Article
Biochemistry & Molecular Biology
Arnold Amusengeri, Asifullah Khan, Oezlem Tastan Bishop
Summary: In this study, the researchers investigated the structural basis and mechanisms of resistance mutations in the DNA-directed RNA polymerase (rpoB) that cause resistance to the anti-tuberculosis drug rifampicin (RIF). Through a combination of molecular docking analysis and molecular dynamics simulations, they identified six mutations that adversely affected RIF binding. These mutations were found to cause conformational changes in rpoB and perturb RIF binding. The researchers believe that this approach can be applied to study other similar cases of drug resistance.
Article
Biochemistry & Molecular Biology
B. S. Ravindranath, S. Vishnu Vinayak, Vivek Chandra Mohan
Summary: Chlamydia felis is a major cause of chronic conjunctivitis in cats without respiratory infections, with zoonotic potential. The emergence of antimicrobial resistance to antibiotics targeting rRNA has complicated the diagnosis and treatment of chlamydial infections, posing challenges for research in this field.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Immunology
Bertin C. Bisimwa, Jean B. Nachega, Robin M. Warren, Grant Theron, John Z. Metcalfe, Maunank Shah, Andreas H. Diacon, Nadia A. Sam-Agudu, Marcel Yotebieng, Andre N. H. Bulabula, Patrick D. M. C. Katoto, Jean-Paul Chirambiza, Rosette Nyota, Freddy M. Birembano, Eric M. Musafiri, Sifa Byadunia, Esto Bahizire, Michel K. Kaswa, Steven Callens, Zacharie M. Kashongwe
Summary: In a study conducted in eastern Democratic Republic of the Congo, it was found that Xpert had a high sensitivity for detecting RIF resistance but a low positive-predictive value for MDR-TB. Comprehensive resistance testing for both INH and RIF should be performed in this setting.
CLINICAL INFECTIOUS DISEASES
(2021)
Article
Multidisciplinary Sciences
Anwar Sheed Khan, Jody E. Phelan, Muhammad Tahir Khan, Sajid Ali, Muhammad Qasim, Gary Napier, Susana Campino, Sajjad Ahmad, Otavio Marques Cabral, Shulin Zhang, Hazir Rahman, Dong-Qing Wei, Taane G. Clark, Taj Ali Khan
Summary: This study conducted genetic analysis on isolates from a high TB endemic province in Pakistan, identifying mutations associated with multidrug-resistant TB. Additionally, internal resistance diversity and heteroresistance were observed, suggesting a complexity that may be linked to high transmission dynamics.
SCIENTIFIC REPORTS
(2021)
Review
Pharmacology & Pharmacy
Gozde Yalcin-Ozkat
Summary: Cancer remains a leading cause of morbidity and mortality worldwide. Efforts to develop anticancer drugs focus on addressing multidrug resistance, with intensive studies using molecular modeling methods to identify new therapeutic molecules. While progress has been made in experimental studies on specific inhibitors for MDR efflux pumps, computational approaches have the potential to accelerate drug development processes.
DRUG RESISTANCE UPDATES
(2021)
Article
Biochemistry & Molecular Biology
Xi Gu, Ying Wang, Hanxun Wang, Hairui Wu, Wei Li, Jian Wang, Ning Li
Summary: This study utilized computational methods to build the structure of ETAR and predict its binding patterns with antagonists, identifying potential ETAR antagonists. Through virtual screening of a Traditional Chinese Medicine database, six compounds with the best binding energies were screened out, providing new therapeutic approaches for treating PAH.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2021)
Article
Genetics & Heredity
Linus Augustin, Nisheeth Agarwal
Summary: We developed a Cas9/gRNA-assisted quantitative Real-Time PCR (CARP) assay to detect drug-resistant mutations in Mycobacterium tuberculosis (Mtb). The CARP assay showed high sensitivity and 100% specificity in recognizing single nucleotide changes associated with drug resistance. This low-cost and rapid diagnostic test holds great promise in the diagnosis and prognosis of tuberculosis patients.
