Article
Virology
Roberto Benoni, Petra Krafcikova, Marek R. Baranowski, Joanna Kowalska, Evzen Boura, Hana Cahova
Summary: The study focuses on the MTase activity involved in viral cap formation, particularly the nsp10-nsp16 MTase. Using a novel LC-MS method, multiple RNA types were identified as substrates of this MTase, presenting a new approach for antiviral drug screening.
Article
Biochemistry & Molecular Biology
Hoang Linh Nguyen, Nguyen Quoc Thai, Mai Suan Li
Summary: The COVID-19 pandemic has led to the need for new drugs, and the NSP16-NSP10 complex has been identified as a potential target. The compound CID 135566620 from PubChem shows promise as an inhibitor and further research is required to test its efficacy against COVID-19.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
Mahmoud A. El Hassab, Tamer M. Ibrahim, Sara T. Al-Rashood, Amal Alharbi, Razan O. Eskandrani, Wagdy M. Eldehna
Summary: This study aimed to identify a potential inhibitor for SARS CoV-2 nsp16, an important target in the virus life cycle. Through virtual screening and molecular dynamics simulations, compound 11 was identified as the best potential nsp16 inhibitor with improved stability and binding free energy compared to Sinefungin.
JOURNAL OF ENZYME INHIBITION AND MEDICINAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Bilal J. M. Aldahham, Khattab Al-Khafaji, Mohanad Yakdhan Saleh, Adel Mohamed Abdelhakem, Amer M. Alanazi, Ataul Islam
Summary: This research explores new heterocyclic compounds as potential inhibitors for SARS-CoV-2 by targeting the Nsp16-Nsp10 protein. Through virtual screening and pharmacokinetics assessment, two compounds were identified as promising inhibitors with strong affinity and stability towards the protein. These findings suggest their potential for future experimental validation.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Chemistry, Physical
Julia Liang, Eleni Pitsillou, Lucy Burbury, Andrew Hung, Tom C. Karagiannis
Summary: This study aimed to identify potential small molecules inhibiting the methyltransferase activity of the SARS-CoV-2 nsp10-nsp16 heterodimer, and ultimately identified oleuropein as a potential inhibitor.
CHEMICAL PHYSICS LETTERS
(2021)
Article
Biochemistry & Molecular Biology
Jose Rogerio A. Silva, Jaime Urban, Edson Araujo, Jeronimo Lameira, Vicent Moliner, Claudio Nahum Alves
Summary: In this study, the mechanism of 2'-O methylation of the viral mRNA cap was evaluated, demonstrating the critical role of TS stabilization in catalysis based on detailed molecular analysis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Anwar Mohammad, Eman Alshawaf, Sulaiman K. Marafie, Mohamed Abu-Farha, Fahd Al-Mulla, Jehad Abubaker
Summary: This study identified four compounds that have the potential to disrupt the nsp10-nsp16 interface interaction in SARS-CoV-2, with one compound demonstrating the most stable complex and strongest binding affinity. This discovery paves the way for further functional studies and the development of potential antiviral drugs.
Article
Chemistry, Physical
Joao Pedro Agra Gomes, Larissa de Oliveira Rocha, Cintia Emi Yanaguibashi Leal, Edilson Beserra de Alencar Filho
Summary: COVID-19 is a significant health problem caused by the SARS-CoV-2 virus. This study utilized computational chemistry to search for potential inhibitors and evaluated various molecular compounds, including those derived from plants in the Brazilian Caatinga biome, the ZINC online molecular database, structural analogues of the enzymatic cofactor S-adenosylmethionine (SAM), and a known inhibitor called sinefungin (SFG). The results identified four compounds from ZINC as the most promising ligands, contributing to the discovery of new molecular hits and potential agents against SARS-CoV-2.
