Review
Biochemistry & Molecular Biology
Weronika Kotkowiak, Anna Pasternak
Summary: G-quadruplexes play a crucial role in nucleic acid structures and can be utilized as regulatory elements in cells. Extending quadruplexes with additional structural elements enhances stability and biological activity, and the specific interaction of G-quadruplexes with target molecules is pivotal. Future applications of G-quadruplex junctions hold promise, and there is still room for development in emerging research areas.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Medicinal
Neha Jain, Uma Shankar, Amit Kumar
Summary: Conserved G-quadruplex motifs have been found in Neisseria meningitidis, which are linked to essential genes involved in cell adhesion, pathogenesis, virulence, and DNA repair.
ACS INFECTIOUS DISEASES
(2022)
Review
Pharmacology & Pharmacy
Joana Figueiredo, Mojgan Djavaheri-Mergny, Lucille Ferret, Jean-Louis Mergny, Carla Cruz
Summary: In this review, we summarize the recent advancements in the development of G4 ligands capable of targeting specific genes associated with the development and progression of lung cancer.
DRUG DISCOVERY TODAY
(2023)
Article
Chemistry, Analytical
Vladimir B. Tsvetkov, Anton Turaev, Nataliia A. Petrunina, Denis M. Melnik, Yuriy M. Khodarovich, Galina E. Pozmogova, Timofei S. Zatsepin, Anna M. Varizhuk, Andrey Aralov
Summary: This study identified a new high throughput screening (HTS) technique that accurately evaluates the impact of ligands on the stability of DNA intervention motifs (iMs), providing a new approach for screening iM ligands.
Article
Biochemistry & Molecular Biology
Jonathan Dickerhoff, Kassandra R. Warnecke, Kaibo Wang, Nanjie Deng, Danzhou Yang
Summary: G-quadruplexes are important secondary structures of nucleic acids, with MycG4 being a commonly studied small-molecule target. The study found that the docking program DOCK 6 with GB/SA rescoring performs better than others, indicating that docking accuracy is mainly limited by scoring functions. Caution should be exercised when using current docking programs to predict G4 DNA-small molecule binding modes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Multidisciplinary
Gitali Devi, Fernaldo Richtia Winnerdy, Jason Cheng Yu Ang, Kah Wai Lim, Anh Tuan Phan
Summary: This study investigates the formation of propeller loops spanning more than three layers in G-quadruplex structures. It was found that native nucleotide sequences are incompatible with this goal, but synthetic non-nucleotide linkers can be used to construct highly stable four-layered intramolecular parallel-stranded G4s. Control over loop design could enhance the engineering of G4-based nanoscaffolds for diverse applications.
Article
Chemistry, Multidisciplinary
Xiaomei He, Jun Yuan, Zi Gao, Yinsheng Wang
Summary: R-loops and DNA G4 structures are enriched in gene promoter regions, and U2AF1 can bind directly to these structures. Binding with R-loops stimulates U2AF1's phase separation and modulates cotranscriptional pre-mRNA splicing.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Biochemistry & Molecular Biology
Ying Bao, Xiaonong Zhang, Xiaoxuan Xiang, Yujing Zhang, Xinhua Guo
Summary: G-quadruplexes (G4s) are important molecules that regulate various physiological functions. Surface-enhanced Raman scattering (SERS) technique can quickly provide structural details of G4s and study their interactions with ligands. This study demonstrates that SERS is a powerful tool for revealing specific interactions between G4s and their ligands.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Biotechnology & Applied Microbiology
Neha Jain, Uma Shankar, Aakriti Singh, Tarun Kumar Sharma, Amit Kumar
Summary: This study identified the significant role of G-quadruplexes (GQs) in N. gonorrhoeae, an obligate human pathogen that causes gonorrhea. Five GQ motifs in the N. gonorrhoeae genome were characterized and shown to be stabilized by the GQ-specific ligand, BRACO-19, in both in vitro and in vivo conditions. BRACO-19 exhibited potent anti-gonococcal activity and altered biofilm formation as well as the adhesion and invasion of human cervical epithelial cells by N. gonorrhoeae. This study advances the knowledge of N. gonorrhoeae biology and provides insights for developing therapeutic measures against this emerging antimicrobial resistant pathogen.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2023)
Article
Chemistry, Medicinal
Rina Kwag, Jieon Lee, Doyoung Kim, Haeun Lee, Miyoung Yeom, Jiwan Woo, Yakdol Cho, Hak Joong Kim, Jeongjin Kim, Gyochang Keum, Byungsun Jeon, Hyunah Choo
Summary: By designing and synthesizing a series of compounds and evaluating their activities and selectivities, it was found that one compound showed good binding affinity and selectivity for 5-HT7R, exhibiting a G protein-biased antagonistic effect. The compound demonstrated inhibitory effects on self-grooming behavior in transgenic mice, indicating that 5-HT7R may be a potential therapeutic target for treating stereotypical behaviors in autism spectrum disorder.