Article
Microbiology
Borys Dolya, Olena Hryhorieva, Khrystyna Sorochynska, Maria Lopatniuk, Iryna Ostash, Vasylyna-Marta Tseduliak, Eva Baggesgaard Sterndorff, Tue Sparholt Jorgensen, Tetiana Gren, Yuriy Dacyuk, Tilmann Weber, Andriy Luzhetskyy, Victor Fedorenko, Bohdan Ostash
Summary: Mutations in the rpoB gene of Streptomyces albidoflavus J1074 have been found to increase its rifampicin resistance and enhance its ability to produce specialized metabolites. Through the isolation and analysis of 14 different rpoB mutants, the study showed that these mutations have a significant impact on the antibiotic production of J1074.
Article
Biochemistry & Molecular Biology
Dian Ayu Eka Pitaloka, Arfan Arfan, Dwi Syah Fitra Ramadhan, Lidya Chaidir
Summary: This study aims to evaluate the impact of mutations found in pyrazinamide monoresistant strains of Mycobacterium tuberculosis on the effectiveness of pyrazinamide for tuberculosis treatment. Five mutations of pyrazinamidase were analyzed, and the results showed that three of these mutations affected the enzyme's activity and led to PZA resistance. However, the other two mutations had no effect. Experimental clarification is needed for further studies on drug resistance in pyrazinamidase.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Infectious Diseases
Jiahui Huang, Feng Zhang, Jumei Zhang, Jingsha Dai, Dongli Rong, Miao Zhao, Juan Wang, Yu Ding, Moutong Chen, Liang Xue, Qihui Gu, Shi Wu, Qingping Wu
Summary: The study revealed the molecular characteristics of rifampin-resistant Staphylococcus aureus in retail food samples in China from 2011 to 2016. The majority of isolates were resistant to multiple antibiotics, with mutations in the rpoB gene contributing to rifampin resistance. Different genetic backgrounds were observed among the strains, highlighting the concerning presence of MRSA in retail food.
Article
Oncology
Haiming Zhuang, Jigang Fan, Mingyu Li, Hao Zhang, Xiuyan Yang, Ligen Lin, Shaoyong Lu, Qing Wang, Yaqin Liu
Summary: The Y96D mutation in KRAS(G12C) causes resistance to the drug AMG510 by impairing the direct interaction between the drug and residue 96, resulting in the opening and loosening of the drug binding pocket.
FRONTIERS IN ONCOLOGY
(2022)
Article
Immunology
Yunfeng Deng, Zichun Ma, Biyi Su, Guanghong Bai, Jianhua Pan, Quan Wang, Long Cai, Yanhua Song, Yuanyuan Shang, Pinyun Ma, Jing Li, Qianxuan Zhou, Gulibike Mulati, Dapeng Fan, Shanshan Li, Yaoju Tan, Yu Pang
Summary: This study developed InnowaveDX MTB/RIF for simultaneous detection of Mycobacterium tuberculosis and rifampicin resistance. InnowaveDX showed a sensitivity of 92.7% for TB detection and 86.4% for rifampicin resistance. Discordant rifampicin susceptibility results between InnowaveDX and Xpert were more frequently observed in samples with very low bacterial load.
EMERGING MICROBES & INFECTIONS
(2023)
Article
Immunology
Pengjiao Ma, Tao Luo, Liang Ge, Zonghai Chen, Xinyan Wang, Rongchuan Zhao, Wei Liao, Lang Bao
Summary: Several rpoB non-RRDR mutations serve as molecular markers for predicting the fitness of clinical rifampin-resistant M. tuberculosis strains. These mutations can enhance the relative fitness of resistant strains and alleviate the decreased RNAP transcription efficiency.
EMERGING MICROBES & INFECTIONS
(2021)
Article
Physics, Fluids & Plasmas
Luana S. Moreira, Douglas D. de Vargas, Mateus H. Kohler
Summary: The introduction of flexibility in water force fields during molecular dynamics simulations of nanoconfined water has a significant impact on viscosity, diffusion, and dipole orientation. The level of confinement and the choice of force-field family greatly influence the behavior of water molecules in nanoconfined systems.
