Article
Biochemistry & Molecular Biology
Xiaojiao Zheng, Chenchen Wang, Na Zhai, Xiaogang Luo, Genyan Liu, Xiulian Ju
Summary: The study investigated a novel series of imidazo[1,2-a]-pyridine derivatives for their binding modes in the GABA(A) receptor binding pocket using various methods. The results provide important information for the development of novel drugs with antipsychotic activities.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Medicinal
Riham M. Bokhtia, Adel S. Girgis, Tarek S. Ibrahim, Fatma Rasslan, Eman S. Nossier, Reham F. Barghash, Rajeev Sakhuja, Eatedal H. Abdel-Aal, Siva S. Panda, Amany M. M. Al-Mahmoudy
Summary: The development of new antibiotics using known scaffolds through molecular hybridization is an effective strategy. In this study, researchers synthesized diverse linezolid conjugates and identified one with promising antibacterial activity. They also developed QSAR and 3D-pharmacophore models to evaluate the drug-like properties of the synthesized compounds.
Article
Chemistry, Medicinal
Stefan Michael Kohlbacher, Matthias Schmid, Thomas Seidel, Thierry Langer
Summary: Pharmacophores are abstract representations of stereoelectronic molecular features used for modeling ligand-receptor interactions and widely applied in fast virtual screening. While much effort has been made to enhance the computational efficiency of the screening process, little attention has been given to automated procedures for optimizing pharmacophores with higher discriminatory power. In this study, an algorithm is proposed that automatically selects features driving pharmacophore model quality using SAR information from validated QPhAR models, leading to a fully automated method for deriving high-quality pharmacophores. Additionally, the QPhAR-generated models are shown to provide insights into (un-)favorable interactions for compounds of interest, guiding researchers.
Article
Chemistry, Multidisciplinary
Stefan M. Kohlbacher, Thierry Langer, Thomas Seidel
Summary: QSAR methods are commonly used in drug discovery, where pharmacophores provide advantageous properties for building quantitative SAR models that can generalize to different datasets with low requirements.
JOURNAL OF CHEMINFORMATICS
(2021)
Review
Biochemistry & Molecular Biology
Marcel P. Goldschen-Ohm
Summary: This article reviews the mechanistic interpretations of functional and structural evidence for the action of benzodiazepines on GABA(A)(alpha 1)(2)(beta X)(2)(gamma 2)(1) receptors.
Article
Biochemistry & Molecular Biology
Vijay H. Masand, Sami A. Al-Hussain, Mithilesh M. Rathore, Sumer D. Thakur, Siddhartha Akasapu, Abdul Samad, Aamal A. Al-Mutairi, Magdi E. A. Zaki
Summary: In this study, a comprehensive quantitative structure-activity relationship (QSAR) analysis was conducted using 561 structurally diverse aurora kinase B inhibitors. The resulting QSAR model showed high statistical performance and successfully identified key pharmacophoric features for inhibiting AKB.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Avinash Kumar, Paridhi Agarwal, Ekta Rathi, Suvarna G. Kini
Summary: Human carbonic anhydrase is a type of metalloenzyme that can catalyze the hydration of carbon dioxide. Certain isoforms of this enzyme are highly expressed in the brain during seizure activity, making them potential targets for antiepileptic drugs. Through computational tools, we have identified and studied some potential inhibitors of a specific isoform of carbonic anhydrase.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Chemistry, Physical
Won Jung Lee, H. Shaun Kwak, Deuk-rak Lee, Chunrim Oh, Eul Kgun Yum, Yuling An, Mathew D. Halls, Chi-Wan Lee
Summary: A new accelerated design scheme for photoinitiators based on an advanced machine learning framework is studied, with over 120 unique oxime ester compounds synthesized and measured for their photosensitivity. An automated machine learning algorithm is used to rapidly identify the best QSPR models and predict photosensitivity. The top-performing models offer clear direction for designing new photoinitiators and three new compounds were successfully synthesized and evaluated as novel photoinitiators, confirming high photosensitivity.
CHEMISTRY OF MATERIALS
(2022)
Article
Chemistry, Medicinal
Mona F. Said, Hanan H. Georgey, Eman R. Mohammed
Summary: The newly synthesized oxadiazolo and thiadiazolo fused pyrimidinones demonstrate promising analgesic properties and excellent pharmacokinetic properties. Among them, the methoxyphenyl piperazinyl derivative 3d shows outstanding analgesic and anti-inflammatory activity.
