Abstract:
:Mimicking receptor flexibility during receptor-ligand binding is a challenging task in computational drug design since it is associated with a large increase in the conformational search space. In the present study, we have devised an in silico design strategy incorporating receptor flexibility in virtual screening to identify potential lead compounds as inhibitors for flexible proteins. We have considered BACE1 (β-secretase), a key target protease from a therapeutic perspective for Alzheimer's disease, as the highly flexible receptor. The protein undergoes significant conformational transitions from open to closed form upon ligand binding, which makes it a difficult target for inhibitor design. We have designed a hybrid structure-activity model containing both ligand based descriptors and energetic descriptors obtained from molecular docking based on a dataset of structurally diverse BACE1 inhibitors. An ensemble of receptor conformations have been used in the docking study, further improving the prediction ability of the model. The designed model that shows significant prediction ability judged by several statistical parameters has been used to screen an in house developed 3-D structural library of 731 phytochemicals. 24 highly potent, novel BACE1 inhibitors with predicted activity (Ki) ≤ 50 nM have been identified. Detailed analysis reveals pharmacophoric features of these novel inhibitors required to inhibit BACE1.
journal_name
Mol Biosystjournal_title
Molecular bioSystemsauthors
Chakraborty S,Ramachandran B,Basu Sdoi
10.1039/c4mb00307asubject
Has Abstractpub_date
2014-10-01 00:00:00pages
2684-92issue
10eissn
1742-206Xissn
1742-2051journal_volume
10pub_type
杂志文章abstract::Protein tyrosine phosphatases (PTPs) constitute a large family of enzymes that play key roles in cell signaling. Deregulation of PTP activity results in aberrant tyrosine phosphorylation, which has been linked to the etiology of several human diseases, including cancer. Since phosphate removal by the PTPs can both enh...
journal_title:Molecular bioSystems
pub_type: 杂志文章,评审
doi:10.1039/b700704n
更新日期:2007-05-01 00:00:00
abstract::To identify an agent with specific activity against human lens epithelial cells (HLECs), we confirmed the presence of glucocorticoid receptors (GRs) and GR-α genes and evaluated whether GRs have a relationship with the apoptotic process in cultured HLECs. We also determined whether the inhibitor RU486 could rescue the...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c1mb05045a
更新日期:2011-06-01 00:00:00
abstract::Conventional methods for detecting single nucleotide polymorphisms (SNPs), including direct DNA sequencing, pyrosequencing, and melting curve analysis, are to a great extent limited by their requirement for particular detection instruments. To overcome this limitation, we established a novel SNP detection technique ut...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/b701645j
更新日期:2007-08-01 00:00:00
abstract::Microbial long chain alcohols and alkanes are renewable biofuels that could one day replace petroleum-derived fuels. Here we report a novel pathway for high efficiency production of these products in Escherichia coli strain BL21(DE3). We first identified the acyl-ACP reductase/aldehyde deformylase combinations with th...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c5mb00268k
更新日期:2015-09-01 00:00:00
abstract::Rhein is a natural product purified from herbal plants such as Rheum palmatum, which has been shown to have anti-angiogenesis and anti-tumor metastasis properties. However, the biological effects of rhein on the behavior of breast cancers are not completely elucidated. To evaluate whether rhein might be useful in the ...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c4mb00451e
更新日期:2014-12-01 00:00:00
abstract::The selective inhibition for JAK2 over the other JAK family kinases (JAK1, JAK3 and TYK2) has shared an immense challenge due to high conservatism. In this paper, the highly JAK2 selective mechanism of the thienopyridine derivative was identified at the molecular level, based on insights into the inhibitory effects of...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c5mb00747j
更新日期:2016-02-01 00:00:00
abstract::Histone deacetylases (HDACs) contribute to regulation of gene expression by mediating higher-order chromatin structures. They assemble into large multiprotein complexes that regulate activity and specificity. We report the development of small molecule probes with class IIa and pan-HDAC activity that contain photoreac...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c6mb00109b
更新日期:2016-05-24 00:00:00
abstract::Non-ribosomal peptide synthetases (NRPSs) are enzymes that catalyze ribosome-independent production of small peptides, most of which are bioactive. NRPSs act as peptide assembly lines where individual, often interconnected modules each incorporate a specific amino acid into the nascent chain. The modules themselves co...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c3mb70594c
更新日期:2014-07-01 00:00:00
abstract::Protein tyrosine phosphatases are crucial regulators of signal transduction and function as antagonists towards protein tyrosine kinases to control reversible tyrosine phosphorylation, thereby regulating fundamental physiological processes. Growing evidence has supported the notion that reversible oxidative inactivati...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c5mb00847f
更新日期:2016-05-24 00:00:00
abstract::In the pathogenesis of renal fibrosis, oxidative stress (OS) enhances the production of reactive oxygen species (ROS) leading to sustained cell growth, inflammation, excessive tissue remodelling and accumulation, which results in the development and acceleration of renal damage. In our previous work (Eltoweissy et al....
