Article
Biochemistry & Molecular Biology
Subhasmita Mahapatra, Nisha Amarnath Jonniya, Suman Koirala, Parimal Kar
Summary: In this study, the phosphorylation-induced conformational dynamics of FGFR1 in both apo and ATP-bound states were investigated using molecular dynamics simulations. The findings reveal that phosphorylation and ATP binding can lead to a fully active configuration of FGFR1 kinase. The formation of a 3-10 helix in the activation loop and strong salt-bridge interactions contribute to the stability and compactness of the structure.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
Samia A. Elseginy
Summary: This study investigated the binding mechanism of two inhibitors, dolutegravir and etravirine, with the Omicron variant of the SARS-CoV-2 virus using various in silico methods. The results revealed hydrogen bonds and salt bridges between the inhibitors and the spike protein of the virus. Key residues involved in the binding were identified. The simulations showed that the conformational changes of the complexes were minimal.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
Nidhi Goswami, Archana Singh, Shiv Bharadwaj, Amaresh Kumar Sahoo, Indrakant K. Singh
Summary: Neuroblastoma is a challenging tumor to develop drugs for due to its heterogeneity. ALYREF protein has been identified as a target for neuroblastoma treatment, and this study used structure-based drug discovery to find potential inhibitors. The study suggests further evaluation of these compounds for development of a drug against neuroblastoma.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
Luis F. Ponce, Karina Garcia-Martinez, Kalet Leon, Pedro A. Valiente
Summary: This research explores the dynamics of PD1 in complex with different PDL1 variants and therapeutic antibodies to understand how binding induces inhibitory signals in T cells. Targeting specific conformations of PD1 may be useful for designing therapies to recover T cells effector functions.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2021)
Article
Multidisciplinary Sciences
Makoto Mizuno, Hideaki Aoyama, Yoshi Fujiwara
Summary: This study introduces a novel method called complex Hilbert principal component analysis (CHPCA) and constructs a synchronization network using Hodge decomposition, which enables the extraction of significant comovements with a time lead/delay in high-dimensional data and identification of the time-structure of correlations. Applied to Japanese beer market data, this method reveals co-movements across multiple products in the consumer choice process and uncovers remarkable customer heterogeneity.
Article
Biochemistry & Molecular Biology
Kristen Rhinehardt, Ming Dong
Summary: This study utilized MD simulations to investigate the protein dynamics and side chain dihedral angles of thermolysin at different temperatures. The findings revealed significant differences in protein structure and side chain angles at different temperatures.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Multidisciplinary Sciences
Shamrat Kumar Paul, Md. Saddam, Khandoker Asiqur Rahaman, Jong-Gu Choi, Sang-Suk Lee, Mahbub Hasan
Summary: This study analyzed the structure and physicochemical properties of GCA protein through modeling and molecular dynamics simulation. The findings revealed the similarity between GCA and grancalcin protein and proposed three potential calcium-binding sites. The simulation results showed that GCA maintained a stable and compact state, primarily composed of alpha helices. These findings have significant implications for the development of potential inhibitors and the identification of binding pockets and residues for drug-like molecules.
Article
Biochemistry & Molecular Biology
Nisha Amarnath Jonniya, Md Fulbabu Sk, Parimal Kar
Summary: This study investigates the structural and conformational properties of WNK kinase isoforms bound to an ATP competitive inhibitor, as well as the effect of phosphorylation on each isoform. The study shows that phosphorylation stabilizes different regions of the protein-inhibitor complexes and leads to different structural dynamics in different isoforms.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Chemistry, Physical
Juan Zhao, Lifei Wang, Huayin Bao, Jianzhong Chen
Summary: The molecular dynamics simulations coupled with structural cluster analysis revealed that mutations A59G and D33E have a significant impact on the structural flexibility and internal dynamics of KRAS, changing its free energy profiles and affecting its binding to effectors.
