Article
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)
Article
Biochemistry & Molecular Biology
Harutyun Sahakyan
Summary: Virtual screening based on molecular docking is a useful method for computer-aided drug design, reducing time and cost of drug development. However, the low accuracy of scoring functions in docking methods is a limitation, necessitating more rigorous calculation methods.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
(2021)
Article
Biochemistry & Molecular Biology
Hazem Abbas Al-Bustany, Selami Ercan, Ebru Ince, Necmettin Pirinccioglu
Summary: This study aims to investigate the binding affinity and molecular interactions of 157 available angucycline compounds with 3CLpro using docking and molecular dynamics simulations. MM-PBSA calculations showed that moromycin A has a better binding energy (-30.42 kcal mol(-1)) compared with other ligands, suggesting its potential as an effective treatment against coronavirus. Further in vitro and in vivo studies are needed to confirm the effectiveness of angucycline compounds.
MOLECULAR DIVERSITY
(2022)
Article
Chemistry, Physical
Yunju Zhang, Liangzhen Zheng, Yanmei Yang, Yuanyuan Qu, Yong-Qiang Li, Mingwen Zhao, Yuguang Mu, Weifeng Li
Summary: This study investigated the structure and energy features of the M-pro dimer of SARS-CoV-2 and SARS-CoV using molecular dynamics simulations. The results showed that the SARS-CoV-2 M-pro dimer is more stable and possibly forms more quickly. Key residues and regions rich in interfacial water were identified as potential targets for the design of anti-SARS-CoV-2 drugs.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Chemistry, Multidisciplinary
Yuchen Sun, Tingjun Hou, Xibing He, Viet Hoang Man, Junmei Wang
Summary: In this study, a transfer free energy-based logP prediction model, FElogP, was developed. The model performed better than other commonly used logP prediction models and was validated using a large set of structurally diverse molecules.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Wemenes Jose Lima Silva, Renato Ferreira de Freitas
Summary: This study investigates the accuracy and efficiency of different computational methods and protocols to predict the free energy of binding for a series of KLK6 inhibitors. The results show that the performance of the methods varied strongly depending on the system. The free energy perturbation (FEP) method showed improved binding affinity predictions and ranked the most potent compounds at the top of the list in a simulation of a real-world drug discovery project.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
(2023)
Article
Biochemistry & Molecular Biology
Chandu Ala, Renuka Parshuram Joshi, Pragya Gupta, Sivaprakash Ramalingam, Murugesan Sankaranarayanan
Summary: In this study, a structure-based virtual screening was performed to identify four potential compounds that can inhibit DNMT1. Additional in vitro and in vivo studies are needed to confirm their clinical effectiveness.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
Trupti S. Chitre, Purvaj V. Hirode, Deepak K. Lokwani, Aniket L. Bhatambrekar, Sayli G. Hajare, Shubhangi B. Thorat, D. Priya, Kunal B. Pradhan, Kalyani D. Asgaonkar, Shirish P. Jain
Summary: A significant three descriptor QSAR model was established to predict the Hec1/Nek2 inhibitory activity of 2-aminothiazoles derivatives, based on which new lead molecules were designed and further studied through ADMET and molecular docking. The study provides insights into the key interactions between the derivatives and Hec1/Nek2 protein, facilitating the development of potential anticancer molecules.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Chemistry, Multidisciplinary
Song Luo, Kaifang Huang, Xiaoyu Zhao, Yalong Cong, John Z. H. Zhang, Lili Duan
Summary: The study found that ritonavir, arbidol, and chloroquine exhibited outstanding binding ability to monomeric M-pro, while chloroquine may not effectively inhibit the activity of M-pro. Hot-spot residues Met165, Hie41, and Gln189 play important roles in binding to monomeric M-pro, while Gln189 and Met165 may be the focus in the discovery and development of anti-COVID-19 drugs in dimeric M-pro systems.
Article
Biochemistry & Molecular Biology
Sunday N. Okafor, Pavimol Angsantikul, Hashim Ahmed
Summary: This research utilized computational tools to screen a large compound library and identified potential HIV-1 protease inhibitors. Two optimized molecules showed promising activity and should be further investigated in vitro and in clinical trials.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Multidisciplinary
Xiaoyu Zhao, Song Luo, Kaifang Huang, Danyang Xiong, John Z. H. Zhang, Lili Duan
Summary: This study investigated the binding mechanisms of four potential drugs with TMPRSS2, demonstrating that camostat, gabexate, and nafamostat have higher binding affinities to TMPRSS2 compared with bromhexine. The molecular dynamics simulations and energy calculations provided valuable insights into the drug-TMPRSS2 interactions, highlighting the potential of these drugs as therapeutic agents targeting TMPRSS2.
