Article
Chemistry, Multidisciplinary
Mouad Lahyaoui, Hafsa El-Idrissi, Taoufiq Saffaj, Bouchaib Ihssane, Nabil Saffaj, Rachid Mamouni, Youssef Kandri Rodi
Summary: In this study, 28 compounds derived from phosphorus-substituted quinoline were investigated for their anti-proliferative activity and binding affinity with proteins related to lung, ovarian, and kidney malignancies. The results suggest that these compounds could be valuable models for the development of more effective anticancer prospects.
ARABIAN JOURNAL OF CHEMISTRY
(2023)
Article
Chemistry, Medicinal
Smriti Sharma, Brij K. Sharma, Surabhi Jain, Puja Gulyani
Summary: This study investigates the use of pyrimidine-based antimicrobial agents for their rapid antimicrobial action. The 2D quantitative structure-activity relationship analysis and docking analysis were performed to identify the compounds with good binding affinity towards Penicillin-binding protein (PBP2a). The results show that compounds 4, 11, and 24 exhibit strong binding affinity towards PBP2a.
LETTERS IN DRUG DESIGN & DISCOVERY
(2022)
Article
Materials Science, Multidisciplinary
Taiwo W. Quadri, Lukman O. Olasunkanmi, Ekemini D. Akpan, Omolola E. Fayemi, Han-Seung Lee, Hassane Lgaz, Chandrabhan Verma, Lei Guo, Savas Kaya, Eno E. Ebenso
Summary: In this study, predictive models for the anticorrosion abilities of pyridazine-based compounds were developed using QSAR, and the essential molecular descriptors of the pyridazines were related to their experimental inhibition efficiencies. The results showed that the ANN model outperformed the MLR model in predicting the anticorrosion abilities of the pyridazine compounds.
MATERIALS TODAY COMMUNICATIONS
(2022)
Review
Biochemical Research Methods
Sanjoy Singh Ningthoujam, Rajat Nath, Sibashish Kityania, Pranab Behari Mazumder, Manabendra Dutta Choudhury, Anupam Das Talukdar, Lutfun Nahar, Satyajit D. Sarker
Summary: This study demonstrates various descriptor selection procedures and regression diagnostics methods that can be used in quantitative structure-activity relationship (QSAR) studies. The results showed that the Boruta approach and genetic algorithm were more effective in selecting potential independent variables, and regression diagnostics using R software helped identify and diagnose model errors, ensuring the reliability of QSAR models. This study provides a accessible and customizable approach for researchers to select appropriate descriptors and diagnose errors in QSAR studies.
PHYTOCHEMICAL ANALYSIS
(2023)
Article
Biochemistry & Molecular Biology
Afaf Zekri, Dalal Harkati, Samir Kenouche, Basil A. Saleh, Radwan Alnajjar
Summary: This study provides a detailed investigation of the interaction between Selective Estrogen Receptor Down-Regulators (SERDs) and Estrogen Receptor alpha (ER alpha) using various methods including quantitative structure-activity relationship, molecular docking, and molecular dynamics simulation. The study establishes an empirical model with better predictive capability and explores the binding mechanism between the compounds and ER alpha. The findings contribute to predicting the anticancer activities of the SERD compounds and improving our understanding of their action mechanism with ER alpha.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Chemistry, Organic
B. Pandit, Y. Vaishnav, S. Bahadur, T. Satapathy
Summary: To address the challenges in treating Mycobacterium tuberculosis, the development of safe medications with novel mechanisms of action is necessary. Utilizing multiple linear regression, partial least squares, and k-nearest neighbor molecular field analysis, 2D and 3D-QSAR models were created and validated. The 2D-QSAR model can explain 85.07% of the total variance, with internal prediction capacity of 77.65% and external prediction capacity of 83.64%. The 3D-QSAR model demonstrates statistical significance and has a predictive capacity of 78.43%. These robust QSAR models are expected to provide an excellent option for drug design.
INDIAN JOURNAL OF HETEROCYCLIC CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
K. D. Asgaonkar, S. M. Patil, T. S. Chitre, S. D. Wani, M. T. Singh
Summary: Tuberculosis is a major global health concern, with drug resistance and HIV co-infections posing significant challenges. This study utilized 2D and 3D QSAR to design new antitubercular drug analogues. The models generated provided insights into key structural requirements for optimizing pharmacophore and guiding future drug discovery efforts.
