Article
Biochemistry & Molecular Biology
Abbas Khan, Hira Waris, Memoona Rafique, Muhammad Suleman, Anwar Mohammad, Syed Shujait Ali, Taimoor Khan, Yasir Waheed, Chenguang Liao, Dong-Qing Wei
Summary: This study provides a basis for understanding the impact of novel mutations on the structure, function, and binding of the new SARS-CoV-2 variants, and serves as a strong impetus for the development of novel drugs against them.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Chemistry, Applied
Alexey A. Kostyukov, Mikhail G. Mestergazi, Anton E. Egorov, Anna M. Shmykova, Anna Shibaeva, Alina A. Markova, Tatyana A. Podrugina, Vladimir I. Pogonin, Eugene Radchenko, Vladimir A. Palyulin, Alexander A. Shtil, Tatiana D. Nekipelova, Iouri E. Borissevitch, Vladimir A. Kuzmin
Summary: This study investigated the photophysical characteristics of a new bis-carbocyanine dye (BCD) and its interaction with human serum albumin (HSA) and DNA. The binding constants of BCD to HSA and DNA were determined, and the fluorescence quantum yield of BCD increased 10-fold after binding to HSA.
Article
Plant Sciences
Xiang Zhou, Zheng Wang, Guangchao Cui, Zimeng Du, Yunlong Qian, Shumei Yang, Minghui Liu, Jixing Guo
Summary: In this study, the cDNA sequence of TrufOBP4 from T. rufivena is cloned and analyzed. The results show that TrufOBP4 has high binding abilities with the host plant volatiles and may play a crucial role in the integrated management of T. rufivena.
Article
Biochemistry & Molecular Biology
Lin-Li Li, Bing-Qiang Xu, Chun-Qin Li, Bo-Liao Li, Kun Luo, Guang-Wei Li, Xiu-Lin Chen
Summary: This study identified four pheromone-binding proteins (PBPs) in Grapholita funebrana, determined their preferred ligands, and investigated the molecular forces maintaining the PBP-pheromone complexes. The results showed high expression of these PBPs in the antennae, with different preferences for different pheromones. Hydrophobic forces, including van der Waals forces and hydrogen bonds, were found to play a crucial role in maintaining the PBP-pheromone complexes. This study enhances our understanding of the sex pheromone recognition mechanisms in G. funebrana and will facilitate the development of novel control strategies.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Chemistry, Physical
Meiru Song, Wei Fu, Yichang Liu, Huiqiao Yao, Ke Zheng, Lin Liu, Jinping Xue, Peng Xu, Yayu Chen, Mingdong Huang, Jinyu Li
Summary: This study systematically investigated the molecular interactions of DOX with HSA at different pH levels, revealing significant effects of environmental pH on their binding. Insights gained from this study may contribute to the design of novel HSA-based microenvironment-responsive drug delivery systems for anticancer therapeutic applications.
JOURNAL OF MOLECULAR LIQUIDS
(2021)
Article
Biochemistry & Molecular Biology
Yingqi Qiu, Yuanmeng Wang, Jiahao Lu, Qinghua Zhu, Li Jia, Fuhou Lei, Liqun Shen, Lihe Jiang, Aiqun Wu
Summary: This study involved the chemical modification of curcumin to obtain tetrahydrocurcumin and demonstrated its enhanced physiological and antioxidant activities compared to curcumin. The computational pharmacology techniques provided a theoretical basis for the development and modification of high-efficiency, low-toxicity drugs that interact with various targets of curcumin in the future.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
Sharat Sarmah, Somdev Pahari, Sourav Das, Vinay Kumar Belwal, Madhurima Jana, Atanu Singha Roy
Summary: The non-enzymatic glycation of plasma proteins significantly reduces the binding affinity of HSA towards chrysin, while the % alpha-helicity of HSA is enhanced upon binding with chrysin. Chrysin mainly binds to subdomain IIA and IIIA of both HSA and gHSA in the interaction study.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2021)
Article
Chemistry, Physical
Imtiyaz Ahmad Bhat, Tasneem Kausar, Aijaz Ahmad Dar, Shahid M. Nayeem, Mohd Akram, Kabir-ud-Din
Summary: This research investigates the interaction between two asymmetric zwitterionic geminis and lysozyme, finding that the n(-)-2-(+)m complex binds more significantly to HEWL than 8(-)-2-(+)16. Fluorescence and CD spectroscopy reveal conformational changes in HEWL upon surfactant addition. Molecular docking identifies the binding sites of the geminis with HEWL, and molecular simulation indicates the formation of stable protein-surfactant complexes.
