Article
Biochemistry & Molecular Biology
Muthumanickam Sankar, K. Langeswaran, Sangavi Jeyachandran, Boomi Pandi
Summary: In this study, computational methods such as pharmacophore modeling, 3DQSAR, molecular docking, DFT, and molecular dynamic simulations were used to identify new, innovative, and effective potential inhibitors against Ebola virus. The results showed promising novel scaffolds with good predictive power and the best binding free energy and docking scores for potential inhibitors were determined through molecular docking and MM-GBSA analysis. Molecular dynamics simulations indicated stable ligand-protein complexes that may improve potent inhibitor development for Ebola viral treatment.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2021)
Article
Biochemistry & Molecular Biology
Ni Made Pitri Susanti, Sophi Damayanti, Rahmana Emran Kartasasmita, Daryono Hadi Tjahjono
Summary: This study aimed to identify potential CDK4/6 inhibitors through virtual screening of the ZINC15 compound database, resulting in two promising compounds, ZINC585292724 and ZINC585291674, based on their favorable binding energy and hydrogen bond stability.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Physical
Prayaga Rajappan Krishnendu, Sonu Benny, Sunil Kumar, Jayalakshmi Jayan, Vaishnav Bhaskar, Leena. K. Pappachen, T. P. Aneesh, Mohamed A. Abdelgawad, Mohammed M. Ghoneim, Orazio Nicolotti, Subin Mary Zachariah, Bijo Mathew
Summary: Anti-inflammatory medications are commonly used over-the-counter drugs due to their relation to inflammation and pain caused by various diseases. Extensive research is required to develop effective and safe anti-inflammatory therapies. A 3D-QSAR model was built using a pharmacophore hypothesis, and virtual screening was used to identify potential compounds for COX-2 inhibition.
JOURNAL OF MOLECULAR STRUCTURE
(2024)
Article
Medicine, Research & Experimental
Mahmoud Ganji, Shohreh Bakhshi, Alireza Shoari, Reza Ahangari Cohan
Summary: This study utilized pharmacophore and QSAR modeling to identify five potential FGFR3 inhibitors for bladder cancer treatment, which showed promising therapeutic properties and low toxicity levels.
JOURNAL OF TRANSLATIONAL MEDICINE
(2023)
Article
Biochemistry & Molecular Biology
P. M. Gurubasavaraja Swamy, Nahid Abbas, Prasad Sanjay Dhiwar, Ekta Singh, Abhishek Ghara, Arka Das
Summary: In this study, a 3D QSAR pharmacophore model was generated using substituted pyrimidine class of Aurora-A kinase inhibitors, revealing the crucial role of molecular features in inhibitory activity. Five potential compounds were identified through screening and docking, demonstrating their distinctive ability to inhibit Aurora-A kinase.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
Milica Radan, Dusan Ruzic, Mirjana Antonijevic, Teodora Djikic, Katarina Nikolic
Summary: This study combined ligand-based and target-based approaches to design novel potent 5-HT2AR antagonists. By conducting molecular dynamic simulations and molecular docking, bioactive conformations of the ligands and different conformations of the 5-HT2AR were obtained, leading to 3D-QSAR modelling and pharmacophore analysis, demonstrating the reliability and predictive power of the created model.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2021)
Article
Biochemistry & Molecular Biology
Ritu Jakhar, Alka Khichi, Dev Kumar, Kiran Sura, Mehak Bhoomika, Mehak Dangi, Anil Kumar Chhillar
Summary: This study highlights the global concern in the medical community regarding the rapid increase in antibiotic resistance. Novel antibacterial agents were developed through virtual screening and molecular docking methods, targeting DNA gyrase as a potential curative target for resistant bacterial strains. The top three compounds identified showed promising binding affinities and were further supported by molecular dynamics simulations.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Chemistry, Multidisciplinary
Na Zhai, Yanming Chen, Chenchen Wang, Fengshou Wu, Xiaogang Luo, Xiulian Ju, Hui Liu, Genyan Liu
Summary: Hyperuricemia is becoming more common and affecting younger populations worldwide. This study established pharmacophore models and performed molecular dynamics simulations to identify potential xanthine oxidase inhibitors. The findings provide useful information for the design and development of new drugs.