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2021)
Article
Chemistry, Medicinal
M. del Carmen Salazar-Lopez, J. Alberto Guevara-Salazar, Monica G. Arellano-Mendoza, Hugo A. Jimenez-Vazquez, Adriana Benavides, Delia Quintana-Zavala
Summary: This study aimed to propose the structural requirements of voltage-dependent sodium channel blockers through a quantitative structure-activity relationship analysis of anticonvulsant drugs. The results showed that polarity, basicity, and electronic density of the drugs are important factors affecting their biological activity as blockers. Derivation of urea is essential for drug activity, which can be in the form of homologues or vinylogues at the ends of the molecule.
MEDICINAL CHEMISTRY
(2021)
Review
Pharmacology & Pharmacy
Ratul Bhowmik, Ajay Manaithiya, Bharti Vyas, Ranajit Nath, Kamal A. Qureshi, Seppo Parkkila, Ashok Aspatwar
Summary: This article discusses various techniques used in tuberculosis drug discovery, including computational approaches. It introduces different databases, methods, approaches, and software used in conducting QSAR, pharmacophore modeling, and molecular docking. The important molecules discovered using these computational approaches and drugs in clinical trials for tuberculosis are also discussed. Finally, the challenges and future perspectives of these techniques in drug discovery are summarized.
FRONTIERS IN PHARMACOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Reem Aljanabi, Lina Alsous, Dima A. Sabbah, Halise Inci Gul, Mustafa Gul, Sanaa K. Bardaweel
Summary: Monoamine oxidases (MAOs) are oxidative enzymes responsible for converting biogenic amines into aldehydes and ketones. Distorted activity of MAOs has been linked to neurological diseases, and recent studies have found unexpected roles of MAOs in tumor progression and metastasis. Chemical inhibition of MAOs may be a valuable therapeutic approach for cancer treatment.
Article
Biochemistry & Molecular Biology
Sonu Benny, Prayaga Rajappan Krishnendu, Sunil Kumar, Vaishnav Bhaskar, Deepthi S. Manisha, Mohamed A. Abdelgawad, Mohammed M. Ghoneim, Ibrahim A. Naguib, Leena. K. Pappachen, Subin Mary Zachariah, Bijo Mathew, T. P. Aneesh
Summary: In this study, reliable models were generated and promising molecules were identified by combining QSAR modelling with the pharmacophore hypothesis-generating technique. The identified molecules were screened, and their chemical features for TS inhibitors were explored.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
Lu Huang, Xulong Wu, Xiaoli Fu, Haoxiang Wang, Biao Tang, Yirong Xiao, Caixia Zhou, Zhiqiao Zhao, Yujun Wan, Hui Chen, Zizhong Tang, Huipeng Yao, Zhi Shan, Tongliang Bu
Summary: In this study, a combination of structure-based drug carriers and molecular docking-based virtual screening was used to screen new potential FGFR1 inhibitors, providing a new approach for further research to explore better therapeutic effects in cancer treatment.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biochemistry & Molecular Biology
Sowmya Andole, Gouthami Thumma, Rajasekhar Reddy Alavala, Kiran Gangarapu
Summary: The present work aimed to develop a Field-based 3D-QSAR model using existing JAK-2 inhibitors. The JAK-STAT pathway is known to be involved in autoimmune diseases and myeloproliferative diseases. A Field-based 3D QSAR model was developed to determine the inhibitory potential of ligands. Virtual screening and molecular docking were performed to validate the results. The study showed the potential for discovering new JAK-2 inhibitors using the developed 3D QSAR model.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Chemistry, Physical