JOURNAL OF MOLECULAR LIQUIDS
(2021)
Article
Pharmacology & Pharmacy
Yuwei Wang, Yifan Guo, Shaojia Qiang, Ruyi Jin, Zhi Li, Yuping Tang, Elaine Lai Han Leung, Hui Guo, Xiaojun Yao
Summary: In this study, the structure-activity relationships and binding modes of a series of anthraquinone derivatives targeting PGAM1 were investigated using 3D-QSAR, molecular docking, and molecular dynamics simulations, which showed satisfactory predictive ability. Molecular dynamics simulations revealed key residues and dominant interactions, as well as stable hydrogen bond formations during the ligand binding process. Overall, the study provided theoretical guidance for the design of new anthraquinone derivatives as PGAM1 inhibitors.
FRONTIERS IN PHARMACOLOGY
(2021)
Article
Physiology
Cheng Qu, Zhao-kai Yang, Su Wang, Hai-peng Zhao, Feng-qi Li, Xin-ling Yang, Chen Luo
Summary: This study investigates the olfactory binding characteristics and expression patterns of H. axyridis antenna specific OBP genes. The findings suggest that HaxyOBP15, with its higher expression in adult stage and broader ligand-binding spectrum, may play a greater role in binding volatiles compared to other HaxyOBPs.
FRONTIERS IN PHYSIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Rohoullah Firouzi, Shahin Sowlati-Hashjin, Cecilia Chavez-Garcia, Mitra Ashouri, Mohammad Hossein Karimi-Jafari, Mikko Karttunen
Summary: The assembly of amyloid-beta peptide (Aβ) into toxic oligomers and fibrils is associated with Alzheimer's disease and dementia. Targeting the monomeric form of Aβ with small molecules or antibodies to disrupt amyloid assembly is a promising therapeutic strategy. This study proposes a computational pipeline, using ensemble docking strategy, to identify catechins' binding sites in monomeric Aβ(42) and explores the crucial interactions for binding. The results suggest that catechins, especially EGCG, can act as potent inhibitors against amyloid aggregation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Food Science & Technology
Huan Liu, Junke Li, Fang Wang, Xuemei Sun, Dengyong Liu, Zhongshuai Wang, Hansheng Gong
Summary: The study comprehensively clarified the effects of glucose glycation-induced structural modifications of myosin on its binding ability with furan derivatives, demonstrating that the binding levels of furan derivatives were obviously affected by the glycation levels of myosin due to the changes of myosin structure and surface.
FOOD RESEARCH INTERNATIONAL
(2023)
Article
Chemistry, Physical
Arup Biswas, Arnab Pal, Debasish Mondal, Somrita Ray
Summary: Gating is a phenomenon in biochemistry that controls the transition between open and closed states of an ion-channel, allowing selective transport. This study uses stochastic resetting to counterbalance the delay caused by gating and predicts when it can enhance the rate of a process without compromising selectivity.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Biochemistry & Molecular Biology
Xunxun Wu, Xiaokun Li, Chunxue Yang, Yong Diao
Summary: In this study, a novel in silico docking and DARTS prediction strategy was proposed, and the targets of natural products were successfully identified through surface plasmon resonance assay and in vitro and in vivo assays.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Inorganic & Nuclear
D. Bharathi, B. Siddlingeshwar, R. Hari Krishna, Elena M. Kirilova, Darshan Devang Divakar, Abdulaziz Abdullah Alkheraif
Summary: This study investigates the interaction of the fluorescent probe 3-MAB with copper oxide and zinc oxide nanoparticles, revealing insights through absorption and fluorescence techniques. Through steady state fluorescence quenching experiments in different solvents, the binding constant, bimolecular quenching rate constant, and binding sites were determined.