JOURNAL OF MOLECULAR STRUCTURE
(2022)
Article
Biochemistry & Molecular Biology
Martin Klima, Aliakbar Khalili Yazdi, Fengling Li, Irene Chau, Taraneh Hajian, Albina Bolotokova, H. Umit Kaniskan, Yulin Han, Ke Wang, Deyao Li, Minkui Luo, Jian Jin, Evzen Boura, Masoud Vedadi
Summary: SARS-CoV-2 nsp10-nsp16 complex is an important enzyme involved in viral RNA capping. Two compounds (SS148 and WZ16) were found to inhibit the activity of nsp16 enzyme, and their binding modes were revealed through crystal structure studies.
Article
Biochemistry & Molecular Biology
Abhilasha Sharma, Jaykant Vora, Dhaval Patel, Sonam Sinha, Prakash C. Jha, Neeta Shrivastava
Summary: This study identified potential phyto-compounds that could be developed as therapeutic candidates for COVID-19. Computational screening revealed several phyto-molecules with high binding affinity against key targets of SARS-CoV-2. ADME profiles and molecular dynamics simulations further validated the drug-like properties and stability of these compounds.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Chemistry, Physical
Said A. H. Vuai, Isaac Onoka, Mtabazi G. Sahini, Hulda S. Swai, Daniel M. Shadrack
Summary: The study demonstrated the inhibitory potential of withanolides from Withania somnifera against SARS-CoV-2 non-structural protein 10 (nsp10), with withanoside IV and withanoside V showing strong inhibition. Further in vitro and in vivo experiments are recommended to validate the anti-SARS-COV-2 potential of these phytochemicals.
MOLECULAR SIMULATION
(2021)
Article
Chemistry, Multidisciplinary
Mahmoud A. El Hassab, Tamer M. Ibrahim, Aly A. Shoun, Sara T. Al-Rashood, Hamad M. Alkahtani, Amal Alharbi, Razan O. Eskandrani, Wagdy M. Eldehna
Summary: A new potential inhibitor for SARS CoV-2 2'-O-methyltransferase (nsp16), molecule AP-20, was proposed and demonstrated superior stability and binding free energy compared to Sinefungin in molecular dynamics simulations and MM-PBSA calculations. Experimental evaluations are recommended to further explore the potential inhibitory effect of AP-20 on the emerging COVID-19 spread. Additionally, in silico ADME profiling showed excellent safety and metabolic stability profile for AP-20.
Article
Biochemical Research Methods
Sultan F. Alnomasy, Bader S. Alotaibi, Ziyad M. Aldosari, Ahmed H. Mujamammi, Ahmad Alzamami, Pragya Anand, Yusuf Akhter, Farhan R. Khan, Mohammad R. Hasan
Summary: The study found that Zyesami has inhibitory effects on the SARS-CoV-2 nsp10/nsp16 complex, which may be used as a drug for COVID-19 treatment.
COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING
(2023)
Article
Biochemistry & Molecular Biology
Alessandra M. Balieiro, Eduarda L. S. Anunciacao, Clauber H. S. Costa, Wesam S. Qayed, Jose Rogerio A. Silva
Summary: This study evaluates inhibitors of MTases enzymes for SARS-CoV-2 and provides structural and energetic analysis using computational modeling techniques. The most potent inhibitor shows lower binding free energy and higher potency than known inhibitors. Additionally, analysis of cell permeability suggests that the inhibitors suffer from poor cell permeability.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Krishnendu Bera
Summary: Drug repurposing using in silico studies identified ravidasvir as a potential inhibitor of 3-Chymotrypsin-like protease (3CL(pro)) of SARS-CoV-2, with promising binding energy and potential for further drug development and optimization in combating COVID-19 pandemic.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biochemistry & Molecular Biology
Rajarshi Roy, Sayan Poddar, Md Fulbabu Sk, Parimal Kar
Summary: In this study, the conformational dynamics of complex glycans on the surface of HIV glycoprotein were investigated using molecular dynamics simulations. The results reveal the influence of adding complex branches on the overall glycan structural dynamics and provide insights into the flexibility and conformational changes of different glycan branches.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
Dharmendra Kashyap, Rajarshi Roy, Parimal Kar, Hem Chandra Jha
Summary: This study screened seven active compounds of plant origins using molecular docking, which showed strong binding affinity with the nucleocapsid protein of SARS-CoV-2 and exhibited good properties. Further research is needed to validate their suitability for clinical trials.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
Rajarshi Roy, Md Fulbabu Sk, Omprakash Tanwar, Parimal Kar
Summary: This study utilized a human metabolites database to screen for potential anti-SARS-CoV-2 compounds, resulting in the identification of new compounds with potential as antiviral drugs. The molecular mechanisms of their binding to the main protease were also elucidated.
