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Intervals and the deduction of drug binding site models

Gordon M. Crippen
1995 Journal of Computational Chemistry  
Determining the site model consists of reducing the uncertainty in the interregion distance intervals, and this uncertainty is described as intervals of intervals.  ...  The geometry of the ligand molecules and the site is described in terms of intervals of internal distances.  ...  Acknowledgments This project was supported by a grant from the National Institute on Drug Abuse (DA06746). Thanks are due to V. N.  ... 
doi:10.1002/jcc.540160412 fatcat:sptd3e2gzret5iktvj6uks7jha

Intervals and the deduction of drug binding site models

G.M. Crippen
Proceedings of the Twenty-Eighth Hawaii International Conference on System Sciences, vol.5  
We describe an extraordinarily objective computer algorithm for deducing the important geometric and energetic features of the common binding Site, starting only from the chemical structures of the ligands  ...  In the search for new drugs, it often occurs that the binding aflnities of several compounds to a common receptor macromolecule are known experimentally, but the structure of the receptor is not known.  ...  With only two regions in three spatial dimensions, The final site model corresponding to the short AA dimer binding weakly and the long A-A isomer binding strongly.  ... 
doi:10.1109/hicss.1995.375332 dblp:conf/hicss/Crippen95 fatcat:i3o2uqlmxndd7ebq72aofzf5bq

An Integrated Multiscale Mechanistic Model for Cancer Drug Therapy

Lei Tang, Jing Su, De-Shuang Huang, Daniel Y. Lee, King C. Li, Xiaobo Zhou
2012 ISRN Biomathematics  
This model will facilitate the analysis and prediction of organ toxicity and provide important pharmacokinetic information with regard to drug clearance rates.  ...  Due to the specific characteristics of cancer, our proposed model focuses on drug effects on malignant solid tumor and specific internal organs as well as the intratumoral and regional extracellular microenvironments  ...  Acknowledgments The author thank Dr. Brian E. O'Neill for his kind help and suggestion and Drs. Zhengzheng Shi, Zheng Li, and Tao Peng for their discussion.  ... 
doi:10.5402/2012/818492 fatcat:h3mnbseddvdjzbgae6br4bz2em

Synthesis and biological evaluation of a fluorescent analog of phenytoin as a potential inhibitor of neuropathic pain and imaging agent

Thomas H. Walls, Scott C. Grindrod, Dawn Beraud, Li Zhang, Aparna R. Baheti, Sivanesan Dakshanamurthy, Manoj K. Patel, Milton L. Brown, Linda H. MacArthur
2012 Bioorganic & Medicinal Chemistry  
Compound 2 incorporated a heptyl side chain and dansyl moiety onto the parent compound phenytoin and produced greater displacement of BTX from sodium channels and greater functional blockade with greatly  ...  Compound 2 reduced mechano-allodynia in a rat model of neuropathic pain and was visualized ex vivo in sensory neuron axons with two-photon microscopy.  ...  Stables at NINDS for help in the evaluation of compound 2 in the Anticonvulsant Drug Development Program.  ... 
doi:10.1016/j.bmc.2012.06.042 pmid:22863530 pmcid:PMC4111572 fatcat:rtnkqw2nhza6jawudtjgr2kmyy

Biodistribution of HuCC49ΔCH2-β-galactosidase in colorectal cancer xenograft model

Yanke Yu, Lanyan Fang, Duxin Sun
2010 International Journal of Pharmaceutics  
At a high dose of 3000 U/ kg, HuCC49ΔCH2-β-galactosidase conjugate saturated the antigen binding sites and yielded decreased tumor/normal tissue ratios compared to 1500 U/kg.  ...  The purpose of this study is to characterize the pharmacokinetics and tissue distribution of HuCC49ΔCH2-β-galactosidase conjugate.  ...  Acknowledgments This study is partially supported by NIH funding RO1 CA 120023, University of Michigan Cancer Center Research Grant (Munn), University of Michigan Cancer Center Core Grant to DS.  ... 
doi:10.1016/j.ijpharm.2009.11.020 pmid:19944136 pmcid:PMC2815147 fatcat:s2fnfeqzkbagddt7bbjhgklp7a

Page 5767 of Psychological Abstracts Vol. 84, Issue 12 [page]

1997 Psychological Abstracts  
receptor binding site accounts for the clinical and biochemical features of this con- dition.  ...  The order of stimulus presentation (Left-First vs Right-First), and the intertarget interval (stimulus onset asynchrony) were varied sys- tematically.  ... 

Allosteric inhibition induces an open WPD-loop: a new avenue towards glioblastoma therapy

Clement Agoni, Pritika Ramharack, Mahmoud E. S. Soliman
2018 RSC Advances  
Structural mechanism of inhibition of NAZ2329 at the allosteric site of PTPRZ, with particular emphasis on the dynamics of the WPD-loop.  ...  Acknowledgements The authors acknowledge the School of Health Sciences, the University of KwaZulu-Natal, Westville Campus for their nancial support.  ...  We also acknowledge the Center for High Performance Computing (CHPC, https://www.chpc.ac.za), Cape Town, for computational resources.  ... 
doi:10.1039/c8ra08427k pmid:35558220 pmcid:PMC9091281 fatcat:ybqtuxnkffdztebupuvtkckedy

HIV decision support: from molecule to man

P.M.A. Sloot, P. V. Coveney, G. Ertaylan, V. Muller, C.A. Boucher, M. Bubak
2009 Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences  
The sheer complexity of the disease stems from the multiscale and highly dynamic nature of the system under study.  ...  ViroLab allows for personalized drug ranking. It is on trial in six hospitals and various virology and epidemiology laboratories across Europe.  ...  The authors would like to thank Breanndán Ó . Nualláin, Alfredo Tirado Ramos and Annemie Vandamme for their valuable feedback.  ... 
doi:10.1098/rsta.2009.0043 pmid:19487205 fatcat:mn62nxoverekdbs55vb6uvjbfa

