Article
Biochemistry & Molecular Biology
Gizem Tatar, Tugba Taskin Tok, Bulent Ozpolat, A. Y. Mehmet
Summary: Protein kinases are successful drug targets, and eEF-2K has been identified as a potential therapeutic target for certain aggressive solid cancers. This study used modeling, docking analysis, and molecular dynamics simulations to understand the binding mechanism of eEF-2K with inhibitors, providing insights for the development of new selective and potential eEF-2K inhibitors.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Environmental Sciences
Wei-hao Yao, Ling-yun Mo, Liu-sen Fang, Li-tang Qin
Summary: A large number of antibiotics have been extensively used in various industries in recent years, which may lead to pollution in the aquatic environment and pose a threat to human health. This study aims to investigate the toxicity mechanism of five antibiotics on luciferase. Through a combination of toxicity testing, molecular docking, molecular dynamics, and binding free energy analysis, the researchers found that the toxicity and binding energy of the antibiotics were correlated. The shape compensation and specific interactions between the antibiotics and luciferase were identified as important factors in their toxicity. This research provides insights into the toxicity mechanisms of antibiotics and contributes to the risk assessment of antibiotic contaminants in the aquatic environment.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2023)
Article
Biochemistry & Molecular Biology
Syarifuddin Husain, Ruzianisra Mohamed, Khairul Bariyyah Abd Halim, Siti Syairah Mohd Mutalip
Summary: In this study, a computational approach was used to identify the protein model of BAP1 and its potential inhibitors. The study revealed the molecular mechanism by which BAP1 regulates cancer and its crystal structure. Docking and simulating experiments showed that rearrangement of specific residues and conformational switching of BAP1 occurred upon binding to ubiquitin. Screening results shortlisted two potential BAP1 inhibitors, and molecular dynamics simulations further confirmed the stability of the BAP1-FDA755 complex.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
Avinash Kumar, Vinay Kumar Singh, Arvind M. Kayastha
Summary: This study determined the three-dimensional structure of fenugreek α-amylase using homology modeling and analyzed its molecular basis and mode of action through molecular dynamics simulations and molecular docking. The study identified functional groupings and binding interactions between the enzyme and its substrate maltose. The research provides valuable insights into the atomic-level molecular underpinnings of α-amylase interaction with maltose.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biotechnology & Applied Microbiology
Xiaoli Qin, Jinfeng Zhong, Yonghua Wang
Summary: This study investigated the interactions between Mut-T1 lipase and various fatty acids through molecular docking and molecular dynamics simulation. The results showed that Mut-T1 lipase had lower binding affinity for shorter-chain caprylic acid, but the complex remained stable during simulation, with decreasing solvent accessible surface area as the chain length of the fatty acid increased.
JOURNAL OF BIOTECHNOLOGY
(2021)
Article
Biochemical Research Methods
Sakshi Singh, Geeta Rai
Summary: This study presents a computational method that successfully designs the structure of IL12R and reveals its tight binding with IL12 ligand. The simulated molecular structure of IL12:IL12R complex provides a promising target complex for future IL12-based drug design.
COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING
(2022)
Article
Biochemistry & Molecular Biology
Satya Narayan Sahu, Sneha Shriparna Satpathy, Chandana Mohanty, Subrat Kumar Pattanayak
Summary: The function of a protein is closely related to its structural properties, and mutations can impact protein functionality. Boerhavia diffusa contains various bioactive compounds, with Boeravinone J showing the best binding affinity to CDKAP1.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biochemistry & Molecular Biology
Sunita Kumari Yadav, Deepak Panwar, Ankita Singh, Meenakshi B. Tellis, Rakesh Shamsunder Joshi, Aparna Dixit
Summary: Aeromonas hydrophila, a Gram-negative bacterium, causes diseases in fish leading to significant losses in the aquaculture industry. The variability in virulence factors and toxins among different Aeromonas strains contributes to the heterogeneity of this bacteria genus. Through phylogenetic analysis and homology modeling, the aerolysin of Ah(EUS112) is identified as a channel protein and a potential drug target. Validation of the model using bioinformatics tools confirms its high quality, and specific drugs show higher affinity for binding to aerolysin and potentially inhibiting pore formation.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biochemistry & Molecular Biology
Yuying Yuan, Mst Nushrat Yiasmin, Nerissa Arviana Tristanto, Yujie Chen, Yaxian Liu, Shuyi Guan, Zijie Wang, Xiao Hua
Summary: The taste mechanism of steviol glycoside (SG) was investigated through molecular docking simulations and molecular dynamics simulations. The results showed that the sweetness intensity of SG can be attributed to its durative concurrent interaction with the receptor's binding site, while the bitterness is determined by the size and structure of the molecule.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2024)
Article
Biochemistry & Molecular Biology
Vishwanath Yadav, Jebin Ahmed, Abhijeet Thakur, Poorvi Vishwakarma, Shubha Singh, Punit Kaur, Arun Goyal
Summary: Structural and conformational insights of a putative beta-1,4-xylosidase (PsGH43F) of glycoside hydrolase family 43 from Pseudopedobacter saltans were investigated. The results revealed the presence of three conserved catalytic amino acid residues and the maximum binding affinity of PsGH43F with xylobiose. These findings are important for understanding the function and mechanism of PsGH43F.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Construction & Building Technology
Aslam Kunhi Mohamed, Stefanie Anne Weckwerth, Ratan K. Mishra, Hendrik Heinz, Robert J. Flatt
Summary: This paper reviews methods of molecular simulation of chemical admixtures, focusing on adsorption behavior and conformations, in order to identify opportunities, challenges, and prospects for future development.
CEMENT AND CONCRETE RESEARCH
(2022)
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
Biochemistry & Molecular Biology
Syed Umair Ahmad, Yasir Ali, Zainab Jan, Salman Rasheed, Noor Ul Ain Nazir, Asif Khan, Shah Rukh Abbas, Abdul Wadood, Ashfaq Ur Rehman
Summary: In this study, computational analysis was performed on the p14ARF protein to identify potential deleterious nsSNPs and evaluate their impact on protein structure, function, and stability. The study discovered four deleterious nsSNPs that significantly affected protein stability and function, potentially leading to the development of various types of cancers.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
Mohsen Sargolzaei, Hossein Nikoofard
Summary: In this study, we designed a suitable ester prodrug of omapatrilat for CNS diseases by considering its ability to penetrate the blood-brain barrier. The most potent stereoisomers against brain carboxylesterase were determined through molecular docking and homology modeling. Molecular dynamics simulation and structural analysis were performed to confirm the suitability of the prodrug structure for crossing the blood-brain barrier and binding to brain carboxylesterase. Additionally, the QM/MM calculation revealed the catalytic reaction mechanism of the prodrug against brain carboxylesterase.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
Rasha Z. Batran, Kuljeet S. Gugnani, Timothy J. Maher, Mohammed A. Khedr
Summary: Through the development of new neuropeptide S receptor antagonists, a series of potential therapeutic derivatives have been identified. By modulating Ca2+ and cAMP signaling, these compounds counteract the stimulatory effects of NPS at both Gq and Gs pathways, showing potential therapeutic effects against anxiety, addiction, and food disorders. Molecular docking and dynamic simulations confirm the stability and efficacy of the top active compounds, suggesting their potential as treatment options.