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
Chemistry, Multidisciplinary
Y. X. Yu, W. T. Liu, H. Y. Li, W. Wang, H. B. Sun, L. L. Zhang, S. L. Wu
Summary: The HIV-1 protease (PR) is considered an efficient target for anti-AIDS drug design. Molecular dynamics simulations and post-processing analysis were used to study the binding mechanism of three drugs (LPV, NFV, ATV) to the PR. The results show that the drugs affect the structural flexibility and dynamics behavior of PR, with common interaction clusters, indicating potential targets for clinically available inhibitors.
SAR AND QSAR IN ENVIRONMENTAL RESEARCH
(2021)
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
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
Chemistry, Applied
Vanaparthi Satheesh, Hemant Kumar Srivastava, Sundaravel Vivek Kumar, Mani Sengoden, Tharmalingam Punniyamurthy
ADVANCED SYNTHESIS & CATALYSIS
(2019)
Article
Biochemical Research Methods
Piyush Agrawal, Harinder Singh, Hemant Kumar Srivastava, Sandeep Singh, Gaurav Kishore, Gajendra P. S. Raghava
BMC BIOINFORMATICS
(2019)
Article
Chemistry, Applied
Kanu Das, Moumita Dutta, Babulal Das, Hemant Kumar Srivastava, Akshai Kumar
ADVANCED SYNTHESIS & CATALYSIS
(2019)
Article
Chemistry, Organic
Gaurav Shukla, Tipu Alam, Hemant Kumar Srivastava, Ritush Kumar, Bhisma K. Patel
Article
Chemistry, Organic
Murugan Vijay, Sundaravel Vivek Kumar, Vanaparthi Satheesh, Periyasamy Ananthappan, Hemant Kumar Srivastava, Sundaram Ellairaja, Vairathevar Sivasamy Vasantha, Tharmalingam Punniyamurthy
Article
Biochemistry & Molecular Biology
Jyoti Gahtori, Suyash Pant, Hemant Kumar Srivastava
MOLECULAR DIVERSITY
(2020)
Article
Biochemistry & Molecular Biology
Suyash Pant, Meenakshi Singh, V. Ravichandiran, U. S. N. Murty, Hemant Kumar Srivastava
Summary: The study identified potential protease inhibitors against SARS-CoV-2 using computational approaches, screening compounds from various databases and conducting docking and molecular dynamics simulations to find promising drugs.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2021)
Article
Chemistry, Inorganic & Nuclear
Vinay Arora, Moumita Dutta, Kanu Das, Babulal Das, Hemant Kumar Srivastava, Akshai Kumar
Article
Chemistry, Organic
Dipanjan Bhattacharyya, Bikash Kumar Sarmah, Sekhar Nandi, Hemant Kumar Srivastava, Animesh Das
Summary: A phosphine-free pincer ruthenium(III) catalyzed beta-alkylation of secondary alcohols with primary alcohols to alpha-alkylated ketones and beta-branched ketones from two different secondary alcohols is reported. This environmentally friendly and atom efficient transformation produces only H2O and H-2 gas as byproducts. The protocol has been successfully scaled up to gram-scale reactions and applied to the functionalization of complex vitamin E and cholesterol derivatives.
Article
Biochemistry & Molecular Biology
N. R. Jena, Suyash Pant, Hemant Kumar Srivastava
Summary: This study explores the mechanisms of inhibiting the RNA-dependent RNA polymerase (RdRp) responsible for virus replication using molecular docking, MD simulations, and MM/GBSA techniques. It finds that Remdesivir (RDV) and Remdesivir monophosphate (RMP) have different effects on RdRp, while artificially expanded genetic information systems (AEGISs) may serve as novel therapeutic candidates against SARS-CoV-2.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Chemistry, Physical
Kanu Das, Eileen Yasmin, Babulal Das, Hemant Kumar Srivastava, Akshai Kumar
CATALYSIS SCIENCE & TECHNOLOGY
(2020)
Article
Chemistry, Multidisciplinary
Sangh Priya Singh, Shashank Tripathi, Anamika Yadav, Ruchir Kant, Hemant Kumar Srivastava, Ajay Kumar Srivastava
CHEMICAL COMMUNICATIONS
(2020)
Article
Chemistry, Multidisciplinary
Moumita Dutta, Kanu Das, Siriyara Jagannatha Prathapa, Hemant Kumar Srivastava, Akshai Kumar
CHEMICAL COMMUNICATIONS
(2020)
Article
Nanoscience & Nanotechnology
Jumi Deka, Kundan Saha, Suresh Kumar, Hemant Kumar Srivastava, Kalyan Raidongia
ACS APPLIED NANO MATERIALS
(2019)
Article
Chemistry, Multidisciplinary
Debojit Bhattacherjee, Abu Sufian, Sulendar K. Mahato, Samiyara Begum, Kaustav Banerjee, Sharmistha De, Hemant Kumar Srivastava, Krishna P. Bhabak
CHEMICAL COMMUNICATIONS
(2019)