JOURNAL OF MEDICINAL CHEMISTRY
(2021)
Article
Cell & Tissue Engineering
Maria Rosaria Ambrosio, Teresa Migliaccio, Fabiana Napolitano, Sarah Di Somma, Giovanni Maneli, Jussara Amato, Bruno Pagano, Antonio Randazzo, Giuseppe Portella, Pietro Formisano, Anna Maria Malfitano
Summary: In this study, the role of G4 motifs in adipogenic differentiation was investigated using human adipose-derived mesenchymal stem cells (ASCs). The results showed that G4 structures were increased in differentiated adipocytes compared to their precursors, and treatment with the G4 ligand Braco-19 reduced G4 content in the mature adipocytes. Furthermore, Braco-19 caused morphological changes and reduced lipid droplet formation and key gene expression in the mature adipocytes. These findings reveal a new role of G4 motifs in human adipocyte differentiation.
STEM CELL RESEARCH & THERAPY
(2023)
Article
Biochemistry & Molecular Biology
Phillip Wulfridge, Qingqing Yan, Nathaniel Rell, John Doherty, Skye Jacobson, Sarah Offley, Sandra Deliard, Kelly Feng, Jennifer E. Phillips-Cremins, Alessandro Gardini, Kavitha Sarma
Summary: CTCF is a critical regulator of genome architecture and gene expression. This study shows that R-loops and G-quadruplex structures facilitate CTCF binding and regulate chromatin organization. The stability of R-loops and G-quadruplex structures can affect CTCF occupancy and gene expression.
Article
Medicine, Research & Experimental
Prativa Majee, Aryamav Pattnaik, Bikash R. Sahoo, Uma Shankar, Asit K. Pattnaik, Amit Kumar, Debasis Nayak
Summary: Research identified potential non-canonical G-quadruplex structures in the Zika virus genome, which can be targeted by ligands like Braco-19 and TMPyP4 to inhibit virus replication and protein production.
MOLECULAR THERAPY-NUCLEIC ACIDS
(2021)
Review
Chemistry, Medicinal
Tiago Santos, Gilmar F. Salgado, Eurico J. Cabrita, Carla Cruz
Summary: This article discusses the progress in the design of G-quadruplex binding ligands and the various methods available to assess the binding interactions. Different experimental approaches, such as structure-based, affinity-based, and high-throughput methods, each have their unique advantages and drawbacks. The combination of these techniques has led to the discovery of numerous G4 ligands for diagnostic and therapeutic purposes.