Article
Physics, Fluids & Plasmas
Luana S. Moreira, Douglas D. de Vargas, Mateus H. Koehler
Summary: This study investigates the effects of introducing flexibility in water force fields on molecular dynamics simulations of nanoconfined water. The results show that viscosity, diffusion, and dipole orientation are greatly influenced by the flexibility and the family of force fields used.
Article
Biochemistry & Molecular Biology
K. Rohini, Pratika Agarwal, B. Preethi, V. Shanthi, K. Ramanathan
APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY
(2019)
Article
Chemistry, Multidisciplinary
Nivya James, V Shanthi, K. Ramanathan
JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY
(2019)
Article
Chemistry, Multidisciplinary
K. Rohini, Roosha Roy, K. Ramanathan, V Shanthi
JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY
(2019)
Article
Chemistry, Medicinal
K. Ramanathan, Sayoni Maiti, V Shanthi, Woong-Hee Shin, Daisuke Kihara
MEDICINAL CHEMISTRY RESEARCH
(2019)
Article
Biochemistry & Molecular Biology
K. Rohini, K. Ramanathan, V. Shanthi
CELL BIOCHEMISTRY AND BIOPHYSICS
(2019)
Article
Biochemistry & Molecular Biology
Nivya James, V. Shanthi, K. Ramanathan
APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY
(2020)
Article
Oncology
Ramanathan Karuppasamy, Shanthi Veerappapillai, Sayoni Maiti, Woong-Hee Shin, Daisuke Kihara
Summary: Non-small cell lung cancer is a leading cause of cancer-related mortality globally, with substandard cure and survival rates, particularly in metastatic diseases. Extended research is needed to establish upcoming generation cancer therapeutics.
SEMINARS IN CANCER BIOLOGY
(2021)
Article
Education, Scientific Disciplines
Anika Jain, Nivya James, Veerapapillai Shanthi, Karuppasamy Ramanathan
INDIAN JOURNAL OF PHARMACEUTICAL EDUCATION AND RESEARCH
(2020)
Article
Chemistry, Multidisciplinary
S. Saranyadevi, V Shanthi
JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY
(2020)
Article
Chemistry, Applied
S. Saranyadevi, K. Ramanathan, V Shanthi
Summary: The study performed in-silico screening of 1574 natural compounds and identified Mucronulatol and 7,4'-dihydroxyhomoisoflavanone as potential lead molecules. These compounds showed cytotoxicity against lung cancer cell lines with IC50 values of 6.74 μM and 8.99 μM.
NATURAL PRODUCT RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Saranyadevi Subburaj, Tanvi Anand Nagrale, Mohd. Mustufa Khan, Nivya James, Ramanathan Karuppasamy, Shanthi Veerappapillai
Summary: This study examined 1,574 compounds to identify potent and nontoxic ALK inhibitors, generating two pharmacophore hypotheses and conducting molecular docking and dynamics studies to confirm their anticancer activity. The results demonstrated that two hits showed better docking scores, binding energies, and drug-likeness properties compared to the reference compound.
BIOTECHNOLOGY AND APPLIED BIOCHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Muthu T. Kumar, K. Rohini, Nivya James, V Shanthi, K. Ramanathan
Summary: Through drug-repurposing study and machine learning-based algorithms, two potential inhibitors were identified in this research. These inhibitors are predicted to bind better with the main protease of Covid-19.
BIOTECHNOLOGY AND APPLIED BIOCHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Nivya James, V. Shanthi, K. Ramanathan
APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY
(2018)
Article
Biochemistry & Molecular Biology
J. Nisha, V. Shanthi
CELL BIOCHEMISTRY AND BIOPHYSICS
(2018)
Review
Medicine, General & Internal
Priyanka Ramesh, Ramanathan Karuppasamy, Shanthi Veerappapillai
BIOMEDICINE-TAIWAN
(2020)