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Search · four archives
28 papers · ranked by Valyu relevance
Zhenrun J. Zhang, Chunyu Wu, Darian Dorantes, Téa Pappas + 4 more
Recent advances in sequencing techniques unveiled the vast potential of ribosomally synthesized and post-translationally modified peptides (RiPPs) encoded in microbiomes. Class I lantibiotics such as nisin A, widely used as a food preservative, have been investigated for their efficacy in killing pathogens. However…
Zhaoxuan Li, Jingling Liu, Jie You, Xin Li + 3 more
'Junli Du' 'M. Natália D.S. Cordeiro'] To fully explore the influence mechanism of interactions between different monomer units of proanthocyanidins (PAs) on biological activity, a path analysis model of the PA structure-activity relationship was proposed. This model subdivides the total correlation between each…
Tianbo Liu, Qianqian Ren, Shuang Wang, Jianing Gao + 5 more
'Shengyu Zhang' 'Yanhong Wang' 'Feng Guan' 'Lesław Juszczak'] Natural polysaccharides are macromolecular substances with great potential owing to their wide biological activity and low toxicity. However, not all polysaccharides have significant pharmacodynamic activity; hence, appropriate chemical modification methods…
Maryam Bayanati, Mohammad Ismail Mahboubi Rabbani, Shirin Sirous Kabiri, Bahareh Mir + 2 more
'Shirin Sirous Kabiri' 'Bahareh Mir' 'Elham Rezaee' 'Sayyed Abbas Tabatabai'] Context Dipeptidyl peptidase 4 (DPP-4) is a serine exopeptidase enzyme that hydrolyzes the amide bond at the N-terminal of peptides. This enzyme converts incretins, such as glucagon-like peptide I and glucose-dependent insulinotropic peptide…
Rattanawan Tangporncharoen, Chuleeporn Phanus-Umporn, Supaluk Prachayasittikul, Chanin Nantasenamat + 2 more
Osteoanabolic agents, or drugs that promote bone formation, have gained considerable attention for osteoporosis management due to their curative and preventive potentials. Sphingosine-1-phosphate receptor 2 (S1PR2) is an attractive drug target, in which its activation leads to osteogenesis-promoting effect.…
Hezha O. Rasul, Dlzar D. Ghafour, Bakhtyar K. Aziz, Bryar A. Hassan + 2 more
'Tarik A. Rashid' 'Arif Kıvrak'] The drug development process is a critical challenge in the pharmaceutical industry due to its timeconsuming nature and the need to discover new drug potentials to address various ailments. The initial step in drug development, drug target identification, often consumes considerable…
Alaa M. Elgohary, Abdo A. Elfiky, Florbela Pereira, Tarek Mohamed Abd El-Aziz + 3 more
Over a span of two years ago, since the emergence of the first case of the novel coronavirus (SARS-CoV-2) in China, the pandemic has crossed borders causing serious health emergencies, immense economic crisis and impacting the daily life worldwide. Despite the discovery of numerous forms of precautionary vaccines along…
Omid Karami, Hanna de Jong, Victor J. Somovilla, Beatriz Villanueva Acosta + 3 more
2,4-dichlorophenoxyacetic acid (2,4-D) is a synthetic analogue of the plant hormone auxin that is commonly used in many in vitro plant regeneration systems, such as somatic embryogenesis (SE). Its effectiveness in inducing SE, compared to the natural auxin indole-3-acetic acid (IAA), has been attributed to the stress…
Jan Sklenicka, Tung Tran, Maria S. Ramirez, Haley M. Donow + 8 more
Resistance to amikacin and other major aminoglycosides is commonly due to enzymatic acetylation by aminoglycoside 6′-N -acetyltransferase type I enzyme, of which type Ib [AAC(6′)-Ib] is the most widespread among Gram-negative pathogens. Finding enzymatic inhibitors could be an effective way to overcome resistance and…
Kim, Hajung, Jueon Park, Choe + 5 more
Quantitative structure–activity relationship assumes a smooth relationship between molecular structure and biological activity. However, activity cliffs defined as pairs of structurally similar compounds with large potency differences break this continuity. Recent benchmarks targeting activity cliffs have revealed that…
Ajaya Kumar Sahoo, Shanmuga Priya Baskaran, Nikhil Chivukula, Kishan Kumar + 1 more
'Kishan Kumar' 'Areejit Samal'] The thyroid stimulating hormone receptor (TSHR) is crucial in thyroid hormone production in humans, and dysregulation in TSHR activation can lead to adverse health effects such as hypothyroidism and Graves' disease. Further, animal studies have shown that binding of endocrine disrupting…
Ioannis G. Riziotis, António J.M. Ribeiro, Neera Borkakoti, Janet M. Thornton
'Janet M. Thornton'] Title: Graphical abstract
Ioannis G. Riziotis, António J. M. Ribeiro, Neera Borkakoti, Janet M. Thornton
Conformational variation in catalytic residues can be captured as alternative snapshots in enzyme crystal structures. Addressing the question of whether active site flexibility is an intrinsic and essential property of enzymes for catalysis, we present a comprehensive study on the 3D variation of active sites of 925…
Markus Dablander, Thierry Hanser, Renaud Lambiotte, Garrett M. Morris
'Garrett M. Morris'] Introduction and Methodology: Pairs of similar compounds that only differ by a small structural modification but exhibit a large difference in their binding affinity for a given target are known as activity cliffs (ACs). It has been hypothesised that QSAR models struggle to predict ACs and that ACs…