CHEMICAL PHYSICS LETTERS
(2021)
Article
Biochemistry & Molecular Biology
Moyad Shahwan, Fahad A. Alhumaydhi, Sharaf E. Sharaf, Badrah S. Alghamdi, Saleh Baeesa, Haythum O. Tayeb, Ghulam Md Ashraf, Anas Shamsi
Summary: Neuronal damage in iron-sensitive brain regions is associated with iron dyshomeostasis and neurodegenerative diseases, particularly Alzheimer's disease (AD). Ferritin plays a key role in iron homeostasis. Natural compound bryostatin may have therapeutic implications for AD. This study explores the binding mechanism of bryostatin 1 with ferritin.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Chemistry, Physical
Bharat Manna, Amit Ghosh
Summary: Xylan, a hemicellulosic feedstock rich in pentose sugars, holds massive potential for biofuel production. Ionic Liquid is a promising solvent for deconstructing lignocellulosic structures, though it can impact xylanase activity during hydrolysis. This study investigates the IL tolerance of a hyperthermophilic xylanase and sheds light on its reduced activity in IL, potentially aiding biofuel production.
JOURNAL OF MOLECULAR LIQUIDS
(2021)
Article
Biochemistry & Molecular Biology
Satyabrata Majumder, Kalyan Giri
Summary: This study investigates the binding mechanism of Viprinin and its derivatives with HIV-1 Vpr using molecular docking, molecular dynamics simulation, MM-PBSA, PCA and Umbrella sampling. The calculations suggest that Viprinin and ViprininD1 have higher binding energy than ViprininD2. Molecular dynamics simulation shows that the ligands are not very stable inside the initial binding pocket.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Polymer Science
Qun Zhang, Dongqing Shao, Peng Xu, Zhouting Jiang
Summary: This study investigated the effect of pulsed and oscillating electric fields on the conformational properties of all-alpha proteins. Molecular dynamics simulations were used to analyze the structural characteristics of the protein samples. The results showed that higher frequencies of the electric field influenced the rapid response to secondary structural transitions, but had a diminished effect on conformational changes measured by RMSD. The dipole moment analysis revealed a direct relationship between the magnitude and frequency of the dipole moment and the strength and frequency of the external electric field. The type of electric field also played a role, with pulsed electric fields leading to larger average values of RMSD and RMSF for the whole protein. Additionally, the secondary structure analysis showed simultaneous transitions of alpha-helix segments to turns or random coils in a pulsed electric field, while different characteristic times were observed in an oscillating electric field. The study also demonstrated that proteins with fewer charged residues or more residues forming alpha-helical structures exhibited higher conformational stability. These findings have important theoretical implications for understanding the effect of frequency and expression form of external electric fields on conformational changes in all-alpha proteins with charged residues and provide guidance for potential applications.
Article
Biochemistry & Molecular Biology
Zahra Musavizadeh, Alessandro Grottesi, Giulia Guarguaglini, Alessandro Paiardini
Summary: The study reveals the impact of phosphorylation on the stability of the A-loop and the effect of conformation disrupting inhibitors on the dynamics of Aurora-A. The presence of a phosphate moiety induces Aurora-A to sample two distinct energy minima, indicating a significant difference in conformational distributions compared to the unphosphorylated state.
Article
Biochemistry & Molecular Biology
Mohammad Raish, Ajaz Ahmad, Shahnawaz Khan, Mohd Abul Kalam
Summary: In this study, three potential compounds were identified through screening of lactate dehydrogenase. These compounds showed exceptional hydrogen bonding ability and high binding scores with the protein. Their strong binding properties and stable interactions make them prime candidates for further research and experimental validation.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Green & Sustainable Science & Technology