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c5mb00887e
更新日期:2016-05-24 00:00:00
abstract::Gene regulatory networks constitute the first layer of the cellular computation for cell adaptation and surveillance. In these webs, a set of causal relations is built up from thousands of interactions between transcription factors and their target genes. The large size of these webs and their entangled nature make it...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/B904960f
更新日期:2009-12-01 00:00:00
abstract::A liquid chromatography coupled with mass spectrometry (LC/MS) based metabonomics approach was applied to characterize the aging of rats, and the anti-aging effect of total flavones of Epimedium (TFE), a traditional Chinese medicine, has also been investigated. Serum samples collected from 4, 10, 18 and 24 month-old r...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/b816407j
更新日期:2009-10-01 00:00:00
abstract::Type 2 diabetes mellitus (T2DM) is increased worldwide in parallel with the obesity epidemic. Potentilla discolor is one of the most important crude materials in Traditional Chinese medicine (TCM) for therapy of hyperglycemia and hyperlipidemia. In this work, a plasma metabonomic approach based on the combination of U...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c4mb00278d
更新日期:2014-11-01 00:00:00
abstract::As a versatile pathogen Staphylococcus aureus can cause various disease patterns, which are influenced by strain specific virulence factor repertoires but also by S. aureus physiological adaptation capacity. Here, we present metabolomic descriptions of S. aureus central metabolic pathways and demonstrate the potential...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c0mb00315h
更新日期:2011-04-01 00:00:00
abstract::New approaches to improve the quality and efficiency of stem cell-derived neurons are important for both research and clinical arenas. Customized subsets of differentiated neurons can be used as model systems to understand the etiology of a variety of complex neurological diseases and disorders. These same neuronal ce...
journal_title:Molecular bioSystems
pub_type: 杂志文章,评审
doi:10.1039/b914822c
更新日期:2010-02-01 00:00:00
abstract::Peptidylarginine deiminase (PAD) catalyzes the posttranslational citrullination of selected proteins in a calcium dependent manner. The PAD4 isoform has been implicated in multiple sclerosis, rheumatoid arthritis, some types of cancer, and plays a role in gene regulation. However, the substrate selectivity of PAD4 is ...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c1mb05089c
更新日期:2011-07-01 00:00:00
abstract::Insight into the molecular mechanism of complex diseases is an important topic in the current bio-medical research. However, different from the single-gene disorders, high heterogeneity of many of the complex diseases prevents scientists from the exact understanding of the etiology. In this study, we used Myelodysplas...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c1mb05018d
更新日期:2011-06-01 00:00:00
abstract::Human mitogen-activated protein kinase (MAPK) family members JNK and p38 are two homologous protein-serine/threonine kinases but play distinct roles in the pathological process of neurological disorders. Selective targeting of JNK over p38 has been established as a potential therapeutic approach to epilepsy and other ...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c6mb00297h
更新日期:2016-07-19 00:00:00
abstract::Differential gene expression governs the development, function and pathology of multicellular organisms. Transcription regulatory networks study differential gene expression at a systems level by mapping the interactions between regulatory proteins and target genes. While microarray transcription profiles are the most...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/B908108a
更新日期:2009-12-01 00:00:00
abstract::The mono-site mutations of the absolutely conserved residues, (464)LGR(466), in the α-helix 5 (h5) of HPV16 L1 completely disrupted the pentamer formation. The implication of this finding is the potential usage of a h5-like peptide as the reagent to interfere with the pentamer formation and stability as an anti-HPV re...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c3mb70550a
