in drug repositioning and personalized tumor treatment. Computational methods for drug repositioning can be divided into four categories, with future directions focusing on more sensitive methods for individualized tumor treatment.
FRONTIERS IN ONCOLOGY
(2021)
Article
Biochemical Research Methods
Fei Li, Ziqiao Zhang, Jihong Guan, Shuigeng Zhou
Summary: In this article, a new model for drug-target interaction (DTI) prediction, MINN-DTI, is proposed. By combining Interformer with an improved CMPNN, MINN-DTI effectively captures the two-way impact between drugs and targets, resulting in better prediction performance and interpretability.
Review
Biochemical Research Methods
Fei Wang, Yulian Ding, Xiujuan Lei, Bo Liao, Fang-Xiang Wu
Summary: Drug repositioning is an important method for exploring new uses of existing drugs in drug discovery, especially in pre-clinical stages. Computational approaches, including machine learning and deep learning, have shown great potential in saving time and reducing costs compared to traditional drug discovery methods.
CURRENT BIOINFORMATICS
(2022)
Article
Biology
Shuyu Wang, Peng Shan, Yuliang Zhao, Lei Zuo
Summary: Drug discovery requires accurate prediction of drug-target interactions through virtual screening. Deep learning methods are more efficient than traditional methods. The GanDTI model, utilizing compound graphs and protein sequences, improves prediction accuracy and classification performance.
COMPUTATIONAL BIOLOGY AND CHEMISTRY
(2021)
Article
Biochemical Research Methods
Yang Li, Guanyu Qiao, Keqi Wang, Guohua Wang
Summary: This paper proposes a new model DTI-MGNN based on multi-channel graph convolutional network and graph attention for predicting drug-target interaction. The model combines topological structure and semantic features to improve the representation learning ability of drug-target interactions, and achieves state-of-the-art results on public datasets.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemical Research Methods
Qi An, Liang Yu
Summary: This study introduces a new method for predicting drug-target interactions in multiplex networks and achieves accurate results that outperform existing algorithms. Additionally, a reasonable model is proposed to address the widespread negative sampling problem, offering new insights for future research.
BRIEFINGS IN BIOINFORMATICS
(2021)
Review
Biotechnology & Applied Microbiology
Hector Hernandez-Parra, Hernan Cortes, Jose Arturo Avalos-Fuentes, Maria Del Prado-Audelo, Benjamin Floran, Gerardo Leyva-Gomez, Javad Sharifi-Rad, William C. Cho
Summary: Parkinson's disease significantly impacts patients' quality of life and healthcare systems economically. Drug repositioning offers new medication alternatives for PD and reduces research time and costs. This review collected evidence of potential candidate drugs for reuse in PD and proposed the reformulation of these drugs into nanocarriers for future repositioning trials. The study also suggested functionalizing the surface of nanoparticles to enhance their ability to cross the blood-brain barrier and improve their affinity for specific brain regions. The main parameters for designing nanoparticles targeting the central nervous system were highlighted.
JOURNAL OF NANOBIOTECHNOLOGY
(2022)
Article
Biochemical Research Methods
Tri Minh Nguyen, Thin Nguyen, Truyen Tran
Summary: By incorporating interaction information from related tasks, the proposed method shows advantages in predicting drug-target interactions compared to other pre-training methods.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Genetics & Heredity
Sree Karani Kondapuram, Mohane Selvaraj Coumar
Summary: This study identifies important autophagy genes and potential drug targets by analyzing the expression levels of genes in 21 cancers. The findings shed light on the role of autophagy in cancer and provide potential targets for cancer treatment.
Article
Mathematics, Applied
Ying Ying Keng, Kiam Heong Kwa, Kurunathan Ratnavelu
Summary: The study demonstrates the significance of central drugs in a drug network for drug repositioning, suggesting that top central drugs are more likely to repurpose their neighboring drugs as new treatment options. This research provides novel insights into complementing drug repositioning efforts and highlights the importance of network centrality measures in guiding systematic analysis.