BULLETIN OF THE UNIVERSITY OF KARAGANDA-CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Prosper Obed Chukwuemeka, Haruna Isiyaku Umar, Opeyemi Iwaloye, Oluwaseyi Matthew Oretade, Christopher Busayo Olowosoke, Oyeyemi Janet Oretade, Michael Omoniyi Elabiyi
Summary: The dysregulation of cyclin-CDK6 interactions has been implicated in human breast cancer, and ATP-competitive inhibitors have been employed for managing breast cancer. In this study, selective predictive models for identifying potent CDK6 inhibitors against human breast cancer cell-lines were established using a dataset of 1,3,4-thiadiazole derivatives. Newly designed compounds, such as C16, showed promising pharmacological activity and selectivity for CDK6, potentially serving as therapeutic options for breast cancer treatment.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Proceedings Paper
Computer Science, Interdisciplinary Applications
Chandrasekhar Gopalakrishnan, Caixia Xu, Yanran Li, Vinutha Anandhan, Sanjay Gangadharan, Meshach Paul, Chandra Sekar Ponnusamy, Rajasekaran Ramalingam, Pengyong Han, Zhengwei Li
Summary: This paper presents a tannin-based QSAR and machine learning pipeline, which uses quantum semi-empirical descriptors and feature selection with a nonlinear artificial neural network. The model achieved good performance in predicting the antioxidant activity of tannins, providing guidance for tannin-based therapeutic design in the future.
INTELLIGENT COMPUTING THEORIES AND APPLICATION, ICIC 2022, PT II
(2022)
Article
Chemistry, Multidisciplinary
Alessandra Biancolillo, Luca Mennitti, Martina Foschi, Federico Marini
Summary: A QSAR model was developed to determine gut permeability of 228 pharmacological drugs under different pH conditions. Molecular descriptors were computed and classification models were calculated using PLS-DA. The models showed high predictive capability with correct classification rates between 80% and 96% in external validation. A feature selection approach, covariance selection, was used to improve predictions and identify the most relevant descriptors for discrimination, which were associated with 2D and 3D structures.
APPLIED SCIENCES-BASEL
(2022)
Article
Biochemistry & Molecular Biology
Utsab Debnath, Saroj Verma, Pankaj Singh, Kavita Rawat, Satish K. Gupta, Raj K. Tripathi, Hefazat H. Siddiqui, Seturam B. Katti, Yenamandra S. Prabhakar
CHEMICAL BIOLOGY & DRUG DESIGN
(2015)
Article
Biochemistry & Molecular Biology
Saroj Verma, Yenamandra S. Prabhakar
CURRENT MEDICINAL CHEMISTRY
(2015)
Article
Chemistry, Medicinal
Saroj Verma, Utsab Debnath, Pooja Agarwal, Kumkum Srivastava, Yenamandra S. Prabhakar
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2015)
Article
Biochemistry & Molecular Biology
Ruchi Saxena, Garima Gupta, Murli Manohar, Utsab Debnath, Pooja Popli, Yenamandra S. Prabhakar, Rituraj Konwar, Sandeep Kumar, Atul Kumar, Anila Dwivedi
INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY
(2016)
Article
Chemistry, Multidisciplinary
Saroj Verma, Shashi Pandey, Pooja Agarwal, Pravesh Verma, Shreekant Deshpande, Jitendra Kumar Saxena, Kumkum Srivastava, Prem M. S. Chauhan, Yenamandra S. Prabhakar
Article
Immunology
R. F. Kamil, U. Debnath, S. Verma, Y. S. Prabhakar
CURRENT HIV RESEARCH
(2018)
Article
Chemistry, Medicinal
Smriti Sharma, Mohammad Saquib, Saroj Verma, Nripendra N. Mishra, Praveen K. Shukla, Ranjana Srivastava, Yenamandra S. Prabhakar, Arun K. Shaw
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2014)
Article
Biochemistry & Molecular Biology
Utsab Debnath, Saroj Verma, Surabhi Jain, Setu B. Katti, Yenamandra S. Prabhakar
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
(2013)
Article
Biochemistry & Molecular Biology
Viney Kumar, Manish K. Gupta, Gagandip Singh, Yenamandra S. Prabhakar
JOURNAL OF ENZYME INHIBITION AND MEDICINAL CHEMISTRY
(2013)
Article
Chemistry, Medicinal
Gagandip Singh, Manish K. Gupta, Viney Kumar, Yenamandra S. Prabhakar
MEDICINAL CHEMISTRY
(2013)