An inhibition model of BPTI to unlinked dengue virus NS2B-NS3 protease

Hua Li, Lei Zhu, Shulin Hou, Jing Yang, Junfeng Wang, Jinsong Liu
2014 FEBS Letters  
However, the lack of structural information on the active conformation of the protease hindered related drug design.  ...  Based on the biochemical and NMR perturbation information, an inhibition model of BPTI to NS2B-NS3 protease is proposed.  ...  We thank Zhiqiang Dong and Liping Gong for their hard work on the linked NS2B-NS3p. This work was supported by the Natural Science Foundation of China (U1232141, U1332142).  ... 
doi:10.1016/j.febslet.2014.05.063 pmid:24931377 fatcat:e5cr4lbxzzfidhp5mgzdlc4hvi

Pharmacokinetics and pharmacodynamics of disopyramide

J Bonde
1991 Danish medical bulletin  
primarily associated with the first binding site of disopyramide.  ...  and second binding site, respectively (Rosenthal 1967).  ... 
pmid:2060320 fatcat:gjddc3tjozdixdxoo7zjlpf77q

DESIGN, In-silico STUDIES, SYNTHESIS, CHARACTERIZATION, AND ANTICONVULSANT ACTIVITIES OF NOVEL THIAZOLE SUBSTITUTED OXAZOLE DERIVATIVES

Singagari Srilakshmi, Raja Sundararajan
2022 RASAYAN Journal of Chemistry  
molecule to find potent and safer antiepileptic drug  ...  In addition, the neurotoxicity of the compounds was also estimated using the rotarod test. Entire tested derivatives displayed varying degrees of antiepileptic and neurotoxicity potency.  ...  ACKNOWLEDGMENT The authors are thankful to the management of Shadan Women's College of Pharmacy, Hyderabad, Telangana, India and GITAM -Deemed to be University, Gandhi Nagar, Rushikonda, Visakhapatnam,  ... 
doi:10.31788/rjc.2022.1516762 fatcat:3apxcgqisve6dc4mftu65jiyfi

Binding of Tetracycline and Chlortetracycline to the Enzyme Trypsin: Spectroscopic and Molecular Modeling Investigations

Zhenxing Chi, Rutao Liu, Hongxu Yang, Hengmei Shen, Jing Wang, Hendrik W. van Veen
2011 PLoS ONE  
In this study, we establish a new strategy to probe the binding modes of TC and CTC with trypsin based on spectroscopic and computational modeling methods.  ...  which bound to a non-active site of trypsin, different from TC due to the Cl atom on the benzene ring of CTC which hinders CTC entering into the S1 binding pocket.  ...  and drugs.  ... 
doi:10.1371/journal.pone.0028361 pmid:22205948 pmcid:PMC3242759 fatcat:c2k5xcz77zgjvbpau6fjy552zy

Signal integration by the CYP1A1 promoter -- a quantitative study

P. Schulthess, A. Loffler, S. Vetter, L. Kreft, M. Schwarz, A. Braeuning, N. Bluthgen
2015 Nucleic Acids Research  
The model unveils how different binding sites cooperate and how they establish the promoter logic; it quantitatively predicts two-dimensional stimulus-response curves.  ...  quantified the regulatory influence of different transcription factor binding sites on gene induction within the promoter.  ...  ACKNOWLEDGEMENTS Technical assistance by Elke Zabinsky and Johanna Mahr is greatly acknowledged. We also thank Dr C. Roland Wolf (Dundee, UK) for the gift of the CYP1A antiserum.  ... 
doi:10.1093/nar/gkv423 pmid:25934798 pmcid:PMC4477655 fatcat:mmgfuqlrnfgrvocm62sdpitzju

Supramolecular Encapsulation of Vitamin B6by Macrocyclic Nanocontainer Cucurbit[7]uril

Wanying Li, Shengke Li, Ian W. Wyman, Donal H. Macartney, Qingwen Zhang, Ying Zheng, Ruibing Wang
2015 Journal of Nanomaterials  
The CB[7] based "nanocapsule" of vitamin B6has been investigated for the first time, via1H NMR and UV-visible spectroscopic titrations (including Job's plot) andab initiomolecular modeling.  ...  Such a nanocapsule could potentially find application in vitamin B6formulation for the purpose of enhancing the stability, absorption, and delivery of this important vitamin.  ...  SRG2014-00025), FDCT Matching Grant from University of Macau (MRG031/ZY/2015/ICMS), and NSERC of Canada for financial support of this research.  ... 
doi:10.1155/2015/574013 fatcat:mj3miofayzal3dnnwgbdgu3xcq

Exploring the inhibitory mechanism of piceatannol on α-glucosidase relevant to diabetes mellitus

Lili Jiang, Zhen Wang, Xiaoyu Wang, Shujuan Wang, Jun Cao, Yong Liu
2020 RSC Advances  
The non-competitive inhibition of piceatannol on α-glucosidase. A combination of dynamic and static process with one binding site. The involvement of hydrophobic interactions and hydrogen bonding.  ...  Dietary recommendations for diabetes or potential antidiabetic drug.  ...  was at a hydrophobic pocket outside of the catalytic site of a-glucosidase, and the binding could block the entrance of other substrates.  ... 
doi:10.1039/c9ra09028b pmid:35495253 pmcid:PMC9049079 fatcat:6xbzenjndbhetmmdssw4rsuy6y
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