Angela Medvedeva, Ksenia Kolomeisky, Anatoly B. Kolomeisky
Understanding how specific molecular substructures control chemical behavior is central to rational molecular design and the development of new materials. However, most current predictive models offer limited mechanistic resolution at the fragmental level. We present a novel physical–chemical computational framework…
Md. Aktar Hossain, Saima Sultana
In silico analysis is a powerful technique to identify better therapeutic interventions. Molecular docking is widely used to screen ligands through analysing binding affinities for target receptors. In this study we screened ligands for two proteins which are potential drug targets: deoxyuridine triphosphate…
Authors not listed
Staphylococcus aureus is a bacterium classified among the ESKAPE pathogens, which are anticipated to pose a significant global health emergency in the coming decades. The FabI enzyme, present in both Gram-positive and Gram-negative bacteria, is a key enzyme involved in fatty acid synthesis II (FAS-II). In this study…
Kenneth López-Pérez, Ramón Alain Miranda-Quintana
Activity cliffs represent an important challenge to tackle in cheminformatics and drug design. One of the most common indicators to quantify them is the SALI index. Here we expose mathematical limitations of SALI’s formulation, the most evident: it is undefined in instances where the similarity between two molecules is…
Fanglei Xue, M L Zhang, Shuqi Li, Xinyu Gao + 4 more
Targeted protein degradation (TPD) induced by small molecules has emerged as a rapidly evolving modality in drug discovery, targeting proteins traditionally considered "undruggable." This strategy induces the degradation of target proteins rather than inhibiting their activity, achieving desirable therapeutic outcomes.…
Edgar López-López, Oscar Robles, Fabien Plisson, José L. Medina-Franco
Peptides are a re-emerged strategy to fight a plethora of diseases and their utility has been expanded to new areas. Now sequence-based peptide design opens up new possibilities to develop peptidic molecular entities. However, its methodological limitations (e.g., its inefficiency in designing large peptides and that…
Torben Gutermuth, Emanuel S. R. Ehmki, Florian Flachsenberg, Patrick Penner + 3 more
Generation of Protein–Ligand Complex Data Sets with Atomistic Detail Authors: Torben Gutermuth, Emanuel S. R. Ehmki, Florian Flachsenberg, Patrick Penner, Sophia M. N. Hönig, Tobias Harren, Matthias Rarey Predicting protein-ligand bioactivities is known to be challenging yet crucial in any drug discovery project. In a…
Ioannis G. Riziotis, Janet M. Thornton
Structural templates are 3D signatures representing protein functional sites, such as ligand binding cavities, metal coordination motifs or catalytic sites. Here we explore methods to generate template libraries and algorithms to query structures for conserved 3D motifs. Applications of templates are discussed, as well…
Authors not listed
Fragment based drug design (FBDD) is like a chess game in that a good or a bad move can dramatically influence the outcome. At the start of the design process, it is important to identify the key binding site residues (hotspots) that can have a substantial impact on ligand efficiency (LE) and binding. Here, we…
Authors not listed
Macrocycles are emerging as a prominent modality in drug discovery, including for conventionally druggable targets for which simpler, acyclic ligands are readily discoverable. Given the additional synthetic challenges associated with macrocyclic chemotypes, we address what benefits macrocycles provided for these highly…
Chris Zhang, Mary Pitman, Anjali Dixit, Sumudu Leelananda + 7 more
DNA-encoded libraries (DELs) provide the means to make and screen millions of diverse compounds against a target of interest in a single experiment. However, despite producing large volumes of binding data at a relatively low cost, the DEL selection process is susceptible to noise, necessitating computational follow-up…
Jiming Chen, Diwakar Shukla
The strigolactone signaling pathway in plants is unconventional among plant hormone signaling pathways in that the receptor also acts as an enzyme that hydrolyzes the strigolactone substrate. While the canonical view of strigolactone hydrolysis is that it occurs via a nucleophilic attack on the butenolide ring of…
Jingwei Zuo, Hakim Hacid
Human Activity Recognition (HAR) has been studied for decades, from data collection, learning models, to post-processing and result interpretations. However, the inherent hierarchy in the activities remains relatively under-explored, despite its significant impact on model performance and interpretation. In this paper…
Chuanchuan Wang, Ahmad Sufril Azlan Mohamed
Group activity recognition is a hot topic in computer vision. Recognizing activities through group relationships plays a vital role in group activity recognition. It holds practical implications in various scenarios, such as video analysis, surveillance, automatic driving, and understanding social activities. The…