BIOORGANIC CHEMISTRY
(2021)
Article
Agriculture, Dairy & Animal Science
Latika Jaiswal, Sachinandan De, Ravi Kant Singh, Rubina Kumari Baithalu
ANIMAL BIOTECHNOLOGY
(2020)
Article
Biochemistry & Molecular Biology
Dhanawantari L. Singha, Jitendra Maharana, Debashis Panda, Budheswar Dehury, Mahendra Kumar Modi, Salvinder Singh
Summary: eIF4A1 shows significantly increased expression in rice under temperature stress, and stronger ATP/Mg2+ binding at higher temperatures, suggesting its heat stress-tolerant capacity in rice.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2021)
Article
Biochemistry & Molecular Biology
Ashutosh Vats, Devika Gautam, Jitendra Maharana, Jatinder Singh Chera, Sushil Kumar, Pramod K. Rout, Dirk Werling, Sachinandan De
MOLECULAR IMMUNOLOGY
(2020)
Article
Chemistry, Physical
Subhraseema Das, Subhrajit Mohanty, Jitendra Maharana, Soumya R. Jena, Jasmine Nayak, Usharani Subuddhi
JOURNAL OF MOLECULAR LIQUIDS
(2020)
Article
Chemistry, Multidisciplinary
Wei-Chieh Cheng, Ting-Yun You, Zhen-Zhuo Teo, Ashik A. Sayyad, Jitendra Maharana, Chih-Wei Guo, Pi-Hui Liang, Chung-Shun Lin, Fan-Chun Meng
CHEMISTRY-AN ASIAN JOURNAL
(2020)
Article
Plant Sciences
Johni Debbarma, Banashree Saikia, Dhanawantari L. Singha, Jitendra Maharana, Natarajan Velmuruagan, Hariprasanna Dekaboruah, Kallare P. Arunkumar, Channakeshavaiah Chikkaputtaiah
Summary: The study identified Xylem sap protein 10 (XSP10) and Salicylic acid methyl transferase (SlSAMT) as potential negative regulatory genes associated with Fusarium wilt of tomato. The expression analysis showed higher expression of XSP10 and SlSAMT in root and flower tissue of different tomato cultivars, with stronger up-regulation in a susceptible cultivar compared to a multiple disease resistant cultivar, indicating the disease susceptibility nature of these genes. Sub-cellular localization analysis revealed that XSP10 mainly localized in the nucleus and SlSAMT in the cytoplasm, and a strong in vivo protein-protein interaction between XSP10 and SlSAMT in regulating responses to Fusarium wilt tolerance in tomato.
PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS
(2021)
Article
Genetics & Heredity
Riwandahun Marwein, Sanjay Singh, Jitendra Maharana, Sanjeev Kumar, Kallare P. Arunkumar, Natarajan Velmurugan, Channakeshavaiah Chikkaputtaiah
Summary: The study identified different levels of resistance in North-East Indian rice cultivars to Bipolaris oryzae, and revealed the importance of early response to the pathogen in suppressing disease progression through systematic RNA seq analysis. The findings provide key regulatory genes for potential functional genetic analysis to develop genetic tolerance to BSD of rice.
Article
Chemistry, Physical
Jitendra Maharana, Diptimayee Maharana, Aritra Bej, Bikash R. Sahoo, Debashis Panda, Sachin B. Wadavrao, Ashutosh Vats, Sukanta K. Pradhan, Sachinandan De
Summary: The study demonstrates the association of NOD2-CARDs with RIP2(CARD) through modeling and molecular dynamics simulations, highlighting the importance of different structural interfaces of NOD2 in CARD-CARD interaction.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Review
Plant Sciences
Dhanawantari L. Singha, Debajit Das, Yogita N. Sarki, Naimisha Chowdhury, Monica Sharma, Jitendra Maharana, Channakeshavaiah Chikkaputtaiah
Summary: Tissue-specific CRISPR/Cas genome editing is a promising approach for crop improvement, bypassing the issues associated with constitutive genome editing and allowing targeted improvement of crops.
Article
Biochemistry & Molecular Biology
Nasir Javaid, Mahesh Chandra Patra, Da-Eun Cho, Maria Batool, Yoongeun Kim, Gwang Muk Choi, Moon Suk Kim, Dae-Hyun Hahm, Sangdun Choi
Summary: A TNF-inhibitory molecule has been discovered that effectively reduces TNF signaling and shows promising results in treating autoimmune diseases such as rheumatoid arthritis. The molecule acts by inhibiting TNF-induced apoptosis and disrupting TNF homotrimerization, thus preventing its association with the TNF receptor.
