Abstract:
:The human cytochrome P450 1A2 is an important drug metabolizing and procarcinogen activating enzyme. An experimental study found that a peripheral mutation, F186L, at ∼26 Å away from the enzyme's active site, caused a significant reduction in the enzymatic activity of 1A2 deethylation reactions. In this paper, we explored the effects of this mutation by carrying out molecular dynamics simulations and structural analyses. We found that the long-range effects of the F186L mutation were through a change in protein flexibility and a collective protein motion that caused the main substrate access channel to be mostly closed in the mutant. Our work is the first that combined both access channel analysis and protein motion analysis to elucidate mechanisms of mutation-induced allostery in a CYP protein. Such structural modeling and analysis approaches may be applied to other CYP proteins and other enzymes with buried active sites and may help guide protein engineering and drug design.
journal_name
J Chem Inf Modeljournal_title
Journal of chemical information and modelingauthors
Zhang T,Liu LA,Lewis DF,Wei DQdoi
10.1021/ci200112bsubject
Has Abstractpub_date
2011-06-27 00:00:00pages
1336-46issue
6eissn
1549-9596issn
1549-960Xjournal_volume
51pub_type
杂志文章abstract::Protein dynamics play a critical role in ligand binding, and different models have been proposed to explain the relationships between protein motion and molecular recognition. Here, we present a study of ligand-binding processes associated with large conformational changes of a protein to elucidate the critical choice...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/acs.jcim.7b00125
更新日期:2017-07-24 00:00:00
abstract::The consistent handling of molecules is probably the most basic and important requirement in the field of cheminformatics. Reliable results can only be obtained if the underlying calculations are independent of the specific way molecules are represented in the input data. However, ensuring consistency is a complex tas...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/ci400724v
更新日期:2014-03-24 00:00:00
abstract::The prediction of Log P is usually accomplished using either substructure or whole-molecule approaches. However, these methods are complicated, and previous whole-molecule approaches have not been successful for the prediction of Log P in very complex molecules. The observed chemical shifts in nuclear magnetic resonan...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/ci049643e
更新日期:2005-03-01 00:00:00
abstract::Screening large libraries of chemicals has been an efficient strategy to discover bioactive compounds; however a portion of the potential for success is limited to the available libraries. Synergizing combinatorial and computational chemistries has emerged as a time-efficient strategy to explore the chemical space mor...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/acs.jcim.6b00648
更新日期:2017-03-27 00:00:00
abstract::Grass weed populations resistant to acetyl-CoA carboxylase-inhibiting (ACCase; EC 6.4.1.2) herbicides represent a major problem for the sustainable development of modern agriculture. In the present study, extensive computational simulations, including homology modeling, molecular dynamics (MD) simulations, and molecul...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/ci900174d
更新日期:2009-08-01 00:00:00
abstract::New hits against HIV-1 wild-type and Y181C drug-resistant reverse transcriptases were predicted taking into account the possibility of some of the known metabolism interactions. In silico hits against a set of antitargets (i.e., proteins or nucleic acids that are off-targets from the desired pharmaceutical target obje...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/ci200203h
更新日期:2011-10-24 00:00:00
abstract::Whereas 400 million distinct compounds are now purchasable within the span of a few weeks, the biological activities of most are unknown. To facilitate access to new chemistry for biology, we have combined the Similarity Ensemble Approach (SEA) with the maximum Tanimoto similarity to the nearest bioactive to predict a...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/acs.jcim.7b00316
更新日期:2018-01-22 00:00:00
abstract::Simulating protein flexibility is a major issue in the docking-based drug-design process for which a single methodological solution does not exist. In our search of new anti-Alzheimer ligands, we were faced with the challenge of including receptor plasticity in a virtual screening campaign aimed at finding new β-secre...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/ci300390h
更新日期:2012-10-22 00:00:00
abstract::Piperine, the bioactive phytochemical from black pepper (Piper nigrum L.), is a nontoxic natural compound exhibiting many physiological and pharmacological properties. They include antioxidant, anti-inflammatory, antimutagenic, antitumor, antiapoptotic, antigenotoxic, antiarthritic, antifungal, antimicrobial, antidepr...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/acs.jcim.5b00514
更新日期:2015-12-28 00:00:00
abstract::The importance of thorough analyses of the secondary structures in proteins as basic structural units cannot be overemphasized. Although recent computational methods have achieved reasonably high accuracy for predicting secondary structures from amino acid sequences, a simple and fundamental empirical approach to char...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/ci900452z
更新日期:2010-04-26 00:00:00
abstract::The anatomical therapeutic chemical (ATC) classification system maintained by the World Health Organization provides a global standard for the classification of medical substances and serves as a source for drug repurposing research. Nevertheless, it lacks several drugs that are major players in the global drug market...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/ci9000844
更新日期:2009-08-01 00:00:00
abstract::Accurate hydrogen placement in molecular modeling is crucial for studying the interactions and dynamics of biomolecular systems. The carboxyl functional group is a prototypical example of a functional group that requires protonation during structure preparation. To our knowledge, when in their neutral form, carboxylic...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/acs.jcim.8b00835
更新日期:2019-05-28 00:00:00
abstract::There is a renewed interest in computer-aided synthesis planning, where the vast majority of approaches require the application of retrosynthetic reaction templates. Here we introduce RDChiral, an open-source Python wrapper for RDKit designed to provide consistent handling of stereochemical information in applying ret...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/acs.jcim.9b00286
更新日期:2019-06-24 00:00:00
abstract::Histone deacetylases (HDACs) are an important class of drug targets for the treatment of cancers, neurodegenerative diseases, and other types of diseases. Virtual screening (VS) has become fairly effective approaches for drug discovery of novel and highly selective histone deacetylase inhibitors (HDACIs). To facilitat...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/ci5005515