Review
Biochemistry & Molecular Biology
Swati Chaudhary, Mohan Kumar, Mahima Kaushik
Summary: G-quadruplexes play significant roles in various diseases and have been extensively studied. Further understanding of these structures and their stabilizing or destabilizing ligands can facilitate future drug discovery.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Review
Medicine, Research & Experimental
Parham Jabbarzadeh Kaboli, Masoomeh Afzalipour Khoshkbejari, Mahsa Mohammadi, Ardavan Abiri, Roya Mokhtarian, Reza Vazifemand, Shima Amanollahi, Shaghayegh Yazdi Sani, Mingxing Li, Yueshui Zhao, Xu Wu, Jing Shen, Chi Hin Cho, Zhangang Xiao
BIOMEDICINE & PHARMACOTHERAPY
(2020)
Review
Pharmacology & Pharmacy
Niloofar Rashidipour, Somayyeh Karami-Mohajeri, Ali Mandegary, Reza Mohammadinejad, Anselm Wong, Melika Mohit, Jafar Salehi, Milad Ashrafizadeh, Amir Najafi, Ardavan Abiri
Editorial Material
Medical Laboratory Technology
S. Jodeiryzaer, M. Farsimadan, A. Abiri, A. Sharafshah, H. Vaziri
BRITISH JOURNAL OF BIOMEDICAL SCIENCE
(2020)
Article
Medicine, Research & Experimental
Mohammad Hassan Moshafi, Saeid Ghasemshirazi, Ardavan Abiri
MEDICAL HYPOTHESES
(2020)
Review
Biochemistry & Molecular Biology
Mohsen Safaei, Gholam-Reza Mobini, Ardavan Abiri, Ali Shojaeian
MOLECULAR BIOLOGY REPORTS
(2020)
Article
Biochemistry & Molecular Biology
Mohammad Amin Langarizadeh, Ardavan Abiri, Saeid Ghasemshirazi, Nazanin Foroutan, Arash Khodadadi, Ehsan Faghih-Mirzaei
Summary: The study found that phlorotannins in marine natural products may have the potential to inhibit the spread of HIV virus, and these compounds have been confirmed as inhibitors of reverse transcriptase and HIV protease. This research paves the way for multifaceted action of marine natural products in combating HIV.
BIOTECHNOLOGY AND APPLIED BIOCHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Elham Mahdevar, Ashkan Safavi, Ardavan Abiri, Amirhosein Kefayat, Seyed Hossein Hejazi, Seyed Mohsen Miresmaeili, Vahid Iranpur Mobarakeh
Summary: A novel multi-epitope vaccine against breast cancer was designed using immunoinformatics approaches and computational methods, showing stability and immunogenicity with approximately 93% to 96% global population coverage for HLA-I and HLA-II. These preliminary results provide a suitable platform for further experimental investigations.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Chemistry, Physical
Mohammad Amin Langarizadeh, Khalil Eskandari, Ardavan Abiri, Marziye Ranjbar Tavakoli, Ali Asadipour, Yaghoub Pourshojaei
Summary: A series of one-pot, atom-economic, parallel three and five-component reactions have been investigated for the synthesis of acridine and bis(2-benzyl-5,5-dimethylcyclohexane-1,3-dione)-N-and 4-disubstituted naphthylamine derivatives under green conditions. The five-component route resulted in unprecedented bis(2-benzyl-5,5-dimethylcyclohexane-1,3-dione)-N-and 4-disubstituted naphthylamine derivatives. The synthesized compounds showed significant scores in in silico analyses, including molecular docking, molecular dynamics, and ADMET prediction tools. Acridine derivatives and N,4-disubstituted naphthylamines exhibited significant interactions with 5-HT2A/C and MAO-A/B, respectively.
JOURNAL OF MOLECULAR STRUCTURE
(2022)
Article
Multidisciplinary Sciences
Hasan Marashi, Maria Beihaghi, Masoud Chaboksavar, Samad Khaksar, Homan Tehrani, Ardavan Abiri
Summary: This study aimed to produce epitopes of CCL21 and IL1 beta as a recombinant protein and evaluate its in vitro anti-tumor and immunogenic activity. The results demonstrated that CCL21/IL1 beta could decrease the survival rate and metastasization of cancer cells, and it has biological activity as a potential effective adjuvant in future in vivo and clinical tests.