Article
Multidisciplinary Sciences
Ruchi Saxena, Vishal Chandra, Murli Manohar, Kanchan Hajela, Utsab Debnath, Yenamandra S. Prabhakar, Karan Singh Saini, Rituraj Konwar, Sandeep Kumar, Kaling Megu, Bal Gangadhar Roy, Anila Dwivedi
Article
Biochemistry & Molecular Biology
Varun Dewaker, Pratik Narain Srivastava, Saroj Verma, Yenamandra S. Prabhakar
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2020)
Article
Biochemistry & Molecular Biology
Varun Dewaker, Ajay K. Srivastava, Ashish Arora, Yenamandra S. Prabhakar
Summary: Histone deacetylases are important enzymes in cellular homeostasis, with HDAC8 being a potential anticancer drug target. By analyzing the ligand sub-structures of HDAC8, new compounds were designed and tested through molecular dynamics simulations, with NC-VI showing the best energy profile for potential use in cancer therapy.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2021)
Article
Biochemistry & Molecular Biology
Varun Dewaker, Pratik Narain Srivastava, Saroj Verma, Ajay K. Srivastava, Yenamandra S. Prabhakar
Summary: The study focused on designing inhibitors with strong affinity in the active site pocket through analyzing protein-ligand interactions at an atomic level. Various structural modifications were attempted based on nonbonding energies (NBEs) calculations, with phenyl moieties identified as the main structural scaffold for improvements. The results showed promising NBEs for new compounds designed, indicating potential for developing improved HDAC2 inhibitors.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biochemistry & Molecular Biology
Utsab Debnath, Amrita Mitra, Varun Dewaker, Yenamandra S. Prabhakar, Raghu Tadala, Kiran Krishnan, Padmakar Wagh, Umashankar Velusamy, Aastha Baliyan, Anura V. Kurpad, Parthasarathi Bhattacharyya, Amit Kumar Mandal
Summary: The spike protein is used to target the human ACE2 receptor for viral fusion into human cells. Interestingly, N-acetyl cysteine can inhibit this viral fusion process by increasing the likelihood of structural deformation of the spike protein. This process may indirectly decrease the intermolecular binding affinity between two enzymes.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Chemistry, Medicinal
Shuang Mei, Su Jiang, Yuting Wang, Han Jing, Peng Yang, Miao-Miao Niu, Jindong Li, Kai Yuan, Yan Zhang
Summary: This study identifies a dual-targeting peptide, AP-1, that effectively inhibits variants of concern (VOCs) of SARS-CoV-2 without impairing host cell viability. The findings suggest that AP-1 could be a promising broad-spectrum agent for treating emerging VOCs of SARS-CoV-2.
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2024)
Article
Chemistry, Medicinal
Hyeonjun Lee, Ju Yeon Lee, Hyunsoo Jang, Hye Young Cho, Minhee Kang, Sang Hyun Bae, Suin Kim, Eunji Kim, Jaebong Jang, Jin Young Kim, Young Ho Jeon
Summary: By using liquid chromatography-tandem mass spectrometry and nuclear magnetic resonance experiments, we identified new chemical moieties that bind to the target sites of the protein of interest, allowing for reversible binding and protein degradation. This method has the potential to expand the application of PROTAC technology.
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2024)
Article
Chemistry, Medicinal
Yingying Li, Xiyou Du, Xinru Kong, Yuelin Fang, Zhijing He, Dongzhu Liu, Hang Wu, Jianbo Ji, Xiaoye Yang, Lei Ye, Guangxi Zhai
Summary: This study proposes a novel nanoplatform based on the autophagy cascade to overcome the obstacles in chemo-immunotherapy. The platform combines chemotherapy and starvation therapy to initiate pro-death autophagy and enhance antigen presentation, while also remodeling the immunosuppressive tumor microenvironment. Furthermore, the study discovers a new therapeutic direction for the respiration inhibitor 3-bromopyruvic acid (3BP) in cancer treatment. Overall, this study offers an opportunity to improve antitumor efficacy and boost immune responses.
