Article
Chemistry, Physical
Ankitkumar Patel, Hardik Bhatt, Bhumika Patel
Summary: This study carried out 3D-QSAR research on Tankyrase inhibitors using various techniques, providing significant insights for the design of novel quinazolinone derivatives as potent inhibitors.
JOURNAL OF MOLECULAR STRUCTURE
(2022)
Article
Biochemistry & Molecular Biology
Bhumi M. Shah, Sneha R. Sagar, Priti Trivedi
Summary: Researchers have identified DPP IV as a target for diabetes treatment, and 3D QSAR studies have helped to determine important structural features of triazole derivatives, leading to the design of novel compounds that may serve as promising DPP IV inhibitors for the treatment of diabetes.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Chemistry, Inorganic & Nuclear
Tong Jian-Bo, Feng Yi, Wang Tian-Hao, Zhang Xing
Summary: In this study, CoMFA, CoMSIA, and HQSAR techniques were utilized to investigate the important characteristic activities of thieno [2,3-d] pyrimidine derivatives for effective antitumor activity. Molecular docking was also employed to study the binding requirements between ligands and receptor proteins, showing promising results that can be used for designing anticancer drugs.
CHINESE JOURNAL OF STRUCTURAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Etibaria Belghalia, Mohamed Ouabane, Salma El Bahi, Hafiz Muzzammel Rehman, Abdelouahid Sbai, Tahar Lakhlifi, Mohammed Bouachrine
Summary: Acute myeloid leukemia, a serious condition affecting stem cells, can be treated using BRD4 inhibitors that suppress cell proliferation. Through molecular modeling techniques and simulation, this study revealed the structural elements and interaction mode of effective BRD4 inhibitors. The incorporation of bulky substituents on the pyridinone ring and hydrophobic/electrostatic substituents on the methoxy-substituted phenyl ring enhanced interactions with the BRD4 target, leading to improved oral bioavailability and non-toxic properties.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Chemistry, Inorganic & Nuclear
Tong Jian-Bo, Xiao Xue-Chun, Luo Ding, Xu Hai-Yin, Wang Jie
Summary: The study used HQSAR and Topomer CoMFA technology to analyze the QSAR of 39 isoquinolone derivatives, with results showing good stability and predictive ability. The Topomer search module was used to define high contribution fragments in the ZINC database and design new isoquinolone compounds with theoretically high inhibitory activity.
CHINESE JOURNAL OF STRUCTURAL CHEMISTRY
(2021)
Article
Chemistry, Inorganic & Nuclear
Chen Xiao-Zhong, Li Guang-Ping, Shen Yan, Hu Yong, Wang Juan, Wang Yuan-Qiang, Lin Zhi-Hua
Summary: This study utilized 3D-QSAR and molecular docking to investigate a series of EED inhibitors, establishing robust and predictive models, designing five new small molecules, and evaluating their ADME properties, providing theoretical guidance for the rational design of novel EED inhibitors.
CHINESE JOURNAL OF STRUCTURAL CHEMISTRY
(2021)
Article
Chemistry, Multidisciplinary
V. K. Vyas, S. Bhati, M. Sharma, P. Gehlot, N. Patel, S. Dalai
Summary: 2,4-Disubstituted quinoline derivatives were designed, synthesized, and evaluated for antimalarial activity based on a 3D-QSAR study. CoMFA and CoMSIA models were used on a dataset of 178 quinoline derivatives, and PLS analysis validated the results. 10 derivatives were synthesized and screened, with compounds #5 and #19 showing maximum reductions of 64% and 57% in parasitaemia level, respectively.
SAR AND QSAR IN ENVIRONMENTAL RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Amina Goudzal, Abdellah El Aissouq, Hicham El Hamdani, El Ghalia Hadaji, Abdelkrim Ouammou, Mohammed Bouachrine
Summary: In this study, a 3D-QSAR analysis was performed on a series of 2, 4, 5-trisubstituted imidazole derivatives to design potent kinase II alpha subunit (CK2) inhibitors. The COMFA and COMSIA models showed excellent performance with high Q(2) and R-2 values. The validity of the models was confirmed through various validation tests. The study's findings provide useful theoretical references for future experimental studies.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
Jian-Bo Tong, Shuai Bian, Xing Zhang, Ding Luo
Summary: A series of mIDH1 inhibitors derived from 3-pyrimidine-4-oxazolidin-2-ketone derivatives were studied by QSAR model to explore key factors inhibiting mIDH1 activity. The generated model was validated by Topomer CoMFA, HQSAR, and PLS methods, and ten new drug molecules were designed using Topomer search technology. The results of molecular docking and ADMET testing showed the effectiveness of the newly designed drug molecules, providing a theoretical basis for the design and validation of novel mIDH1 inhibitor anticancer drugs in the future.