NEW JOURNAL OF CHEMISTRY
(2022)
Article
Chemistry, Physical
Swati Krishna, T. P. Krishna Murthy, G. Divyashri, Manikanta Murahari, Rohit Shukla, S. Birendra Kumar, Tiratha Raj Singh
Summary: The study designed drugs with anticancer potential by combining features of synthetic drugs and phytochemicals. Effective compounds were screened using ligand-based pharmacophore model and quantitative structure-activity relationship studies. Docking, ADMET, and molecular dynamics simulation studies confirmed the high activity and good stability of the identified compounds.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Biochemical Research Methods
V Divya, V. L. Pushpa
Summary: A study was conducted to generate and validate various categorical QSAR models for identifying molecules with drug-like properties in human breast cancer cells, ultimately selecting 25 potential lead molecules.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2021)
Article
Biochemistry & Molecular Biology
Vibhu Jha, Salvatore Galati, Valerio Volpi, Lidia Ciccone, Filippo Minutolo, Flavio Rizzolio, Carlotta Granchi, Giulio Poli, Tiziano Tuccinardi
Summary: ACLY is an important enzyme involved in fatty acid synthesis and could be a promising target for anticancer drug design. Through virtual screening, compound VS1 with potential inhibitory activity was identified, showing a 2.5 times higher potency than the reference inhibitor 2-hydroxycitrate.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2021)
Article
Biochemistry & Molecular Biology
Apoorva M. Kulkarni, Vikas Kumar, Shraddha Parate, Gihwan Lee, Sanghwa Yoon, Keun Woo Lee
Summary: This study used computational methods to screen potential KRAS G12D inhibitors and conducted analyses such as pharmacophore modeling, molecular docking, and molecular dynamics simulations. The results showed that four hit compounds have a strong affinity towards KRAS G12D and form stable interactions with key residues. These findings provide strong support for further in vitro testing.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Narimene Chahbaoui, Saida Khamouli, Marwa Alaqarbeh, Salah Belaidi, Leena Sinha, Samir Chtita, Mohammed Bouachrine
Summary: This study explores the potential of curcumin derivatives as pancreatic cancer therapy targets using computational approaches, and demonstrates the feasibility and effectiveness of this treatment method through modeling and experiments.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Chemistry, Physical
Xiao-Zhong Chen, Xiu-Yan Yu, Chen Dai, Qiu-Yang Huang, Yan Shen, Juan Wang, Yong Hu, Zhi-Hua Lin
Summary: This study identified novel potential CypD inhibitors through screening of the ZINC database and molecular docking, providing a basis for the treatment of acute pancreatitis.
JOURNAL OF MOLECULAR STRUCTURE
(2022)
Article
Biochemistry & Molecular Biology
Zhili Yin, Shaohui Liu, Xiaoyue Yang, Mengguo Chen, Jiangfeng Du, Hongmin Liu, Longhua Yang
Summary: In this study, virtual screening methods were used to identify potential novel compounds targeting the substrate-binding pocket of LSD1. Through drug-likeness evaluation, ADMET screening, molecular dynamics simulations, and binding free energy screening, one and four hit compounds were identified. These compounds can be categorized into two groups, amide and 1,2,4-triazolo-4,3-& alpha;-quinazoline. Among them, Compound 4 showed the strongest binding affinity. The study also revealed that van der Waals interactions and FAD play important roles in the binding mechanisms of the hit compounds.
Article
Biochemistry & Molecular Biology
Vipul Kumar, Jaspreet Kaur Dhanjal, Priyanshu Bhargava, Ashish Kaul, Jia Wang, Huayue Zhang, Sunil C. Kaul, Renu Wadhwa, Durai Sundar
Summary: A study examined the binding potential of natural compounds Withaferin-A, Withanone, and caffeic acid phenethyl ester to the cell surface receptor TMPRSS2 using molecular docking and molecular dynamics simulations. The results showed that Withanone had stronger interactions with TMPRSS2 and was able to induce changes in its allosteric site. Furthermore, Withanone downregulated TMPRSS2 mRNA expression, suggesting its potential dual action in blocking SARS-CoV-2 entry into host cells.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biochemistry & Molecular Biology
Rajkumar Singh Kalra, Vipul Kumar, Jaspreet Kaur Dhanjal, Sukant Garg, Xiaoshuai Li, Sunil C. Kaul, Durai Sundar, Renu Wadhwa
Summary: Research shows that withanolides derived from Ashwagandha have potential therapeutic effects against the SARS-CoV-2 virus by inhibiting the ACE2 protein. Among them, stem extracts demonstrate higher inhibitory potency.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Oncology
Rajkumar S. Kalra, Gaurav S. Soman, Pradeep B. Parab, Avinash M. Mali, Sagar S. Varankar, Rutika R. Naik, Swapnil C. Kamble, Jaspreet K. Dhanjal, Sharmila A. Bapat
Summary: The monoclonal antibody mAb150 targets cancer stem cells, promoting their reentry into the cell cycle and disrupting tumor dormancy, leading to effective tumor targeting.
