Analysis of Binding Determinants for Different Classes of Competitive and Noncompetitive Inhibitors of Glycine Transporters by Kamil Łątka, Marek Bajda

“…The results of this study indicate that two amino acids, Gly373 and Leu476 in GlyT-1 and the corresponding Ser479 and Thr582 in GlyT-2, are mainly responsible for the selective binding of ligands within the S1 site. Apart from these, one pocket of the S2 site, which lies between TM3 and TM10, may also be important. …”
Get full text

An auto lifting device to lift manhole cover with ergonomics consideration by Wan Draman, Wan Nur A'tiqah, Abang Abdul Majid, Dayang Laila, Ishak, Muhammad Ikman, Rosli, M. U., M., Lailina N., Ismail, Ras Izzati

“…The manhole cover has one pocket which is to lock it and ensure that nobody open it. …”
Get full text

Deciphering the Binding of Salicylic Acid to <i>Arabidopsis thaliana</i> Chloroplastic GAPDH-A1 by Igor Pokotylo, Denis Hellal, Tahar Bouceba, Miguel Hernandez-Martinez, Volodymyr Kravets, Luis Leitao, Christophe Espinasse, Isabelle Kleiner, Eric Ruelland

“…A simulation in water of the complex between SA and the protein allowed us to determine that only one pocket—a surface cavity around Asn35—would efficiently bind SA in the presence of solvent. …”
Get full text

Affimer-mediated locking of p21-activated kinase 5 in an intermediate activation state results in kinase inhibition by Heather L. Martin, Amy L. Turner, Julie Higgins, Anna A. Tang, Christian Tiede, Thomas Taylor, Sitthinon Siripanthong, Thomas L. Adams, Iain W. Manfield, Sandra M. Bell, Ewan E. Morrison, Jacquelyn Bond, Chi H. Trinh, Carolyn D. Hurst, Margaret A. Knowles, Richard W. Bayliss, Darren C. Tomlinson

“…Co-crystallization revealed that PAK5-Af17 bound in the P+1 pocket of PAK5, locking the kinase into a partial activation state. …”
Get full text

Glycosylation of the primary binding pocket of a subtilisin protease causes a remarkable broadening in stereospecificity in peptide synthesis by Matsumoto, K, Davis, B, Jones, J

“…Site-selective glycosylation at position 166 at the base of the primary specificity S1 pocket in the serine protease subtilisin Bacillus lentus (SBL) created glycoproteins that are capable of catalyzing the coupling reactions of not only L- amino acid esters but also D-amino acid esters to give the corresponding dipeptides in good yields as a result of greatly broadened substrate specificities that can be rationalized by the interaction of the glycans acting as chiral auxiliaries in stereochemically mismatched pairs.…”

Identification of 13 Guanidinobenzoyl- or Aminidinobenzoyl-Containing Drugs to Potentially Inhibit TMPRSS2 for COVID-19 Treatment by Xiaoqiang Huang, Robin Pearce, Gilbert S. Omenn, Yang Zhang

“…These results suggest that the proposed compounds, in addition to Camostat and Nafamostat, could be effective TMPRSS2 inhibitors for COVID-19 treatment by occupying the S1 pocket with the hallmark positively charged groups.…”
Get full text

Mechanism of auxin perception by the TIR1 ubiquitin ligase. by Tan, X, Calderon-Villalobos, L, Sharon, M, Zheng, C, Robinson, C, Estelle, M, Zheng, N

“…Anchored to the base of the TIR1 pocket, auxin binds to a partially promiscuous site, which can also accommodate various auxin analogues. …”

Identification of <i>N</i>-Acyl Hydrazones as New Non-Zinc-Binding MMP-13 Inhibitors by Structure-Based Virtual Screening Studies and Chemical Optimization by Doretta Cuffaro, Aleix Gimeno, Bianca Laura Bernardoni, Riccardo Di Leo, Gerard Pujadas, Santiago Garcia-Vallvé, Susanna Nencetti, Armando Rossello, Elisa Nuti

“…Here we have developed a virtual screening workflow aimed at identifying selective non-zinc-binding MMP-13 inhibitors by targeting the deep S1′ pocket of MMP-13. Three ligands were found to inhibit MMP-13 in the µM range, and one of these showed selectivity over other MMPs. …”
Get full text

ACE Inhibitory Peptides Derived from Muscovy Duck (<i>Cairina moschata</i>) Plasma by Zongshuai Zhu, Haoyu Guo, Yan Xu, Anthony Pius Bassey, Ahtisham Ali, Ming Huang, Jichao Huang

“…The peptide VALSSLRP revealed high ACE inhibitory activity (91.67 ± 0.73%) because this peptide bound tightly to the S1′ pocket and formed 3 hydrogen bonds. Meaningfully, this work provides some new information about the generation of ACE–IPs derived from duck blood plasma.…”
Get full text

Revealing the mechanistic interactions of profenofos and captan pesticides with serum protein via biophysical and computational investigations by Kamonrat Phopin, Waralee Ruankham, Supaluk Prachayasittikul, Virapong Prachayasittikul, Tanawut Tantimongcolwat

“…Both pesticides bound preferentially to the site I pocket of BSA, where the hydrophobic interaction was the main binding mode of PF, and the electrostatic interaction drove the binding of CT. …”
Get full text

DNA Origami Disguises Herpes Simplex Virus 1 Particles and Controls Their Virulence by Raina M. Borum, Avery E. Lin, Xiangyi Dong, Mingxuan Kai, Yi Chen