更新日期:2015-02-23 00:00:00
abstract::Water is the natural medium of molecules in the cell and plays an important role in protein structure, function and interaction with small molecule ligands. However, the widely used molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) method for binding energy calculation does not explicitly take account of wa...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/ci4001794
更新日期:2014-02-24 00:00:00
abstract::The ongoing search for fast Li-ion conducting solid electrolytes has driven the deployment surge on density functional theory (DFT) computation and materials informatics for exploring novel chemistries before actual experimental testing. Existing structure prototypes can now be readily evaluated beforehand not only to...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/ci500752n
更新日期:2015-06-22 00:00:00
abstract::Telomere maintenance is a universal cancer hallmark, and small molecules that disrupt telomere maintenance generally have anticancer properties. Since the vast majority of cancer cells utilize telomerase activity for telomere maintenance, the enzyme has been considered as an anticancer drug target. Recently, rational ...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/acs.jcim.5b00336
更新日期:2015-12-28 00:00:00
abstract::In this work, we report an ab initio investigation based on density functional theory calculations within van der Waals D3 corrections to investigate the adsorption properties and activation of CO2 on transition-metal (TM) 13-atom clusters (TM = Ru, Rh, Pd, Ag), which is a key step for the development of subnano catal...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/acs.jcim.9b00792
更新日期:2020-02-24 00:00:00
abstract::Nonfibrillar neurotoxic amyloid β (Aβ) oligomer structures are typically rich in β-sheets, which could be promoted by metal ions like Zn(2+). Here, using molecular dynamics (MD) simulations, we systematically examined combinations of Aβ40 peptide conformations and Zn(2+) binding modes to probe the effects of secondary...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/acs.jcim.5b00063
更新日期:2015-06-22 00:00:00
abstract::Growing data sets with increased time for analysis is hampering predictive modeling in drug discovery. Model building can be carried out on high-performance computer clusters, but these can be expensive to purchase and maintain. We have evaluated ligand-based modeling on cloud computing resources where computations ar...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/ci500580y
更新日期:2015-01-26 00:00:00
abstract::On the order of hundreds of absorption, distribution, metabolism, excretion, and toxicity (ADME/Tox) models have been described in the literature in the past decade which are more often than not inaccessible to anyone but their authors. Public accessibility is also an issue with computational models for bioactivity, a...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/acs.jcim.5b00143
更新日期:2015-06-22 00:00:00
abstract::A novel pharmacophore descriptor Flexophore is presented, which considers molecular flexibility when comparing descriptor similarities. The descriptor is a complete reduced graph of the underlying molecule. Its nodes are represented by enhanced MM2 atom types, while the edge descriptions encode the molecular flexibili...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/ci700359j
更新日期:2008-04-01 00:00:00
abstract::Generation and prioritization of new molecules are the most central part of the drug design process. Matched molecular series analysis (MMSA) has recently been proposed as a formal approach that captures both of these key elements of design. In order to better understand the power of MMSA and its specific limitations,...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/acs.jcim.0c00269
更新日期:2020-06-22 00:00:00
abstract::LEAFY (LFY) is a plant-specific transcription factor, with a variety of roles in different species. LFY contains a conserved DNA-binding domain (DBD) that determines its DNA-binding specificity. Recently, the structures of the dimeric LFY-DBD bound to different DNA motifs were successively solved by X-ray crystallogra...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/ci500705j
更新日期:2015-04-27 00:00:00
abstract::We have applied the two most commonly used methods for automatic matched pair identification, obtained the optimum settings, and discovered that the two methods are synergistic. A turbocharging approach to matched pair analysis is advocated in which a first round (a conservative categorical approach that uses an analo...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/acs.jcim.7b00335
更新日期:2017-10-23 00:00:00
abstract::Partial covalent interactions (PCIs) in proteins, which include hydrogen bonds, salt bridges, cation-π, and π-π interactions, contribute to thermodynamic stability and facilitate interactions with other biomolecules. Several score functions have been developed within the Rosetta protein modeling framework that identif...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/acs.jcim.7b00398
更新日期:2018-05-29 00:00:00
abstract::Large corpora of kinase small molecule inhibitor data are accessible to public sector research from thousands of journal article and patent publications. These data have been generated employing a wide variety of assay methodologies and experimental procedures by numerous laboratories. Here we ask the question how app...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/ci300403k
更新日期:2013-01-28 00:00:00
abstract::A kinetic, reactivity-binding model has been proposed to predict the regioselectivity of substrates meditated by the CYP1A2 enzyme, which is responsible for the metabolism of planar-conjugated compounds such as caffeine. This model consists of a docking simulation for binding energy and a semiempirical molecular orbit...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/ci800001m
更新日期:2008-05-01 00:00:00
abstract::The human DNA-repair O (6)-alkylguanine DNA alkyltransferase (MGMT or hAGT) protein protects DNA from environmental alkylating agents and also plays an important role in tumor resistance to chemotherapy treatment. Available inhibitors, based on pseudosubstrate analogs, have been shown to induce substantial bone marrow...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/ci700447r
更新日期:2008-04-01 00:00:00
abstract::The antiproliferative factor (APF) involved in interstitial cystitis is a glycosylated nonapeptide (TVPAAVVVA) containing a sialylated core 1 α-O-disaccharide linked to the N-terminal threonine. The chemical structure of APF was deduced using spectroscopic techniques and confirmed using total synthesis. The synthetic ...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/ci400147s
更新日期:2013-05-24 00:00:00