MOLECULAR DIVERSITY
(2022)
Article
Pharmacology & Pharmacy
Yuwei Wang, Yifan Guo, Shaojia Qiang, Ruyi Jin, Zhi Li, Yuping Tang, Elaine Lai Han Leung, Hui Guo, Xiaojun Yao
Summary: In this study, the structure-activity relationships and binding modes of a series of anthraquinone derivatives targeting PGAM1 were investigated using 3D-QSAR, molecular docking, and molecular dynamics simulations, which showed satisfactory predictive ability. Molecular dynamics simulations revealed key residues and dominant interactions, as well as stable hydrogen bond formations during the ligand binding process. Overall, the study provided theoretical guidance for the design of new anthraquinone derivatives as PGAM1 inhibitors.
FRONTIERS IN PHARMACOLOGY
(2021)
Article
Food Science & Technology
Yijie Yang, Qi Tian, Shiming Li, Bo Li
Summary: In this study, 3D-QSAR analysis was performed to investigate the structure-activity relationship of collagen hydrolysate peptides. The results showed that Hyp, rather than Pro, had a greater impact on improving antiplatelet activity. The predicted peptide EOGE exhibited antiplatelet activity and inhibited thrombus formation.
Article
Chemistry, Multidisciplinary
Fangfang Wang, Wei Yang, Ran Li, Zhihai Sui, Guijuan Cheng, Bo Zhou
Summary: Through 3D-QSAR and molecular dynamics simulations, the structure-activity relationships and mechanism of actions of FAK inhibitors were investigated, predicting the inhibitory activities of novel inhibitors and guiding the optimization of FAK inhibitors with higher inhibitory activities.
ARABIAN JOURNAL OF CHEMISTRY
(2021)
Article
Chemistry, Inorganic & Nuclear
Tong Jian-Bo, Zhang Xing, Bian Shuai, Luo Ding
Summary: In this study, HQSAR and Topomer CoMFA methods were used to establish QSAR models for anti-HIV drugs targeting CCR5. Topomer search technology was utilized for molecular design. Through molecular docking and ADMET prediction, potential active residues A/ASN425, A/GLY198, and A/TRP427 were identified, and 40 newly designed anti-HIV drugs with main ADMET properties were proposed. These results provide a theoretical basis for future experimental verification of new compounds.
CHINESE JOURNAL OF STRUCTURAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Agata Zieba, Tuomo Laitinen, Jayendra Z. Patel, Antti Poso, Agnieszka A. Kaczor
Summary: The study successfully constructed 3D-QSAR CoMFA and CoMSIA models for a series of 31 FAAH inhibitors with 1,3,4-oxadiazol-2-one moiety, which showed good statistical parameters and were validated using various techniques. The field contributions in the CoMFA and CoMSIA models varied, influencing the ligand-enzyme interactions in different ways.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Multidisciplinary
Fangfang Wang, Wei Yang, Bo Zhou
Summary: In this study, a theoretical approach was used to investigate the structure-activity relationship and mechanism of action of novel GyrB inhibitors. The results demonstrated the stability and predictability of the CoMFA and CoMSIA models. Molecular docking and MD simulations revealed the key amino acids and binding modes at the active site. These findings provide valuable guidance for the discovery and design of new GyrB inhibitors.
ARABIAN JOURNAL OF CHEMISTRY
(2022)
Article
Chemistry, Medicinal
Sravani Pulya, Tarun Patel, Milan Paul, Nilanjan Adhikari, Suvankar Banerjee, Ganesh Routholla, Swati Biswas, Tarun Jha, Balaram Ghosh
Summary: A promising HDAC3 inhibitor with high potency and selectivity has been developed through the synthesis of a series of novel compounds. It exhibits strong cytotoxicity against cancer cells and minimal toxicity against normal cells. This compound also increases acetylation levels of specific proteins, induces cell cycle arrest and apoptosis, and modulates gene expression.