“…The optimized origami:HSV1 molar ratios led to characteristic packaging geometries ranging from dispersed “HSV1 pockets” to agglomerated “HSV1 sleeves”. “Pockets” were disguised from cells in HeLa and B16F10 cells and were 44.2% less infective than naked HSV1 particles. …”
Get full text

Proteomic data and structure analysis combined reveal interplay of structural rigidity and flexibility on selectivity of cysteine cathepsins by Livija Tušar, Jure Loboda, Francis Impens, Piotr Sosnowski, Emmy Van Quickelberghe, Robert Vidmar, Hans Demol, Koen Sedeyn, Xavier Saelens, Matej Vizovišek, Marko Mihelič, Marko Fonović, Jaka Horvat, Gregor Kosec, Boris Turk, Kris Gevaert, Dušan Turk

“…Abstract Addressing the elusive specificity of cysteine cathepsins, which in contrast to caspases and trypsin-like proteases lack strict specificity determining P1 pocket, calls for innovative approaches. Proteomic analysis of cell lysates with human cathepsins K, V, B, L, S, and F identified 30,000 cleavage sites, which we analyzed by software platform SAPS-ESI (Statistical Approach to Peptidyl Substrate-Enzyme Specific Interactions). …”
Get full text

Recent Update on Applications of Quaternary Ammonium Silane as an Antibacterial Biomaterial: A Novel Drug Delivery Approach in Dentistry by Ranjeet Ajit Bapat, Abhishek Parolia, Tanay Chaubal, Ho Jan Yang, Prashant Kesharwani, Khoo Suan Phaik, Seow Liang Lin, Umer Daood

“…The compound can attach to S1' pockets on matrix metalloproteinases (MMPs), leading to massive MMP enzyme inhibition, making it one of the most potent protease inhibitors. …”
Get full text

Nonstandard peptide binding revealed by crystal structures of HLA-B*5101 complexed with HIV immunodominant epitopes. by Maenaka, K, Maenaka, T, Tomiyama, H, Takiguchi, M, Stuart, D, Jones, E

“…In both complexes, the hydrogen-bonding network in the N-terminal anchor (P1) pocket is rearranged as a result of the replacement of the standard tyrosine with histidine at position 171. …”

The Molecular Docking and Inhibition Kinetics of Angiotensin I-Converting Enzyme Inhibitory Peptides Derived from Soft-Shelled Turtle Yolk by Nhung Thi Phuong Nong, Christoper Caesar Yudho Sutopo, Wei-Ting Hung, Ping-Hsun Wu, Jue-Liang Hsu

“…The result revealed that WLQL would dock into the S1 pockets of ACE, while LPSW interacted with ACE’s secondary binding site. …”
Get full text

Potent antiviral agents fail to elicit genetically-stable resistance mutations in either enterovirus 71 or Coxsackievirus A16. by Kelly, J, De Colibus, L, Elliott, L, Fry, E, Stuart, D, Rowlands, D, Stonehouse, N

“…In silico modelling suggested that the mutations prevented the compounds from binding the VP1 pocket in the capsid. Although both viruses developed resistance to these potent pocket-binding compounds, the acquired mutations were associated with large fitness costs and reverted to WT phenotype and sequence rapidly in the absence of inhibitors. …”

Neoprzewaquinone A Inhibits Breast Cancer Cell Migration and Promotes Smooth Muscle Relaxation by Targeting PIM1 to Block ROCK2/STAT3 Pathway by Guiying Zhao, Yali Ren, Jie Yan, Tingrui Zhang, Peng Lu, Jieting Lei, Huanan Rao, Xin Kang, Zhixing Cao, Fu Peng, Cheng Peng, Chaolong Rao, Yuzhi Li

“…Molecular docking simulations revealed that NEO enters the PIM1 pocket, thereby triggering multiple interaction effects. …”
Get full text

A cheminformatics-biophysics correlate to identify promising lead molecules against matrix metalloproteinase-2 (MMP-2) enzyme: A promising anti-cancer target by Faris Alrumaihi

“…The compounds docked deeply inside the pocket interacting with S1 pocket residues. The docked complexes dynamics in real time at cellular environment was then done to decipher the stable binding conformation and intermolecular interactions network. …”
Get full text

Chemically modified "polar patch" mutants of subtilisin in peptide synthesis with remarkably broad substrate acceptance: designing combinatorial biocatalysts. by Matsumoto, K, Davis, B, Jones, J

“…The introduction of polar and/or homochiral auxiliary substituents, such as X=oxazolidinones, alkylammonium groups, and carbohydrates at position 166 at the base of the primary specificity S(1) pocket created SBL CMMs S166C-S-X with strikingly broad structural substrate specificities. …”

Deaza-modification of MR1 ligands modulates recognition by MR1-restricted T cells by Haihong Jin, Nicole A. Ladd, Andrew M. Peev, Gwendolyn M. Swarbrick, Meghan Cansler, Megan Null, Christopher T. Boughter, Curtis McMurtrey, Aaron Nilsen, Karen M. Dobos, William H. Hildebrand, Deborah A. Lewinsohn, Erin J. Adams, David M. Lewinsohn, Melanie J. Harriff

“…In assessing the dynamics of each ligand in the MR1 pocket, we found that DMRL and DZ exhibit differential dynamics of both the ribityl moiety and the aromatic backbone, which may contribute to ligand recognition. …”
Get full text