Meghdad Pirsaheb, Sajad Moradi, Mohsen Shahlaei, Xiangke Wang, Negin Farhadian
JOURNAL OF CLEANER PRODUCTION
(2019)
Article
Chemistry, Physical
Sajad Moradi, Solmaz Khani, Mohabbat Ansari, Mohsen Shahlaei
JOURNAL OF MOLECULAR LIQUIDS
(2019)
Article
Chemistry, Multidisciplinary
Abbas Hemati Azandaryani, Soheila Kashanian, Mohsen Shahlaei, Katayoun Derakhshandeh, Marjan Motiei, Sajad Moradi
PHARMACEUTICAL RESEARCH
(2019)
Article
Environmental Sciences
Meghdad Pirsaheb, Sajad Moradi, Mohsen Shahlaei, Xiangke Wang, Negin Farhadian
JOURNAL OF ENVIRONMENTAL MANAGEMENT
(2019)
Article
Spectroscopy
Sajad Moradi, Negin Farhadian, Fatemeh Balaei, Mohabbat Ansari, Mohsen Shahlaei
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2020)
Article
Engineering, Electrical & Electronic
Maryam Haghighi, Mohsen Shahlaei, Mohsen Irandoust, Alireza Hassanpour
JOURNAL OF MATERIALS SCIENCE-MATERIALS IN ELECTRONICS
(2020)
Article
Chemistry, Analytical
Giti Paimard, Mohsen Shahlaei, Pouran Moradipour, Hamzeh Akbari, Mahsa Jafari, Elham Arkan
SENSORS AND ACTUATORS B-CHEMICAL
(2020)
Article
Spectroscopy
Mahtab Amoorahim, Mohammad Reza Ashrafi-Kooshk, Sajjad Esmaeili, Mohsen Shahlaei, Sajad Moradi, Reza Khodarahmi
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2020)
Article
Chemistry, Multidisciplinary
Amir Kiani, Mohsen Shahlaei, Mahdi Rahpeyma, Hadi Adibi
Summary: Angiogenesis plays a crucial role in cancer progression and other non-neoplastic diseases. Isatin-based compounds have shown potential as anticancer agents, with some exhibiting antiangiogenic effects. Specifically, (Z)-3-((5-(benzylthio)-4H-1,2,4-triazol-3-yl)imino)-5-haloindolin-2-one macromolecules showed the highest cytotoxicity and ability to reduce MMP-2 and MMP-9 levels in cancer cell lines. Further investigation is needed to understand the molecular mechanisms of these compounds.
JOURNAL OF THE IRANIAN CHEMICAL SOCIETY
(2021)
Article
Engineering, Electrical & Electronic
Maryam Haghighi, Mohsen Shahlaei, Kiumars Bahrami, Homa Targhan
Summary: A new electrochemical sensor using RGO/Ti-MOF-modified GCE was introduced for the electro-catalytic oxidation and determination of Propranolol, showing high sensitivity and low detection limit. The synthesized composite exhibited excellent performance in phosphate buffer solution, significantly reducing the oxidation over-potential of Propranolol.
JOURNAL OF MATERIALS SCIENCE-MATERIALS IN ELECTRONICS
(2021)
Article
Biology
Kosar Sadat Ebrahimi, Mohabbat Ansari, Mahdieh S. Hosseyni Moghaddam, Zohre Ebrahimi, Zohre Salehi, Mohsen Shahlaei, Sajad Moradi
Summary: This study investigated the inhibitory potential of secondary metabolites from endophytic fungi against the new coronavirus RNA-dependent RNA polymerase using computational methods. Two fungal metabolites, 18-methoxy cytochalasin J and pyrrocidine A, were identified as promising candidates for inhibiting COVID-19 based on their high binding energy, protein instability, strong complex formation, and pharmacokinetic properties. Further laboratory evaluation of these compounds is recommended.
COMPUTERS IN BIOLOGY AND MEDICINE
(2021)
Article
Chemistry, Multidisciplinary
Maryam Haghighi, Mehdi Rezaei, Payam Sariaslani, Sajad Moradi, Mohsen Shahlaei
Summary: A modified carbon paste electrode based on nanomagnetic core-shell and reduced graphene oxide was developed for sensitive determination of lamotrigine, with a detection limit of 0.7 nM. The electrochemical sensor was successfully applied for quantification of lamotrigine in tablet and plasma samples under optimized conditions.
MONATSHEFTE FUR CHEMIE
(2021)
Article
Chemistry, Multidisciplinary
Meghdad Pirsaheb, Sajad Moradi, Mohsen Shahlaei, Negin Farhadian
NEW JOURNAL OF CHEMISTRY
(2020)
Review
Chemistry, Multidisciplinary
Sajad Moradi, Amin Nowroozi, Mohsen Shahlaei
Article
Pharmacology & Pharmacy
Seyran Saeidi, Elham Esmaeili, Mohabbat Ansari, Sajad Moradi, Mohsen Shahlaei
JOURNAL OF REPORTS IN PHARMACEUTICAL SCIENCES
(2019)