APPLIED MATHEMATICS AND COMPUTATION
(2021)
Review
Biochemistry & Molecular Biology
Judit Olah, Tibor Szenasi, Attila Lehotzky, Victor Norris, Judit Ovadi
Summary: Protein-protein interactions (PPIs) play a crucial role in fundamental processes and are associated with pathological conditions. However, discovering drugs that can modulate PPIs poses challenges and limitations.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Clinical Neurology
Paulami Chatterjee, Debjani Roy
CURRENT ALZHEIMER RESEARCH
(2016)
Article
Biochemistry & Molecular Biology
Paulami Chatterjee, Debjani Roy
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2017)
Article
Neurosciences
Paulami Chatterjee, Debjani Roy, Nitin Rathi
JOURNAL OF ALZHEIMERS DISEASE
(2018)
Article
Multidisciplinary Sciences
Paulami Chatterjee, Malay Bhattacharyya, Sanghamitra Bandyopadhyay, Debjani Roy
Review
Microbiology
Paulami Chatterjee, Gabriele Sass, Wieslaw Swietnicki, David A. Stevens
Article
Infectious Diseases
Gabriele Sass, Hasan Nazik, Paulami Chatterjee, David A. Stevens
Summary: Pseudomonas aeruginosa has mechanisms to compete with Aspergillus fumigatus under both limiting and non-limiting iron conditions. The switch from iron-denial-based to toxin-based antifungal activity can have implications for the evolution of the microbiome in clinical settings where the two pathogens co-exist. Important differences in iron response between P. aeruginosa laboratory strains PA14 and PAO1 were also uncovered.
Article
Microbiology
Gabriele Sass, David J. Larwood, Marife Martinez, Paulami Chatterjee, Melissa O. Xavier, David A. Stevens
Summary: Nikkomycin Z has demonstrated efficacy against disseminated coccidioidomycosis, showing a greater reduction in CFU in organs compared to fluconazole. A dose of >= 200 mg/kg of body weight/day of oral nikZ was particularly effective and well tolerated in all organs. Developing an extended release formulation of nikZ may provide continuous systemic concentrations and further benefits in treatment.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2021)
Article
Immunology
Gabriele Sass, Hasan Nazik, Paulami Chatterjee, Pallabi Shrestha, Marie-Christine Groleau, Eric Deziel, David A. Stevens
Summary: Pseudomonas aeruginosa produces antifungal factors such as pyoverdine and pyocyanin on agar, which are different from those produced in liquid cultures. These factors depend on quorum sensing and are regulated by the availability of ferric iron. Rhamnolipids and elastase appear to be major mediators of Pseudomonas' antifungal activity on a solid surface.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
Article
Biophysics
Efthymia Iliana Matthaiou, Husham Sharifi, Christian O'Donnell, Wayland Chiu, Clark Owyang, Paulami Chatterjee, Ihsan Turk, Laura Johnston, Theresa Brondstetter, Karen Morris, Guang-Shing Cheng, Joe L. Hsu
Summary: This study examined the potential of pirfenidone for treating bronchiolitis obliterans syndrome (BOS). The 52-week trial found that approximately 59% of participants tolerated the recommended dose and no severe adverse events were attributed to the drug. Treatment with pirfenidone was shown to stabilize pulmonary function and improve patient-reported outcomes, suggesting its efficacy for BOS treatment.
BONE MARROW TRANSPLANTATION
(2022)
Article
Biotechnology & Applied Microbiology
Paulami Chatterjee, Debjani Roy, Malay Bhattacharyya, Sanghamitra Bandyopadhyay
Article
Biochemistry & Molecular Biology
Paulami Chatterjee, Debjani Roy
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2017)
Article
Biochemistry & Molecular Biology
Soojung Hahn, Gyuri Kim, Sang-Man Jin, Jae Hyeon Kim
Summary: This study utilized three-dimensional intestinal organoids to investigate the effects of metformin on inflammatory bowel disease (IBD) and found that metformin can enhance intestinal barrier function and reduce levels of inflammatory cytokines.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
V. V. Sudarev, M. S. Gette, S. V. Bazhenov, O. M. Tilinova, E. V. Zinovev, I. V. Manukhov, A. I. Kuklin, Yu. L. Ryzhykau, A. V. Vlasov
Summary: This study investigated the self-assembly processes of ferritin-based protein complexes and obtained structurally characterized oligomeric states. These results provide new potential and opportunities for the application of ferritin in various fields.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Yalda Sabaghi, Farnaz Pourfarzad, Leila Zolghadr, Azita Bahrami, Tahereh Shojazadeh, Alireza Farasat, Nematollah Gheibi
Summary: p-Coumaric acid (p-CA) is a plant compound with anti-cancer activities. This study designed a nano-liposomal carrier containing p-CA to enhance its effectiveness against melanoma cells. The findings showed that the liposomal form of p-CA had a greater impact on the cells. Kinetic modeling indicated that the best fitting model was zero-order.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
M. D. Nazmul Hasan, Md Mahfuzur Rahman, Al Asmaul Husna, Nobuhiro Nozaki, Osamu Yamato, Naoki Miura
Summary: This study investigated the expression of ncRNAs other than miRNAs in different histologic subtypes of canine mammary gland tumors (MGT). Three aberrantly expressed ncRNAs were identified as potential biomarkers for differentiating MGT subtypes. YRNA and tRFs expression levels were found to be decreased in metastatic compared to primary MGT cell lines.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Seine A. Shintani