INORGANIC CHEMISTRY COMMUNICATIONS
(2021)
Article
Chemistry, Organic
Gitumoni Kalita, Sharat Sarmah, Atanu Singha Roy, Paresh Nath Chatterjee
Summary: This study presents a facile method for the synthesis of 2,2-disubstituted-2H-1-benzopyrans using easily accessible tertiary propargylic alcohols and phenolic derivatives. A sulfonated tetraphenylethylene-based hypercrosslinked polymer (THP-SO3H) was used as a heterogeneous organocatalyst. The catalyst can be easily recovered and reused up to five consecutive cycles with minimal loss in catalytic efficiency. The binding interaction of the synthesized benzopyrans with human serum albumin was investigated using fluorescence spectroscopy and molecular docking techniques.
JOURNAL OF HETEROCYCLIC CHEMISTRY
(2023)
Review
Biochemistry & Molecular Biology
Subhomoi Borkotoky, Debajit Dey, Zaved Hazarika
Summary: SARS-CoV-2, the virus causing COVID-19, binds to the ACE2 receptor through its spike protein, and mutations in the spike protein may affect vaccine efficacy and neutralizing antibodies. Therefore, understanding the detailed interactions between ACE2 and the spike protein is crucial for preventing virus transmission and therapeutic development.
MOLECULAR BIOLOGY REPORTS
(2023)
Article
Materials Science, Biomaterials
Mahabul Haque, Ibemhanbi Konthoujam, Sona Lyndem, Sudipta Koley, Kripamoy Aguan, Atanu Singha Roy
Summary: This study synthesized biocompatible zinc sulphide (ZnS) quantum dots (QDs) using a plant leaf extract as an immobilizing and stabilizing agent. The ZnS QDs exhibited antibacterial activity against E. coli and E. faecalis, cytotoxic effects on HeLa cell line, and were used as fluorescence probes for bilirubin and rifampicin detection. The QDs also formed complexes with human serum albumin (HSA) protein and enhanced the binding affinities with other ligands.
JOURNAL OF MATERIALS CHEMISTRY B
(2023)
Review
Biochemistry & Molecular Biology
Indu Kumari, Dinesh Lakhanpal, Sandeep Swargam, Anupam Nath Jha
Summary: Leishmaniasis is a deadly tropical disease found in different clinical forms. Various techniques, including next-generation sequencing, have been used to detect and study the disease. These studies have provided valuable insights into the population structure, virulence, and drug resistance of Leishmania. Advanced CRISPR technology has also been employed to understand the role of individual genes in the disease.
CURRENT PROTEIN & PEPTIDE SCIENCE
(2023)
Article
Pharmacology & Pharmacy
Saynaz A. Choudhary, Debarun Patra, Archana Sinha, Sayani Mazumder, Rajat Pant, Raju Chouhan, Anupam Nath Jha, Biswa Mohan Prusty, Debasis Manna, Sajal K. Das, Kulbhushan Tikoo, Durba Pal, Suman Dasgupta
Summary: Increasing evidence suggests that vanillin and its analogs are potent toll-like receptor signaling inhibitors, effectively reducing inflammation. However, the underlying molecular mechanism is still unclear. This study reveals that vanillin inhibits toll-like receptor 4 activation by targeting the MyD88-dependent pathway and suppressing IRAK4 activity. It also shows that vanillin can block constitutively activated IRAK4/1 and NF-kappa B activation, indicating its potential therapeutic application in managing inflammatory diseases.
EUROPEAN JOURNAL OF PHARMACOLOGY
(2023)
Article
Chemistry, Physical
Sona Lyndem, Upasana Hazarika, P. Athul, Anindita Bhatta, Vivek Prakash, Anupam Nath Jha, Atanu Singha Roy
Summary: This study investigated the molecular recognition of bovine hemoglobin with 7-hydroxycou-marin and 4-methyl-7-hydroxycoumarin. The results showed that the binding of these fluorescent compounds to hemoglobin is reversible and occurs through a static quenching mechanism. Hydrophobic forces and hydrogen bonding play important roles in the binding process.
JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY A-CHEMISTRY
(2023)
Article
Biochemical Research Methods
Debanjan Saha, Anupam Nath Jha
Summary: This study aimed to find effective inhibitors of Leishmania donovani using a multi-target approach. First, inhibitors of two key enzymes were collected and screened using drug metabolism and effectiveness analysis. 15 potential inhibitors were identified through molecular docking simulations and molecular dynamics analysis. One plant-derived compound (Lig_3) showed promising inhibitory effects on both targets.
