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Biochemistry & Molecular Biology
Muthu Kumar Thirunavukkarasu, Ramanathan Karuppasamy
Summary: The study screened a candidate with high binding affinity in MEK protein from a library of 11,808 compounds, and suggested that Nebivolol may be an excellent candidate for MEK inhibition in NSCLC patients in the future.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
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Biochemistry & Molecular Biology
Xi Gu, Ying Wang, Mingxing Wang, Jian Wang, Ning Li
Summary: Molecular modeling methods were utilized to study the structural requirements of a series of Akt1 allosteric inhibitors, resulting in the design of 15 novel compounds. Through molecular docking, 3D-QSAR, and molecular dynamics simulation, key insights were gained for the discovery of potent Akt1 inhibitors.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2021)
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Virology
Bruno Stein Barbosa Menechino, Rodrigo Bentes Kato, Helena Cristina Ferreira Franz, Pedro Eduardo Almeida da Silva, Marcus Corat, Daniel Ferreira de Lima Neto
Summary: This study investigated the interaction between the envelope proteins of ZIKV and DENV with the DC-SIGN receptor. The results suggest a better competitive interaction between ZIKV and the DC-SIGN receptor, especially in the CRD portion.
Article
Chemistry, Physical
D. Kumar, M. K. Meena, K. Kumari, R. Kumar, I Bahadur, P. Jain, P. Singh
Summary: Researchers are seeking effective drugs to treat chikungunya viral infections by inhibiting nsp3 activity, but the temperature may affect the inhibition of nsp3 of CHIKV by CMPD104.
JOURNAL OF MOLECULAR LIQUIDS
(2021)
Article
Biochemistry & Molecular Biology
Yiwen Wang, Fen Yang, Dongliang Yan, Yalin Zeng, Benzheng Wei, Jianzhong Chen, Weikai He
Summary: In this study, the mechanism of BACE1 identification for three inhibitors was comparatively determined using molecular dynamics simulations and binding free energy calculations. The presence of the inhibitors affects the structural stability, flexibility, and internal dynamics of BACE1. The binding free energy calculations reveal that hydrophobic interactions play a decisive role in the binding between the inhibitors and BACE1. Residue-based free energy decomposition analysis suggests that specific residues contribute significantly to the inhibitor-BACE1 binding, providing insights for future drug design for AD treatment.
Article
Biology
Shriram D. Ranade, Shankar G. Alegaon, U. Venkatasubramanian, A. Soundarya Priya, Rohini S. Kavalapure, Jagdish Chand, Sunil S. Jalalpure, D. Vinod
Summary: This study aimed to design, synthesize, and evaluate 4-aminoquinoline hybrid compounds as potential Eg5 inhibitors. Compounds 6c, 6d, 6g, and 6h showed sensitivity to Eg5 inhibition based on data from Malachite green and steady state ATPase assays. Compound 4 and 6c exhibited promising inhibitory activity, with IC50 values of 2.32 ± 0.23 μM and 1.97 ± 0.23 μM, respectively. Molecular docking, MM/GBSA calculations, and molecular dynamic simulations were performed to evaluate the interactions between ligands and the binding site of the kinesin spindle protein, indicating that these 4-aminoquinoline Schiff's base hybrids may be potential candidates for Eg5 inhibitors. Further in-vivo research is needed.
COMPUTATIONAL BIOLOGY AND CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Angamba Meetei Potshangbam, Apana Nandeibam, Thongamba Amom, Nongdam Potshangbam, Hamidur Rahaman, Ravindranath Singh Rathore, Laishram Rajendrakumar Singh, Aslam Khan
Summary: Alzheimer's disease is a progressive neurological disorder affecting millions worldwide, with limited effective treatments available. Research is exploring the potential of medicinal plants to treat the disease, utilizing receptor-based computational methods to identify compounds with inhibitory activity against AChE.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biochemistry & Molecular Biology
Sofia D'Souza, S. Balaji, K. Prema
Summary: This study successfully developed new 3CL protease inhibitors using 2D and 3D QSAR models, and validated their inhibitory effects on SARS-CoV through molecular docking and molecular dynamics simulations. The newly designed compounds showed higher interaction energies with active site residues and improved pharmacokinetic properties.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biochemistry & Molecular Biology
Banoth Karan Kumar, Faheem, Kondapalli Venkata Gowri Chandra Sekhar, Rupal Ojha, Vijay Kumar Prajapati, Aravinda Pai, Sankaranarayanan Murugesan
Summary: This study identified potential ligands that may act as inhibitors of SARS-CoV-2 M-pro through computational screening. The molecules SN00293542 and SN00382835 showed the highest docking scores and demonstrated stability through molecular dynamics studies.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Chemistry, Multidisciplinary
Y. Y. Yin, J. Zhao, L. L. Zhang, X. Y. Xu, J. Q. Liu
Summary: The study utilized molecular dynamics simulations to decipher the molecular mechanism of inhibitor binding to A-FABP, revealing that van der Waals interactions play a crucial role. Additionally, the binding of inhibitors affects conformational changes of A-FABP and contributes significantly to stabilization. Furthermore, it was found that certain residues have stronger binding strengths with specific inhibitors, providing insights for the development of clinically available inhibitors.
SAR AND QSAR IN ENVIRONMENTAL RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Farideh Sadeghkhani, Zahra Hajihassan, Sajjad Gharaghani
Summary: This study identified two potential TLR8 agonists with favorable pharmacological features, which could be used for future experimental studies. The compounds showed advantages over Motolimod, and their flexibility and energy levels were compared to provide insights for further research.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
Jian Gao, Yinchuan Wang, Kaihang Li, Jinyuan Zhang, Xiaoju Geng
Summary: Myc is a master transcriptional regulator that relies on dimerization with its partner Max, while Omomyc is a peptide inhibitor that competitively inhibits Myc-Max binding. Stabilizers of Max-Max can increase the stability of Omomyc homodimer. Through molecular dynamics simulation and energy calculation, it was found that Omomyc homodimer is more stable than Max-Max, with hydrophobic characteristics suggesting potential Omomyc-Omomyc stabilizers.
JOURNAL OF MOLECULAR MODELING
(2022)
Article
Biochemistry & Molecular Biology
P. S. Lakshmi Soukya, A. Sajeli Begum
Summary: This study identifies several natural compounds, including rutin and myricetin, as potential inhibitors of the Fatty Acid Synthase (FASN) enzyme. These compounds show promising inhibitory effects on FASN and may have implications for the treatment of diseases such as cancer.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
Chiara Luise, Dina Robaa, Pierre Regenass, David Maurer, Dmytro Ostrovskyi, Ludwig Seifert, Johannes Bacher, Teresa Burgahn, Tobias Wagner, Johannes Seitz, Holger Greschik, Kwang-Su Park, Yan Xiong, Jian Jin, Roland Schule, Bernhard Breit, Manfred Jung, Wolfgang Sippl
Summary: The study developed novel analogs of the A366 inhibitor, revealing key structural features for Spindlin1 inhibitory activity through molecular modeling and in vitro testing. Different protocols were tested to identify a fast computer-aided method to discriminate active compounds, leading to the discovery of some selective compounds.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Ahmed Samir, Wael M. Elshemey, Abdo A. Elfiky
Summary: The interaction between the C-terminal domain (CTD) of the polymerase acidic (PA) component of flu A RNA polymerase and heptad repeats from human polymerase II CTD was computationally studied. A unique compound was found to effectively bind to the active site residues in each of the three RdRps, potentially inhibiting the activity of the viruses. This in silico analysis suggests a promising novel lead to block flu A RdRp.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)