Summary: In this study, the researchers used signal analysis to study the instantaneous amplitude and phase of sarcomeric oscillations in skeletal muscle. They identified two types of oscillations, sarcomeric oscillations and sarcosynced oscillations, and visualized their behavior during propagating waves. The researchers discovered the presence of sarcomeric defect holes and sarcomeric collision holes, which are important indicators for understanding the oscillation properties of sarcomeres. This finding has important implications for improving our understanding of muscle function and its regulatory mechanisms.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Shuanglin Zhang, Yuzhong Jia, Guolan Ma, Yanyan Yang, Zhenzhen Cao, Antao Luo, Zefu Zhang, Shihan Li, Jie Wen, Hanfeng Liu, Jihua Ma
Summary: Bupleurum is an antiarrhythmic agent that may exert its effects by inhibiting L-type calcium channels.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Tomotaka Ohkubo, Yasuhiko Matsumoto, Hiroaki Sasaki, Kaoru Kinoshita, Yuki Ogasawara, Takashi Sugita
Summary: This study found that Citrobacter koseri inhibits the growth of Staphylococcus epidermidis, disrupting the balance between S. epidermidis and Staphylococcus aureus, and exacerbating inflammation in atopic dermatitis.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Toshifumi Asano, Philipp Sasse, Takao Nakata
Summary: A Cre recombination-based fluorescent reporter system was developed to monitor cell-cell fusion. The system successfully detected the formation of multinuclear myotubes and placental syncytiotrophoblast. This tool could facilitate the study of cell-to-cell fusion.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Ke Shi, Yunlong Shan, Xiao Sun, Kuida Chen, Qiong Luo, Qiang Xu
Summary: This study found that low expression of TP53INP2 is associated with poor survival in colorectal cancer (CRC) patients. As the malignancy of CRC progresses, TP53INP2 expression gradually decreases. Knockdown of TP53INP2 promotes CRC cell proliferation and tumor growth. Mechanistically, TP53INP2 deficiency decreases phosphorylation of beta-catenin, leading to increased accumulation and enhanced nuclear translocation and transcriptional activity. Additionally, TP53INP2 sequesters TIM50, inhibiting its activation of beta-catenin. In conclusion, downregulation of TP53INP2 promotes CRC progression by activating beta-catenin.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Martina Rossi, Fabio Tomaselli, Alejandro Hochkoeppler
Summary: Oligomeric enzymes are known for their higher catalytic rates compared to monomeric enzymes, but the extent of additivity in their activity is still not well understood. This study used tetrameric rabbit lactate dehydrogenase as a model to examine the kinetics of its catalytic action. Surprisingly, when the concentration of the limiting reactant exceeded that of a single subunit, there was a significant slowdown in the enzyme's conformational rearrangements.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Amin Sahraei, Mohammad Javad Shamsoddini, Fakhrossadat Mohammadi, Leila Hassani
Summary: This study explored the inhibitory effects of gallium curcumin, indium curcumin, and vanadyl curcumin on the amyloid fibrillation of hen egg white lysozyme, as well as the binding interactions of these metal complexes with the enzyme. The results showed that indium curcumin and vanadyl curcumin exhibited higher binding affinities and stronger inhibitory effects on amyloid fibrillation compared to gallium curcumin.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Takahiro Sasaki, Yoshiki Kuse, Shinsuke Nakamura, Masamitsu Shimazawa
Summary: PGRN deficiency plays a significant role in cardiac remodeling and arrhythmias post-myocardial infarction (MI), potentially by promoting metabolic abnormalities in macrophages.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Hongwei Zhao, Yiqiang Li, Yibo Zhang, Chi Zhang
Summary: Electrical brain stimulation technology is commonly used to treat brain neurological disorders, but it can cause side effects. This study investigated the impact of electric fields on nerve fibers and revealed the possible origin of side effects. The findings provide guidance for selecting electrical parameters in clinical stimulation therapy.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Julia S. Scott, Lake-Ee Quek, Andrew J. Hoy, Johannes V. Swinnen, Zeyad D. Nassar, Lisa M. Butler
Summary: The fatty acid elongation enzyme ELOVL5 plays a critical role in promoting metastasis in prostate cancer. Knocking down ELOVL5 leads to the accumulation of malonyl-CoA, which inhibits fatty acid oxidation in mitochondria. This study highlights the importance of fatty acid elongation in regulating cell viability and provides a potential target for prostate cancer treatment.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
Article
Biochemistry & Molecular Biology
Zan Zhou, Wen-jun Jiang, Li Li, Jun-qiang Si
Summary: This study investigates the effect of noise exposure on cognitive function in mice and explores the underlying molecular mechanisms. The findings suggest that noise exposure leads to increased inflammation, increased phosphorylation of Tau protein, and decreased levels of postsynaptic density protein, resulting in cognitive impairment.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2024)