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2024)
Article
Chemistry, Medicinal
Bingsi Wang, Mingxu Ma, Yusen Dai, Pengfei Yu, Liang Ye, Wenyan Wang, Chunjie Sha, Huijie Yang, Yingjie Yang, Yunjing Zhu, Lin Dong, Shujuan Wei, Linlin Wang, Jingwei Tian, Hongbo Wang
Summary: Breast cancer is a common malignant tumor in women, and drug resistance remains a clinical challenge. In this study, a novel compound, G-5b, was developed with potent antagonistic and degradation activities comparable to the current drug fulvestrant. G-5b also showed improved stability and solubility. Mechanistically, G-5b engages the proteasome pathway to degrade ER, inhibiting the ER signaling pathway and inducing apoptosis and cell cycle arrest. In animal models, G-5b exhibited superior pharmacokinetics and pharmacodynamics properties. Overall, G-5b is a promising long-acting SERD worthy of further investigation and optimization.
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2024)
Article
Chemistry, Medicinal
Karoline B. Waitman, Larissa C. de Almeida, Marina C. Primi, Jorge A. E. G. Carlos, Claudia Ruiz, Thales Kronenberger, Stefan Laufer, Marcia Ines Goettert, Antti Poso, Sandra V. Vassiliades, Vinicius A. M. de Souza, Monica F. Z. J. Toledo, Neuza M. A. Hassimotto, Michael D. Cameron, Thomas D. Bannister, Leticia Costa-Lotufo, Joa o A. Machado-Neto, Mauricio T. Tavares, Roberto Parise-Filho
Summary: A series of hybrid inhibitors combining pharmacophores of known kinase inhibitors and benzohydroxamate HDAC inhibitors were synthesized and evaluated for their anticancer activity and pharmacokinetic properties. Compounds 4d-f exhibited promising cytotoxicity against hematological cells and moderate activity against solid tumor models. Compound 4d showed potent inhibition of multiple kinase targets and had stable interactions with HDAC and members of the JAK family. These compounds showed selective cytotoxicity with minimal effects on non-tumorigenic cells and favorable pharmacokinetic profiles.
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2024)
Article
Chemistry, Medicinal
Michal Sulik, Diana Fontinha, Dietmar Steverding, Szymon Sobczak, Michal Antoszczak, Miguel Prudencio, Adam Huczynski
Summary: This study describes the synthesis of the first-in-class ivermectin derivatives obtained through derivatization of the C13 position, along with the unexpected rearrangement of the macrolide ring. These derivatives show potential for antiparasitic activity and are important for the development of new antiparasitic agents.
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2024)
Article
Chemistry, Medicinal
Jun Liu, Qiu-Xian Chen, Wen-Fu Wu, Dong Wang, Si -Yu Zhao, Jia-Hao Li, Yi-Qun Chang, Shao-Gao Zeng, Jia-Yi Hu, Yu-Jie Li, Jia-Xin Du, Shu-Meng Jiao, Hai-Chuan Xiao, Qiang Zhang, Jun Xu, Jian-Fu Zhao, Hai -Bo Zhou, Yong-Heng Wang, Jian Zou, Ping-Hua Sun
Summary: A new anti-infective drug strategy has been discovered to attenuate virulence and modulate inflammation caused by drug-resistant Pseudomonas aeruginosa infections. Compound 5f inhibits biofilm formation, macrophage migration, and inflammatory response induced by P. aeruginosa, showing potential as a novel candidate against drug-resistant infections.
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2024)
Article
Chemistry, Medicinal
Liuzeng Chen, Ke Wang, Lingyun Wang, Wei Wang, Lifan Wang, Jia Li, Xiaohan Liu, Mengya Wang, Banfeng Ruan
Summary: In this study, a series of novel anti-inflammatory compounds were designed and synthesized based on the natural product pterostilbene skeleton. Among them, compound 8 showed the highest activity and exhibited its effects through inhibition of pro-inflammatory cytokines by blocking the NF-KB/MAPK signaling pathway. Compound 8 also demonstrated a good relieving effect on acute colitis in mice and showed good safety in acute toxicity experiments.
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2024)
Article
Chemistry, Medicinal
Si-Min Liang, Gui-Bin Liang, Hui-Ling Wang, Hong Jiang, Xian-Li Ma, Jian-Hua Wei, Ri-Zhen Huang, Ye Zhang
Summary: A series of novel multi-target antitumor agents were designed, synthesized, and evaluated. Some compounds exhibited significant antitumor activity and one compound showed excellent efficacy, limited toxicity, and low resistance. Further mechanism studies revealed that the compound exerted antitumor effects through multiple pathways.
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2024)