MOLECULAR DIVERSITY
(2023)
Review
Biochemistry & Molecular Biology
Subhasmita Mahapatra, Nisha Amarnath Jonniya, Suman Koirala, Kapil Dattatray Ursal, Parimal Kar
Summary: Fibroblast Growth Factor (FGF) ligands and their receptors, FGFR, play a crucial role in chemoresistance in several malignancies. Dysfunction of FGF/FGFR signaling pathways in tumor cells affects drug effectiveness. Overexpression and mutation of FGF/FGFR induce regulatory changes in signaling pathways, leading to drug resistance. Inhibition of FGF/FGFR through various therapeutic approaches may provide solutions to this problem.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
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
Suman Koirala, Rajarshi Roy, Sunanda Samanta, Subhasmita Mahapatra, Parimal Kar
Summary: Recent findings have emphasized the important role of dual leucine zipper kinase (DLK) in neuronal degeneration. Saraswatharishta (SWRT), a traditional Indian medicine, has shown effectiveness in treating neurodegenerative diseases. This study aims to explore the detailed mechanism of action of phytochemicals in SWRT against DLK. By screening over 500 phytochemicals derived from the main ingredients of SWRT, four novel compounds were identified and further investigated through molecular dynamics simulations. Among these compounds, CID16066851 from Acorus calamus showed the most stable interaction with DLK. The study identified key residues and highlighted the significance of electrostatic and van der Waals interactions in the binding process. The findings suggest potential for future drug development targeting neurodegenerative conditions.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
Suman Koirala, Sunanda Samanta, Subhasmita Mahapatra, Kapil Dattatray Ursal, Sayan Poddar, Parimal Kar
Summary: This study identified novel compounds that may serve as potential antivirals against monkeypox virus (MPXV) and revealed the molecular mechanisms underlying their binding with the target enzyme TMPK.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
Sayan Poddar, Rajarshi Roy, Parimal Kar
Summary: In this study, the conformational dynamics of histo-blood group antigens and their interactions with VP8* domain of rotavirus genotypes were investigated using molecular dynamics simulations. The study revealed changes in the dynamic behavior of glycans due to linkage variations. The binding affinity was calculated, revealing the impact of glycan linkage on binding. Additionally, key amino acids and monosaccharides contributing to protein-ligand binding were identified.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Chemistry, Multidisciplinary
Md Fulbabu Sk, Sunanda Samanta, Sayan Poddar, Parimal Kar
Summary: This study investigated the structural dynamics and drug resistance mechanisms of neuraminidase N7. The results revealed that the mutant systems showed significant conformational changes and a mutation led to drug resistance. The study suggests that drug resistance can be reduced by strengthening the hydrogen bond contacts between the drug and the mutant N7 or preserving closed cavity conformations.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
S. Samanta, M. F. Sk, S. Koirala, P. Kar
Summary: The study identified a potential medication, lead1, for treating Syk-associated diseases through screening and molecular dynamics simulations. Lead1 exhibited similar binding free energy to a control drug and one of its structural analogues showed improved binding free energy. The analogue could be further explored for developing effective therapeutics against Syk-associated diseases.
SAR AND QSAR IN ENVIRONMENTAL RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Dharmendra Kashyap, Suman Koirala, Rajarshi Roy, Vaishali Saini, Nidhi Varshney, Pranit Hemant Bagde, Sunanda Samanta, Parimal Kar, Hem Chandra Jha
Summary: This study identifies FDA-approved antibiotics that can be repurposed against VacA of H. pylori and explores their molecular mechanism of interaction with VacA through molecular simulations.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)