PHYTOCHEMICAL ANALYSIS
(2023)
Editorial Material
Genetics & Heredity
Anupam Nath Jha
FRONTIERS IN GENETICS
(2023)
Article
Food Science & Technology
Sadia Nudrat, Piyusaranjan Giri, Dasuklang Lyngdoh Nongbri, Kalpana Kumari, Sana Quraishi, Madhurima Jana, Kripamoy Aguan, Atanu Singha Roy
Summary: This study investigated the molecular interactions and inhibitory effects of two bioactive coumarin derivatives, 7-hydroxycoumarin and 4-methyl-7-hydroxycoumarin, on the main food allergen from egg white, ovalbumin. The results showed that these coumarin derivatives could effectively inhibit OVA aggregation and induce conformational changes of OVA.
ACS FOOD SCIENCE & TECHNOLOGY
(2023)
Review
Pharmacology & Pharmacy
Priya Kumari, Afrin Mamud, Anupam Nath Jha
Summary: Leishmaniasis is a vector-borne disease caused by a protozoan parasite, with no effective medicine/vaccine available. The development of new drugs is crucial, and a vaccine could be a low-risk and effective alternative. Although no vaccine has successfully passed clinical trials, the successful development of a vaccine for canine leishmaniasis provides hope.
CURRENT DRUG TARGETS
(2023)
Article
Plant Sciences
Debanjan Saha, Nayan Jyoti Borah, Anupam Nath Jha
Summary: The study aimed to find potential drugs against visceral leishmaniasis by selecting essential therapeutic targets and conducting molecular simulations and analysis. Several compounds were identified as potential inhibitors for pyridoxal kinase and sterol alpha-14 demethylase, which play crucial roles in the pathogenicity of Leishmania donovani.
SOUTH AFRICAN JOURNAL OF BOTANY
(2023)
Article
Chemistry, Multidisciplinary
Sona Lyndem, Upasana Hazarika, Anindita Bhatta, Vivek Prakash, Anupam Nath Jha, Atanu Singha Roy
Summary: This study aims to comprehensively explain the binding interaction of bioactive esculetin and esculin with bovine hemoglobin and determine the anti-fibrillation properties of these compounds. The results showed a static quenching mechanism for the BHb-esculin complex and a combined quenching mechanism for the BHb-esculetin complex. The binding affinity was higher for the BHb-esculetin complex, possibly due to the lower binding distance between a β-Trp37 residue and esculetin. The study also revealed the structural and anti-fibrillation effects of esculin and esculetin on bovine hemoglobin.
NEW JOURNAL OF CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Girgis Obaid, Menitte Eroy, Jie Zhao, Shazia Bano, Mari Mino-Kenudson, Tayyaba Hasan
Summary: The presence of desmoplasia in pancreatic ductal adenocarcinoma (PDAC) is associated with poor treatment outcomes and reduced drug delivery. By analyzing collagen subtypes in PDAC tumors following different treatment regimens, immunofluorescence profiling can predict long-term survival and tumor growth inhibition. This information can aid in personalized treatment and improve patient survival.
JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY
(2024)
Article
Biochemistry & Molecular Biology
Fatemeh Malekpour, Rashin Bahrami, Mahshid Hodjat, Neda Hakimiha, Behnam Bolhari, Aidin Sooratgar, Soheil Niavarzi
Summary: This study investigated the effect of photobiomodulation (PBM) therapy using an 808 nm diode laser on cellular modulation mechanisms in regenerative endodontic procedures (REPs). The results showed that PBM treatment significantly increased cell viability and migration, and enhanced the release of TGF-131 from dentin.
JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY
(2024)
Article
Biochemistry & Molecular Biology
Pranathi Tata, Ramakrishnan Ganesan, Jayati Ray Dutta
Summary: Thin film coatings with potent antibacterial properties are widely used in medical devices, frequently touched surfaces, and food packaging. However, achieving antibacterial performance under both light and dark conditions remains a challenge. In this study, we successfully prepared AgBr-coated ZnO nanorod thin film architecture using a unique surfactant-mediated solution-phase spin-coating approach. The resulting structures showed dual functionality as antimicrobial agents and photosensitizers, effectively enhancing the visible-light photodisinfection efficacy of ZnO nanorods. The concentration of the surfactant-based precursor solution could be modulated to control the AgBr content. Additionally, components like urea and lactic acid were found to enhance the photocatalytic efficiency of the structures.
JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY
(2024)