Article
Biochemistry & Molecular Biology
Ningning Fan, Steffen Hirte, Johannes Kirchmair
Summary: In this study, three strategies for maximizing the virtual screening performance of pairwise comparison methods for 2D and 3D molecular structures were explored. The integration of 2D and 3D methods using a parallel selection strategy showed the clearest advantages. The integrated approach yielded higher AUC values, EF1%, and SRR1% compared to using 2D and 3D methods separately with a single query molecule.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Mukesh Tandi, Nancy Tripathi, Animesh Gaur, Balasubramanian Gopal, Sandeep Sundriyal
Summary: Virtual screening is an important method in drug discovery that relies on a virtual library of compounds. Ugi reaction is a reliable multi-component reaction that produces a peptidomimetic scaffold, and recent research has renewed interest in it due to its potential for further chemical modifications. A library of small molecules derived from Ugi reaction was collated for virtual screening, and the analysis shows that these molecules are 'clean', drug-like, and have a structurally distinct space compared to FDA-approved oral drugs and inhibitors of protein-protein interactions. The molecules in this library consist of diverse ring systems, many of which have not been exploited for drug design, making it a valuable resource for virtual screening.
MOLECULAR DIVERSITY
(2022)
Article
Biochemistry & Molecular Biology
Oluwakemi Ebenezer, Maryam A. Jordaan, Nkululeko Damoyi, Michael Shapi
Summary: Noroviruses are non-enveloped viruses causing acute gastroenteritis in humans. The RNA-dependent RNA polymerase is a critical target for developing anti-norovirus agents. Compounds CID-57930781 and CID-44396095 show promising potential as human norovirus inhibitors.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Multidisciplinary
Sascha Jung, Helge Vatheuer, Paul Czodrowski
Summary: The article introduces an open-source command line tool for ligand-based virtual screening, which enables rapid screening of large compound databases to identify similar structures.
JOURNAL OF CHEMINFORMATICS
(2023)
Article
Chemistry, Multidisciplinary
Manuel S. Sellner, Amr H. Mahmoud, Markus A. Lill
Summary: In this study, a transformer model was trained to autoencode tokenized SMILES strings using a custom loss function that preserves similarities in latent space. By reducing the similarity between molecules to their Euclidian distance in latent space, the model can perform independent of the similarity metric it was trained on. The method was tested using 2D similarity and showed promise for high-content screening with time-consuming 3D similarity metrics.
JOURNAL OF CHEMINFORMATICS
(2023)
Article
Automation & Control Systems
Mridul Krishna Gogoi, Rituparna Chutia
Summary: Crop selection involves various risk factors, and probabilistic methods and possibilistic analysis can be used to evaluate these risks, with linguistic variables observed as fuzzy numbers. The goal of fuzzy risk analysis is to transform final risks into communicable linguistic variables, using similarity measure as a tool for transformation.
ENGINEERING APPLICATIONS OF ARTIFICIAL INTELLIGENCE
(2022)
Article
Biochemical Research Methods
Zhenla Jiang, Jianrong Xu, Aixia Yan, Ling Wang
Summary: The study evaluated 15 3D molecular similarity programs against two datasets and found that some academic tools may outperform commercial software in terms of virtual screening performance; 3D similarity VS tools exhibit considerable capability in capturing active compounds with new chemotypes; Multiple conformers generally improve performance for most 3D similarity tools.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Neurosciences
Sepideh Tabrik, Mehdi Behroozi, Lara Schlaffke, Stefanie Heba, Melanie Lenz, Silke Lissek, Onur Gunturkun, Hubert R. Dinse, Martin Tegenthoff
Summary: This study examined how 3D shape features of objects form two congruent and interchangeable visual and tactile perceptual spaces in healthy male and female participants. The results indicate that both modalities share the same shape features to form highly similar veridical spaces. This finding suggests that visual and tactile systems might apply similar cognitive processes to sensory inputs that enable humans to rely merely on one modality in the absence of another to recognize surrounding objects.
Article
Biochemical Research Methods
Yue Zhao, Xiang-Gui Wang, Zhong-Ye Ma, Guo-Li Xiong, Zhi-Jiang Yang, Yan Cheng, Ai-Ping Lu, Zhi-Jun Huang, Dong-Sheng Cao
Summary: PARP1 inhibitors are important for ovarian and breast cancer therapies, but current inhibitors have some disadvantages. By employing various virtual screening methods and discovering molecules with novel frameworks, the screening efficiency can be improved, laying the foundation for broader clinical applications.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Engineering, Civil
Kwang-Lim Ko, Jun-Sang Yoo, Chang-Woo Han, Jungyeop Kim, Seung-Won Jung
Summary: As autonomous driving technologies progress, occupants can be freed from driving, allowing for more diverse interactions with vehicles. However, most existing in-vehicle occupant monitoring systems focus on tracking the face or head of occupants, with limited studies on detecting their poses. This paper presents a novel framework specialized for the estimation of 3D human pose and shape in an in-vehicle environment using a single image. By introducing the HIVE dataset, which consists of synthesized humans with various shapes and poses in vehicle images, along with a pose prior derived from a variational autoencoder trained with in-vehicle human pose data, the proposed method shows significantly improved performance compared to state-of-the-art methods for real-world test images captured in vehicles under different conditions.