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2022)
Article
Chemistry, Medicinal
Sandip Kumar Baidya, Suvankar Banerjee, Nilanjan Adhikari, Tarun Jha
Summary: MMPs with medium-size S1' pockets are considered promising biomolecular targets in cancer, cardiovascular diseases, and neurodegenerative diseases. Despite the difficulty in designing selective MMPIs due to structural resemblance among these MMPs, the variability and uniqueness of their S1' pockets make them potential targets for selective MMPI design.
JOURNAL OF MEDICINAL CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
S. Banerjee, S. K. Baidya, N. Adhikari, T. Jha
Summary: This study conducted a comparative QSAR analysis to identify the structural components of benzothiazine-derived HDAC8 inhibitors and provided references for the development of potent HDAC8-selective inhibitors. The results validated the efficacy of diverse modelling techniques and predicted new molecules.
SAR AND QSAR IN ENVIRONMENTAL RESEARCH
(2022)
Review
Pharmacology & Pharmacy
Amit Kumar Halder, Soumya Mitra, Maria Natalia D. S. Cordeiro
Summary: This article reviews the recent developments in the design of multi-target drugs for the treatment of major depressive disorders. Case studies focusing on design strategies and challenges are discussed. The authors suggest exploring potential biological targets and utilizing computational modeling techniques for further research.
EXPERT OPINION ON DRUG DISCOVERY
(2023)
Article
Biochemistry & Molecular Biology
Suvankar Banerjee, Shristi Kejriwal, Balaram Ghosh, Goverdhan Lanka, Tarun Jha, Nilanjan Adhikari
Summary: Angiogenesis, mediated by VEGF, is crucial for tumor progression, invasion, and metastasis. Small molecule VEGFR-2 inhibitors have limited usage due to severe toxicities, therefore, novel and cost-effective inhibitors are needed. In this study, a set of thiourea-based inhibitors were analyzed using fragment-based QSAR, molecular docking, and molecular dynamics simulation to understand their structural attributes and binding pattern. The findings suggest that certain structural features are important for VEGFR-2 inhibition while others are detrimental. The study also explored the significance of urea and thiourea binding at the active site for future molecule design.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Chemistry, Physical
Suvankar Banerjee, Sandip Kumar Baidya, Nilanjan Adhikari, Balaram Ghosh, Tarun Jha
Summary: COVID-19 is a devastating global disease with high transmissibility and mutations, and the lack of potential therapeutics has made it a crisis. Natural molecules, such as glycyrrhizin and its derivatives, show promise as a therapeutic strategy against COVID-19. This review discusses the therapeutic implications of glycyrrhizin and its derivatives, as well as their potential role in traditional Chinese medicine. Derivatization of glycyrrhizin and combination therapy with other anti-SARS-CoV-2 agents could lead to the development of novel treatments for COVID-19.
JOURNAL OF MOLECULAR STRUCTURE
(2023)
Article
Chemistry, Multidisciplinary
S. Banerjee, S. K. Baidya, B. Ghosh, T. Jha, N. Adhikari
Summary: This study explored the structural and sub-structural fingerprints responsible for modulating MMP-9 inhibition through classification-dependent analysis. Based on these findings, new lead compounds were designed and validated, potentially serving as novel MMP-9 inhibitors in the future.
SAR AND QSAR IN ENVIRONMENTAL RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Jigme Sangay Dorjay Tamang, Suvankar Banerjee, Sandip Kumar Baidya, Balaram Ghosh, Nilanjan Adhikari, Tarun Jha
Summary: In this study, the crucial structural contributions of dibenzofuran and dibenzothiophene derivatives towards MMP-12 inhibitory activity were determined using 2D and 3D-QSAR techniques. The study identified that the carboxylic group enhances binding with catalytic Zn2+ ion, i-propyl sulfonamido carboxylic acid contributes positively towards MMP-12 inhibition, and the dibenzofuran moiety confers stable binding at the S1 & PRIME; pocket. Molecular docking and MD simulation studies revealed the stable and compact binding between these compounds at the MMP-12 active site. These findings can aid in the development of selective and potent lead molecules for MMP-12-associated diseases.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
Suvankar Banerjee, Shraddha Dumawat, Tarun Jha, Goverdhan Lanka, Nilanjan Adhikari, Balaram Ghosh
Summary: HDAC3 is an emerging target for the discovery of novel drug candidates against diseases including cancer. A machine learning method and chemical space exploration were used to analyze the structure of HDAC3 inhibitors and identify key features for HDAC3 inhibition.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Chemistry, Medicinal
Sravani Pulya, Ambati Himaja, Milan Paul, Nilanjan Adhikari, Suvankar Banerjee, Ganesh Routholla, Swati Biswas, Tarun Jha, Balaram Ghosh
Summary: HDAC3 modulation shows promise for breast cancer treatment, particularly for triple-negative cases. Novel pyrazino-hydrazide-based HDAC3 inhibitors have been designed and synthesized, with lead compound 4i demonstrating potent HDAC3 inhibition and strong cytotoxicity against triple-negative breast cancer cells. Compound 4i also exhibits favorable pharmacokinetic properties and shows therapeutic efficacy in a tumor-bearing mouse model.