Review
Chemistry, Medicinal
Mohammad Amin Langarizadeh, Alieh Ameri, Marziye Ranjbar Tavakoli, Ardavan Abiri, Hamid Forootanfar
Summary: Studies have shown that the Trimethoxyphenyl (TMP) group exhibits diverse bioactivity effects, including anticancer, antibacterial, antiviral, antiparasitic, and anti-inflammatory properties. The TMP-bearing compounds hold potential as valuable agents across a wide range of biomedical applications.
MEDICINAL CHEMISTRY RESEARCH
(2023)
Review
Urology & Nephrology
Mohammadsadegh Hamzehnejadi, Marziye Ranjbar Tavakoli, Ardavan Abiri, Ali Ghasempour, Mohammad Amin Langarizadeh, Hamid Forootanfar
Summary: Phosphodiesterase inhibitors as topical therapy for erectile dysfunction show promise as effective alternative treatment with reduced side effects, interactions, and contraindications, potentially playing a role in mild to moderate cases.
SEXUAL MEDICINE REVIEWS
(2022)
Review
Pharmacology & Pharmacy
Ardavan Abiri, Marc Lavigne, Masoud Rezaei, Sanaz Nikzad, Peyman Zare, Jean-Louis Mergny, Hamid-Reza Rahimi
Summary: G-quadruplexes (G4s) are noncanonical nucleic acid structures that have gained increasing recognition in recent years, particularly in virology. G4 ligands are known to target viral transcription and replication, and both viral and cellular G4s may be potential targets for antiviral therapeutics. This review covers various aspects of G-quadruplexes in both host and viral contexts, highlighting the importance of studying G4s for future antiviral drug discovery.
PHARMACOLOGICAL REVIEWS
(2021)
Article
Immunology
Ashkan Safavi, Amirhosein Kefayat, Elham Mahdevar, Ardavan Abiri, Fatemeh Ghahremani
Review
Biology
Mohammad Amin Langarizadeh, Marziye Ranjbar Tavakoli, Ardavan Abiri, Ali Ghasempour, Masoud Rezaei, Alieh Ameri
Summary: The emergence of the novel coronavirus sparked numerous clinical trials globally in search of effective drugs and treatment protocols; Corticosteroids can suppress inflammation during COVID-19 infection, but also come with a range of side effects; Certain corticosteroids like methylprednisolone and dexamethasone have shown significant efficacy, particularly for COVID-19 patients on mechanical ventilation.
Article
Biochemical Research Methods
Saranya Krishnan, Shina Sasi, Preshobha Kodakkattumannil, Salima Al Senaani, Geetha Lekshmi, Martin Kottackal, Khaled M. A. Amiri
Summary: This study aimed to develop an efficient DNA extraction protocol suitable for diverse plant species and tissues. A reliable and consistent protocol was described for the extraction of high-quality DNA from difficult-to-extract plant species. The optimized protocol was successful in extracting high-quality DNA from various plant species and tissues, making it useful for genomic studies of recalcitrant plants.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Eisaku Hokazono, Saori Fukumoto, Takeshi Uchiumi, Susumu Osawa
Summary: This study proposes a method for detecting nucleic acid amplification using pyrophosphate, which requires only two reagents and an automated analyzer. The technique has high sensitivity and reproducibility, and can detect pyrophosphate within 10 minutes. Therefore, this method has the potential to be a new, rapid, and simple detection technique for amplified nucleic acids.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Drew S. Sowersby, L. Kevin Lewis
Summary: SURE electrophoresis is a new method for concentrating samples in gels, which allows efficient detection of highly dilute DNA samples. This approach generates single bands with enhanced signal intensities and minimal band broadening.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Hongyi Liang, Guoliang Yin, Guangxi Shi, Zhiyong Liu, Xiaofei Liu, Jingwei Li
Summary: The mechanism of Echinacoside (ECH) in treating breast cancer (BC) was explored through network pharmacology and experimental validation. It was found that ECH plays an important role in anti-BC by regulating the PI3K/AKT/HIF-1 alpha/VEGF signaling pathway, and it exhibits multi-target and multi-pathway effects.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Daniel S. Kantner, Emily Megill, Anna Bostwick, Vicky Yang, Carmen Bekeova, Alexandria Van Scoyk, Erin L. Seifert, Michael W. Deininger, Nathaniel W. Snyder