更新日期:2014-04-01 00:00:00
abstract::The protein kinase C (PKC) family of serine/threonine kinases is an attractive drug target for the treatment of cancer and other diseases. Diacylglycerol (DAG), phorbol esters and others act as ligands for the C1 domain of PKC isoforms. Inspection of the crystal structure of the PKCδ C1b subdomain in complex with phor...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c2mb05452c
更新日期:2012-04-01 00:00:00
abstract::Regular physical activity is associated with a reduced risk of coronary heart disease, as it probably modifies the balance between free-radical generation and antioxidant activity. On the other hand, however, acute physical activity increases oxygen uptake and leads to a temporary imbalance between the production of r...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c0mb00106f
更新日期:2011-03-01 00:00:00
abstract::Epithelial ovarian cancer (EOC) is the most lethal of gynecologic malignancies due to the high rate of recurrence and poor prognosis. Predicting the prognosis in patients with EOC is clinically challenging, partly because appropriate biomarkers of recurrence have yet to be explored. In this prospective study, pre-trea...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c4mb00407h
更新日期:2015-02-01 00:00:00
abstract::The eIF4E-binding protein 1 (4EBP1) has long been known to be completely unstructured without any secondary structures, which contributed significantly to the proposal of the induced fit mechanism for target binding of intrinsically disordered proteins. We show here that 4EBP1 is not completely unstructured, but conta...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c4mb00532e
更新日期:2015-02-01 00:00:00
abstract::The knowledge available about the application and generation of induced pluripotent stem cells (iPSC) has grown since their discovery, and new techniques to enhance the reprogramming process have been described. Among the new approaches to induce iPSC that have gained great attention is the use of small molecules for ...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c3mb70159j
更新日期:2013-11-01 00:00:00
abstract::Matrix metalloproteinases (MMPs) consist of a class of proteins required for normal tissue function. Their over expression is associated with many disease states and hence the interest in MMPs as drug targets. Almost all MMP inhibitors have been reported to fail in clinical trials due to lack of specificity. Zinc in t...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c5mb00003c
更新日期:2015-04-01 00:00:00
abstract::Epithelial to mesenchymal transition (EMT) is a biological process that plays a crucial role in cancer metastasis. Although studies regarding the EMT mechanisms are usual in terms of gene expression and protein functions, little is known about the involvement of lipids in EMT. In this work, an untargeted lipidomic ana...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c5mb00413f
更新日期:2015-12-01 00:00:00
abstract::With the advent of new cancer therapies in the last few years, the goals of reducing disease burden and improving quality of life are frequently achieved. Yet despite the advances seen with numerous monotherapies, a multimodality approach that targets different aspects of tumor biology may yield the greatest clinical ...
journal_title:Molecular bioSystems
pub_type: 杂志文章,评审
doi:10.1039/b911313b
更新日期:2009-11-01 00:00:00
abstract::The major mechanical function of talin is to couple the β-integrin cytoplasmic tails to actin filaments. A variety of β-integrin tails contain conserved binding motifs for talin, and recent research shows that β-integrins differ both in affinity to talin and preferences for other cytoplasmic adaptor proteins. While ta...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c4mb00341a
更新日期:2014-12-01 00:00:00
abstract::Blockage of the interactions between immunologic checkpoint protein PD-1 and its ligand PD-L1 showed efficacy for cancer treatment. X-ray structures have captured static conformational snapshots of PD-1 and revealed that the CC' loop adopts an open conformation in the apo-protein but turns into a closed form and inter...
journal_title:Molecular bioSystems
pub_type: 杂志文章
doi:10.1039/c7mb00036g
更新日期:2017-05-02 00:00:00