IEEE TRANSACTIONS ON INTELLIGENT TRANSPORTATION SYSTEMS
(2023)
Article
Biochemistry & Molecular Biology
Maiia E. Bragina, Antoine Daina, Marta A. S. Perez, Olivier Michielin, Vincent Zoete
Summary: SwissSimilarity is a web tool for virtual screening of chemical libraries to find molecules similar to a compound of interest. The new version offers additional methods for estimating molecular similarity and improved user experience.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Computer Science, Artificial Intelligence
Fouaz Berrhail, Hacene Belhadef, Mohammed Haddad
Summary: LBVS plays a crucial role in the early stage of drug discovery, solving time and cost issues associated with traditional methods. The proposed method based on Deep Convolutional Neural Network (DCNN) demonstrates superior performance compared to conventional methods through new learning representation for chemical compounds.
EXPERT SYSTEMS WITH APPLICATIONS
(2022)
Article
Computer Science, Information Systems
Bingwen Hu, Ping Liu, Zhedong Zheng, Mingwu Ren
Summary: This paper proposes an image-based virtual try-on network that fits desired clothing onto a reference person under diverse poses, outperforming existing methods and being robust to data noise.
IEEE TRANSACTIONS ON MULTIMEDIA
(2022)
Article
Chemistry, Medicinal
Nattanan Jiwacharoenchai, Rungroj Saruengkhanphasit, Worawat Niwetmarin, Supaporn Seetaha, Kiattawee Choowongkomon, Somsak Ruchirawat, Chatchakorn Eurtivong
Summary: By conducting a similarity search on the U.S. Enhanced National Cancer Institute Database Browser 2.2, compounds related to a known EGFR-TK inhibitor were identified. Five candidates with strong antiproliferative activities against overexpressed EGFR-TK cancer cell lines were selected through virtual screening and bioactivity testing. Molecular docking analysis and physicochemical property calculations suggested their potential as drug-like orally active compounds.
BIOORGANIC & MEDICINAL CHEMISTRY LETTERS
(2022)
Article
Computer Science, Hardware & Architecture
Jeronimo S. Garcia, Savins Puertas-Martin, Juana L. Redondo, Juan Jose Moreno, Pilar M. Ortigosa
Summary: In this study, an algorithm called OptiPharm was designed to improve the sequential methods and showed excellent results. To further enhance the quality of predictions and reduce experimentation time, a parallelized version of the software, called pOptiPharm, was proposed. The results demonstrated that pOptiPharm outperformed sequential OptiPharm and reduced computation time proportionally to the number of processing units considered.
JOURNAL OF SUPERCOMPUTING
(2023)
Article
Chemistry, Medicinal
Xi Jiang, Ashutosh Kumar, Yasutaka Motomura, Tian Liu, Yong Zhou, Kazuyo Moro, Kam Y. J. Zhang, Qing Yang
JOURNAL OF MEDICINAL CHEMISTRY
(2020)
Article
Biochemistry & Molecular Biology
Rahul Kaushik, Kam Y. J. Zhang
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2020)
Article
Biochemical Research Methods
Yashpal Singh Malik, Mohd Ikram Ansari, Jobin Jose Kattoor, Rahul Kaushik, Shubhankar Sircar, Anbazhagan Subbaiyan, Ruchi Tiwari, Kuldeep Dhama, Souvik Ghosh, Shailly Tomar, Kam Y. J. Zhang
Summary: The interaction between the SARS-CoV-2 spike glycoprotein and the ACE2 cell receptor is crucial for virus attachment to human cells, and certain mutations in the S-protein can strengthen binding affinity to ACE2. Recombination events in SARS-CoV-2 strains are frequent, suggesting a common origin with predecessors and genetic exchange between potential reservoirs and human hosts. Comprehensive analysis of codon bias in SARS-CoV-2 indicates adaptation in other animal hosts and potential use in experimental animal models for drug and vaccine development research.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Chandran Remya, K. Dileep, E. Jayadevi Variyar, Kam Y. J. Zhang, R. Omkumar, C. Sadasivan
Summary: This study identified two potent AChE inhibitors from the ZINC database using in silico approaches and validated their in vitro effects. These inhibitors showed strong selectivity towards AChE and did not cause significant reductions in cell viability of HEK-293 cells and primary cortical neurons. Additionally, they exhibited promising neuroprotective properties against glutamate-induced excitotoxicity in primary cortical neurons.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Biochemistry & Molecular Biology
K. Dileep, Naoki Sakai, Kentaro Ihara, Miyuki Kato-Murayama, Akiko Nakata, Akihiro Ito, D. M. Sivaraman, Jay W. Shin, Minoru Yoshida, Mikako Shirouzu, Kam Y. J. Zhang
Summary: Alzheimer's disease is a major public health concern with limited therapeutic options. Inhibiting sQC to prevent the formation of neurotoxic pGlu-Aβ offers a promising disease-modifying therapy for AD. A novel sQC inhibitor, Cpd-41, was identified with unique binding mode and moderate toxicity, making it a potential candidate for designing high affinity sQC inhibitors.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Agriculture, Multidisciplinary
Qi Chen, Wei Chen, Ashutosh Kumar, Xi Jiang, Matej Janezic, Kam Y. J. Zhang, Qing Yang
Summary: Chitinases in nematodes play crucial roles in various processes of their lifecycle, and a study on the crystal structure of a representative chitinase in Caenorhabditis elegans has provided insights for the development of inhibitors targeting this enzyme. The researchers successfully identified novel inhibitors through hierarchical virtual screening, which may pave the way for improving the inhibitory activities in future studies.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Matej Janezic, Kalarickal V. Dileep, Kam Y. J. Zhang
Summary: This study reveals that missense mutations of human choline acetyltransferase may affect its structure and function through various mechanisms, such as disrupting secondary structures, perturbing the P-loop, disrupting connecting loops, and affecting the phosphorylation process. It underscores the necessity for further genomic research to better understand the pathology of CHAT.