Summary: This study compared the results of different methods for measuring the amount of acetyl-Coenzyme A. The colorimetric ELISA kit did not produce interpretable results, while the fluorometric enzymatic kit showed comparable results to the LC-MS-based methods depending on the matrix and extraction conditions. LC-MS/MS and LC-HRMS methods produced well-aligned results, especially when using stable isotope-labeled internal standards.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Jingyan Xu, Hanying Tan, Xionghui Ma, Linjing Su, Zhi Zhang, Yuhao Xiong
Summary: This study investigates the co-catalytic capabilities of MoO3 nanosheets in enhancing the enzyme-like catalytic activity of a two-dimensional ultrathin Fe(III)-modified covalent triazine framework (Fe-CTF) under neutral pH conditions. The Fe-CTF/MoO3 co-catalytic system exhibits enzyme-mimicking activity and enables the development of a colorimetric method for glucose detection. Furthermore, a straightforward one-pot colorimetric method is established for screening XOD inhibitors.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Lichao Zhang, Kang Xiao, Xueting Wang, Liang Kong
Summary: A novel fusion technology was designed to identify FAD-binding sites, achieving the best results on two independent test datasets and outperforming existing methods significantly. The high performance and certainty of the method were demonstrated through statistical tests and cross-entropy loss analysis.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Abdulkadir Kilic, Mehmet Aslan, Abdulkadir Levent
Summary: This study developed a simple, rapid, sensitive, and selective voltammetric technique for the electrochemical characterization and detection of the highly risky drug Edoxaban. The optimized voltammetric method showed good analytical working range and was successfully applied to urine and tablet samples.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Su Hyun Kim, Nara Shin, Jong-Min Jeon, Jeong-Jun Yoon, Jeong Chan Joo, Hee Taek Kim, Shashi Kant Bhatia, Yung-Hun Yang
Summary: To address environmental issues caused by traditional plastics, bioplastics have gained attention as alternatives. Although bioplastics have better degradability, their degradation still takes longer than anticipated. This study proposes a novel screening method to identify bioplastic degraders faster, saving time and providing more quantitative data.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Irem Okman Kocoglu, Pinar Esra Erden, Esma Kilic
Summary: In this study, an electrochemical biosensor based on carbon nanofibers and ionic liquid modification was constructed for tyramine detection. The biosensor showed linear response, low detection limit, high sensitivity, and exhibited good reproducibility, stability, and anti-interference ability.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Liana U. Akhmetzianova, Timur M. Davletkulov, Assol R. Sakhabutdinova, Alexey Chemeris, Irek M. Gubaydullin, Ravil R. Garafutdinov
Summary: A new program called LAMPrimers iQ has been developed for high-quality LAMP primer design, and its advantages in providing higher specificity and reliable detection of viral RNA were validated using SARS-CoV-2 coronavirus RNA as a model target.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Tommaso Pileri, Alberto Sinibaldi, Agostino Occhicone, Norbert Danz, Elena Giordani, Matteo Allegretti, Frank Sonntag, Peter Munzert, Patrizio Giacomini, Francesco Michelotti
Summary: This study developed a biosensing device based on one-dimensional photonic crystal to detect HER2 in breast cancer. The device combines label-free and fluorescence operation modes, allowing for real-time and accurate detection in less than 20 minutes. It offers a promising technique for combined label-free and fluorescence detection in disease diagnosis and therapeutic monitoring.
ANALYTICAL BIOCHEMISTRY
(2024)