Ahmet Mentes, Nan-Jie Deng, R. S. K. Vijayan, Junchao Xia, Emilio Gallicchio, Ronald M. Levy
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2016)
Article
Biochemistry & Molecular Biology
Nanjie Deng, William F. Flynn, Junchao Xia, R. S. K. Vijayan, Baofeng Zhang, Peng He, Ahmet Mentes, Emilio Gallicchio, Ronald M. Levy
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
(2016)
Article
Biochemistry & Molecular Biology
Allan Haldane, William F. Flynn, Peng He, R. S. K. Vijayan, Ronald M. Levy
Article
Biochemistry & Molecular Biology
Ansuman Biswas, Arpit Shukla, R. S. K. Vijayan, Jeyaraman Jeyakanthan, Kanagaraj Sekar
JOURNAL OF STRUCTURAL BIOLOGY
(2017)
Article
Biochemistry & Molecular Biology
Joseph D. Bauman, Disha Patel, Steven F. Baker, R. S. K. Vijayan, Amy Xiang, Ajit K. Parhi, Luis Martinez-Sobrido, Edmond J. LaVoie, Kalyan Das, Eddy Arnold
ACS CHEMICAL BIOLOGY
(2013)
Article
Microbiology
Partha Palit, Abhijit Hazra, Arindam Maity, R. S. K. Vijayan, Prabu Manoharan, Sukdeb Banerjee, Nirup B. Mondal, Nanda Ghoshal, Nahid Ali
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2012)
Article
Biochemistry & Molecular Biology
Ajit K. Parhi, Amy Xiang, Joseph D. Bauman, Disha Patel, R. S. K. Vijayan, Kalyan Das, Eddy Arnold, Edmond J. LaVoie
BIOORGANIC & MEDICINAL CHEMISTRY
(2013)
Article
Chemistry, Medicinal
R. S. K. Vijayan, Neha Trivedi, Sudipendra Nath Roy, Indrani Bera, Prabu Manoharan, Pavan V. Payghan, Dhananjay Bhattacharyya, Nanda Ghoshal
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2012)
Article
Chemistry, Medicinal
Joseph D. Bauman, Disha Patel, Chhaya Dharia, Marc W. Fromer, Sameer Ahmed, Yulia Frenkel, R. S. K. Vijayan, J. Thomas Eck, William C. Ho, Kalyan Das, Aaron J. Shatkin, Eddy Arnold
JOURNAL OF MEDICINAL CHEMISTRY
(2013)
Article
Biochemistry & Molecular Biology
R. S. K. Vijayan, Dhananjay Bhattacharyya, Nanda Ghoshal
JOURNAL OF MOLECULAR MODELING
(2012)
Article
Chemistry, Physical
Nanjie Deng, Stefano Forli, Peng He, Alex Perryman, Lauren Wickstrom, R. S. K. Vijayan, Theresa Tiefenbrunn, David Stout, Emilio Gallicchio, Arthur J. Olson, Ronald M. Levy
JOURNAL OF PHYSICAL CHEMISTRY B
(2015)
Article
Biochemistry & Molecular Biology
R. S. K. Vijayan, Eddy Arnold, Kalyan Das
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2014)
Article
Chemistry, Medicinal
Hye Yeon Sagong, Ajit Parhi, Joseph D. Bauman, Disha Patel, R. S. K. Vijayan, Kalyan Das, Eddy Arnod, Edmond J. LaVoie
ACS MEDICINAL CHEMISTRY LETTERS
(2013)
Correction
Oncology
Jacqulyne P. Robichaux, Yasir Y. Elamin, R. S. K. Vijayan, Monique B. Nilsson, Lemei Hu, Junqin He, Fahao Zhang, Marlese Pisegna, Alissa Poteete, Huiying Sun, Shuai Li, Ting Chen, Han Han, Marcelo Vailati Negrao, Jordi Rodon Ahnert, Lixia Diao, Jing Wang, Xiuning Le, Funda Meric-Bernstam, Mark Routbort, Brent Roeck, Zane Yang, Victoria M. Raymond, Richard B. Lanman, Garrett M. Frampton, Vincent A. Miller, Alexa B. Schrock, Lee A. Albacker, Kwok-kin Wong, Jason B. Cross, John V. Heymach
Article
Biochemistry & Molecular Biology
Qinfang Sun, Vijayan S. K. Ramaswamy, Ronald Levy, Nanjie Deng
Summary: This study focuses on designing small molecules to disrupt or enhance known protein-protein interactions, using a novel thermodynamic free energy cycle for rational design of allosteric inhibitors of HIV-1 integrase. The results obtained can inform the discovery of new allosteric inhibitors through dissecting the multifunctional mechanisms of existing compounds. The developed free energy protocol can be broadly applied to quantitatively study the effects of small molecules on modulating protein-protein interactions.