JOURNAL OF CELLULAR BIOCHEMISTRY
(2021)
Article
Biochemical Research Methods
Naveen Kumar, Rahul Kaushik, Chandana Tennakoon, Vladimir N. Uversky, Sonia Longhi, Kam Y. J. Zhang, Sandeep Bhatia
Summary: Research has shown that the abundance and function of intrinsically disordered proteins in viral proteomes vary widely depending on virus genome types and taxonomically divergent hosts. These proteins are primarily involved in key virus-host interactions and regulation of host antiviral immune responses. These findings provide promising targets for the design of novel therapeutics.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Jeroen P. M. Vrancken, Hiroki Noguchi, Kam Y. J. Zhang, Jeremy R. H. Tame, Arnout R. D. Voet
Summary: Symmetric proteins are of interest for their ability to create larger assemblies and incorporate metal ions in them. By studying the mechanism behind the formation of cadmium-chloride nanocrystals via truncation, mutation, and circular permutations, researchers also explore the interaction of biologically relevant metal ions with these proteins. The results suggest that symmetric proteins can serve as a scaffold to create complex metal-based assemblies with potential applications in bionanotechnology and biocatalysis.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Sourya Bhattacharya, Aditya K. Padhi, Vivek Junghare, Neeladrisingha Das, Debashish Ghosh, Partha Roy, Kam Y. J. Zhang, Saugata Hazra
Summary: This study evaluated the inhibitory potential of various beta-lactamase inhibitors against Bla1, a class-A betalactamase encoded by Bacillus anthracis. Tazobactam and Avibactam were identified as good inhibitors with better inhibition efficiency. Molecular dynamics simulations were carried out to understand the dynamics and stability of Bla1-inhibitor complexes. The study helps in comprehending the catalytic divergence of betalactamases and developing new generation therapeutics less prone to antimicrobial resistance.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Chemistry, Medicinal
Erma Fatiha Muhammad, Ashutosh Kumar, Habibah A. Wahab, Kam Y. J. Zhang
Summary: A new class of AChE inhibitors, 1,2,4-triazolylthioethanones, was identified using a virtual screening approach. These compounds showed IC50 values ranging from 0.15 +/- 0.07 to 3.32 +/- 0.92 μM, and could potentially serve as a starting point for novel therapeutics for Alzheimer's disease.
MOLECULAR INFORMATICS
(2021)
Article
Developmental Biology
Vishnu Mishra, Archita Singh, Nidhi Gandhi, Shabari Sarkar Das, Sandeep Yadav, Ashutosh Kumar, Ananda K. Sarkar
Summary: Submergence-induced hypoxic condition negatively affects plant growth and development, and causes early onset of senescence. A miRNA called miR775 plays a crucial role in post-submergence recovery by regulating the expression of genes related to ethylene signaling and ABA biosynthesis pathways.
Article
Biochemistry & Molecular Biology
Wei Chen, Qi Chen, Ashutosh Kumar, Xi Jiang, Kam Y. J. Zhang, Qing Yang
Summary: Nematode chitinases play crucial roles in various physiological processes, and small-molecule inhibitors show potential for controlling nematode pests. By studying the crystal structure, a series of novel inhibitors were discovered, with compound PP28 showing the most potent activity. This research provides a structural basis for the development of novel nematode chitinase inhibitors.
JOURNAL OF ENZYME INHIBITION AND MEDICINAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Aditi Mhaske, K. Dileep, Mukesh Kumar, Mukta Poojary, Kavita Pandhare, Kam Y. J. Zhang, Vinod Scaria, B. K. Binukumar
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2020)
Letter
Cell Biology
Xuetian Yue, Fangnan Wu, Jianming Wang, Kaitlin Kim, Bindu Santhamma, Kalarickal V. Dileep, Kam Y. J. Zhang, Suryavathi Viswanadhapalli, Ratna K. Vadlamudi, Gulzar Ahmed, Zhaohui Feng, Klaus Nickisch, Wenwei Hu
JOURNAL OF MOLECULAR CELL BIOLOGY
(2020)