Article
Chemistry, Multidisciplinary
Jyoti Kode, Jitendra Maharana, Asif Amin Dar, Shayanti Mukherjee, Nikhil Gadewal, Dilep Kumar Sigalapalli, Satyanshu Kumar, Debashis Panda, Soumyajit Ghosh, Supriya Suman Keshry, Prabhudutta Mamidi, Soma Chattopadhyay, Trupti Pradhan, Vaishali Kailaje, Sunil Inamdar, Vidula Gujjarwar
Summary: Recent global health concern has led to the investigation of natural medicinal plant resources as alternative treatments for COVID-19 infection and inflammation. In this study, a phytochemical called 6-shogaol was explored as a potential anti-inflammatory and anti-COVID-19 agent. 6-shogaol was found to efficiently inhibit SARS-CoV2 replication and regulate the expression of inflammasome pathway molecules. Compared to existing drugs, 6-shogaol demonstrated similar efficacy and better safety in terms of physicochemical properties and clinical toxicity. This study provides important insights for the further development of 6-shogaol as a potential therapeutic agent against inflammation and viral infections.
Article
Agriculture, Dairy & Animal Science
Rupali Khan, Sachinandan De, Rahul Dewangan, Rajendra Tamboli, Reeshu Gupta
Summary: This study aimed to determine the polymorphism in the 7th exon of the beta-casein gene (CSN2) in different domestic and exotic cattle breeds. The results showed that the A1A1 genotype was absent in all domestic breeds, and the A2A2 genotype was highest in the Gir breed. The study also found that the Gir, Sahiwal, Tharparkar, and Motu breeds have a high potential for A2 milk production.
ANIMAL BIOTECHNOLOGY
(2023)
Article
Microbiology
Ila Singh, Mayank Roshan, Ashutosh Vats, Manisha Behera, Devika Gautam, Shiveeli Rajput, Chanchal Rana, Sachinandan De
Summary: This study investigated the virulence factors, antibiotic resistance profile, and biofilm production potential of 46 MRSA isolates from 300 bovine mastitis milk samples. The results showed a high level of resistance among MRSA isolates, with 46 and 42 isolates resistant to cefoxitin and oxacillin, respectively. The study also identified various virulence factors and antibiotic resistance determinants in the MRSA isolates. Microtiter plate assay revealed that 29 MRSA isolates were capable of producing biofilms.
CURRENT MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Shiveeli Rajput, Devika Gautam, Ashutosh Vats, Chanchal Rana, Manisha Behera, Mayank Roshan, Ashutosh Ludri, Sachinandan De
Summary: AQPs are membrane proteins that transport water across cellular membranes, while AQGPs are a subfamily that transport small solutes. They play roles in various physiological processes in mammals. However, the conservation patterns, phylogenetic relationships, and evolution of AQPs in mammals remain unexplored.
JOURNAL OF MOLECULAR EVOLUTION
(2023)
Article
Genetics & Heredity
Johni Debbarma, Banashree Saikia, Dhanawantari L. L. Singha, Debajit Das, Ajay Kumar Keot, Jitendra Maharana, Natarajan Velmurugan, Kallare P. P. Arunkumar, Palakolanu Sudhakar Reddy, Channakeshavaiah Chikkaputtaiah
Summary: Fusarium wilt is a devastating fungal disease in tomato caused by Fusarium oxysporum f. sp. lycopersici, leading to reduced yield and production. Xylem sap protein 10 (XSP10) and Salicylic acid methyl transferase (SlSAMT) are two negative regulatory genes associated with Fusarium wilt in tomato. CRISPR/Cas9 has emerged as a promising technique to target these susceptible genes and increase tolerance/resistance to plant diseases. In this study, the efficiency of CRISPR/Cas9-mediated editing of XSP10 and SlSAMT genes was validated in tomato, and dual-gene editing showed stronger tolerance to Fusarium wilt than single-gene editing. Stable transformation of tomato further confirmed that dual-gene CRISPR-edited lines exhibited higher tolerance to Fusarium wilt compared to single-gene-edited lines.