TRANSLATIONAL ONCOLOGY
(2022)
Article
Oncology
Anissa Nofita Sari, Jaspreet Kaur Dhanjal, Ahmed Elwakeel, Vipul Kumar, Hazna Noor Meidinna, Huayue Zhang, Yoshiyuki Ishida, Keiji Terao, Durai Sundar, Sunil C. Kaul, Renu Wadhwa
Summary: A combination of low doses of Wi-A and CAPE, two natural compounds found in Ashwagandha leaves and propolis, respectively, exhibits potent anti-migratory and anti-angiogenic activities. This combination acts on cell adhesion/tight junction proteins and inhibits Wnt/β-catenin signaling pathways, leading to the downregulation of EMT-signaling proteins. These findings suggest that this combination may be a potential therapeutic option for metastatic and aggressive cancers.
Article
Biochemistry & Molecular Biology
Vidhi Malik, Navaneethan Radhakrishnan, Sunil C. Kaul, Renu Wadhwa, Durai Sundar
Summary: The study suggests that Withaferin-A and Withanone from Ashwagandha have potential as natural drugs for the treatment of Chronic Myeloid Leukemia. These compounds interact with the protein kinase ABL, and inhibition of ABL may contribute to their anticancer activity.
Article
Biochemistry & Molecular Biology
Navaneethan Radhakrishnan, Sunil C. Kaul, Renu Wadhwa, Durai Sundar
Summary: The development of drugs that selectively target cancer cells while being safe for normal cells is crucial in cancer treatment. This study used in silico molecular models to investigate the impact of phosphatidylserine (PS) exposure on the membrane permeation of natural compounds in cancer cells. The findings showed that PS exposure facilitated the permeation of certain compounds in cancer cell membranes, suggesting the potential of PS exposure-based models for studying drug selectivity in cancer cells.
Review
Biochemistry & Molecular Biology
Jaspreet Kaur Dhanjal, Rajkumar Singh Kalra
Summary: Cancer is a disease caused by perturbed genes, with driver mutations dictating the functional impacts and progression of the disease. Recently, there has been significant attention on identifying driver events from genomic alterations to develop precision cancer therapies. Predicting cancer drivers using genetic signatures and protein structures can provide more clinically relevant evidence than genetic variations alone.
CURRENT PROTEIN & PEPTIDE SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Dhvani Sandip Vora, Yugesh Verma, Durai Sundar
Summary: Efforts have been made to improve the efficiency and reduce the off-target effects of the CRISPR/Cas9 genome editing tool. By incorporating novel features, such as binding energy, better machine learning models have been developed for predicting Cas9 activity.
Article
Virology
Neha Quadir, Jasdeep Singh, Anwar Alam, Asrar Ahmad Malik, Syed Asad Rahman, Subhash Hira, Nasreen Zafar Ehtesham, Durai Sundar, Seyed Ehtesham Hasnain
Summary: The acquisition of multiple mutations, including immune-escape mutations, by Omicron allows it to maintain a selection advantage within the population. Despite lower hospitalization and death rates, the surges in Omicron variants can still offset public health measures and disrupt healthcare facilities. The BA.4/BA.5 variants are found to be more severe than the earlier-emerged Omicron variants. Active COVID-19 surveillance can help understand the evolution and transmission patterns of new variants. The sudden decline in reported cases in low- and middle-income countries needs to be addressed to prevent undetected spread.
Editorial Material
Genetics & Heredity
Jaspreet Kaur Dhanjal, Rajkumar Singh Kalra, Dhanendra Tomar, Amrendra K. Ajay
FRONTIERS IN GENETICS
(2023)
Article
Biochemistry & Molecular Biology
Dhvani Sandip Vora, Shashank Yadav, Durai Sundar
Summary: CRISPR/Cas9 technology allows precise genome editing and has contributed to various scientific and medical advancements. However, the unintentional off-target effects create a burden on the genome and hinder further research. Recent off-target prediction tools have used machine learning and deep learning techniques to better understand the potential off-targets, as the rules governing Cas9 activity are still not fully understood.
Article
Biochemical Research Methods
K. Ramki, G. Thiruppathi, Selva Kumar Ramasamy, P. Sundararaj, P. Sakthivel
Summary: A chromone-based ratiometric fluorescent probe L2 was developed for the selective detection of Hg(II) in a semiaqueous solution. The probe exhibited enhanced fluorescence in its aggregated state and even higher fluorescence when chelated with Hg(II). The probe demonstrated high sensitivity and specificity for Hg(II) detection and was successfully applied for imaging Hg(II) in a living model.
Article
Biochemical Research Methods
Qun Zhang, Rui Yang, Gang Liu, Shiyan Jiang, Jiarui Wang, Juqiang Lin, Tingyin Wang, Jing Wang, Zufang Huang
Summary: This research aims to develop a cost-effective and portable method for measuring creatinine levels using the enhanced Tyndall effect phenomenon. The method offers a promising solution for monitoring renal healthcare in resource-limited settings.