JOURNAL OF MEDICINAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Shuvam Sar, Soumya Mitra, Parthasarathi Panda, Subhash C. Mandal, Nilanjan Ghosh, Amit Kumar Halder, Maria Natalia D. S. Cordeiro
Summary: In this study, various in silico modeling approaches were used to investigate a diverse dataset of structurally distinct human soluble epoxide hydrolase (sEH) inhibitors. Predictive and validated models were developed to understand the structural requirements for achieving higher inhibitory potential. The results highlighted the important roles played by topological characteristics, 2D pharmacophore features, and specific physicochemical properties in enhancing inhibitory potential. The findings from the QSAR modeling studies were validated using molecular dynamics (MD) simulations, providing crucial insights into receptor-ligand interactions.
Article
Chemistry, Multidisciplinary
S. K. Baidya, S. Banerjee, B. Ghosh, T. Jha, N. Adhikari
Summary: In this study, the impact of various structures and spatial attributes on MMP-2 inhibition was investigated through computational modeling methods. The study found that favorable steric, electrostatic, and hydrophobic substituents at the terminal phenyl ring play a crucial role in MMP-2 inhibition. Additionally, key amino acid residues and their stable binding interactions with the molecules were identified.
SAR AND QSAR IN ENVIRONMENTAL RESEARCH
(2023)
Article
Chemistry, Multidisciplinary
Suvankar Banerjee, Sandip Kumar Baidya, Balaram Ghosh, Suvendu Nandi, Mahitosh Mandal, Tarun Jha, Nilanjan Adhikari
Summary: In this study, a quantitative structural assessment of meprin beta inhibitors was performed using non-linear pattern recognition techniques and binding mode analysis. The study identified various structural attributes and designed highly effective inhibitors for meprin beta. Molecular dynamics simulation also confirmed the stability of these inhibitors at the active site. Therefore, this study provides valuable tools for identifying and designing potent inhibitors for meprin beta-related pathophysiological conditions.
NEW JOURNAL OF CHEMISTRY
(2023)
Review
Chemistry, Medicinal
Suvankar Banerjee, Sandip Kumar Baidya, Nilanjan Adhikari, Tarun Jha
Summary: This review investigates newer MMPIs patented after the COVID-19 period for an updated perspective on MMPIs. The study found a significant decrease in the number of new patent applications in the post-COVID-19 period, despite the disclosure of several MMP-related patents up to 2020. In addition to major MMPs, attention has recently been focused on other isoforms (such as MMP-3 and MMP-7) for drug development. The selectivity and bioavailability of isoforms are major concerns in the development of effective MMPIs. Theoretical approaches and experimental methodologies can be adopted to develop novel MMPIs with improved pharmacokinetic profiles. Extensive research on the role of MMPs in cancer and the mechanisms of such MMPs in other diseases is needed for the development of novel MMPIs.
EXPERT OPINION ON THERAPEUTIC PATENTS
(2023)
Article
Biochemical Research Methods
Sandip Kumar Baidya, Suvankar Banerjee, Balaram Ghosh, Tarun Jha, Nilanjan Adhikari
Summary: This study utilized classification-based QSAR techniques and fragment-based data mining to analyze different MMP-9 inhibitors, revealing the importance of certain molecular fragments in MMP-9 inhibition. These findings have implications for the development of effective MMP-9 inhibitors in the future.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2024)