Abstract:
:Current research has shown cell-penetrating peptides and antimicrobial peptides (AMPs) as probable vectors for use in drug delivery and as novel antibiotics. It has been reported that the higher the therapeutic index (TI) the higher would be the bacterial cell penetrating ability. To the best of our knowledge, no in-silico study has been performed to determine bacterial cell specificity of the antimicrobial cell penetrating peptides (aCPP's) based on their TI. The aim of this study was to develop a quantitative structure activity relationship (QSAR) model, which can estimate antimicrobial potential and cell-penetrating ability of aCPPs against S. aureus, to confirm the relationship between the TI and aCPPs and to identify specific descriptors responsible for aCPPs penetrating ability. Molecular dynamics (MD) simulation was also performed to confirm the membrane insertion of the most active aCPPs obtained from the QSAR study. The most appropriate pharmacophore was identified to predict the aCPP's activity. The statistical results confirmed the validity of the model. The QSAR model was successful in identifying the optimal aCPP with high activity prediction and provided insights into the structural requirements to correlate their TI to cell penetrating ability. MD simulation of the best aCPP with 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayer confirmed its interaction with the membrane and the C-terminal residues of the aCPP played a key role in membrane penetration. The strategy of combining QSAR and molecular dynamics, allowed for optimal estimation of ligand-target interaction and confirmed the importance of Trp and Lys in interacting with the POPC bilayer. Communicated by Ramaswamy H. Sarma.
journal_name
J Biomol Struct Dynjournal_title
Journal of biomolecular structure & dynamicsauthors
Faya M,Kalhapure RS,Dhumal D,Agrawal N,Omolo C,Akamanchi KG,Govender Tdoi
10.1080/07391102.2018.1484814subject
Has Abstractpub_date
2019-06-01 00:00:00pages
2370-2380issue
9eissn
0739-1102issn
1538-0254journal_volume
37pub_type
杂志文章abstract::EcoRII DNA methyltransferase (M.EcoRII) recognizes the DNA sequence 5'.CC*T/AGG.3' and catalyzes the transfer of the methyl group from S-adenosyl-L-methionine to the C5 position of the inner cytosine residue (C*). We obtained several DNA duplexes containing photoactive 5-iodo-2'-deoxyuridine (i(5)dU) or 5-[4-(3-(trifl...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2002.10506860
更新日期:2002-12-01 00:00:00
abstract::Transcription factor NAM-B1 has a major role in the process of senescence, which results in higher Fe and Zn concentrations in grains of wild wheat (T. durum; Td). The absence of the wild type NAMB1 in T. aestivum (Ta), one of the cardinal crops essential for more than 1/3rd of the global population, affects Fe and Zn...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2019.1680435
更新日期:2020-08-01 00:00:00
abstract::An important regulatory domain of NF-[Formula: see text]B Essential Modulator (NEMO) is a ubiquitin-binding zinc finger, with a tetrahedral CYS3HIS1 zinc-coordinating binding site. Two variations of NEMO's zinc finger are implicated in various disease states including ectodermal dysplasia and adult-onset glaucoma. To ...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2017.1363662
更新日期:2018-08-01 00:00:00
abstract::Many bacterial genomes have been sequenced and stored in public databases now, of which Reference Sequence (RefSeq) is the most widely used one. However, the annotation in RefSeq is still unsatisfactory. The present analysis is focused on the re-annotation of an important plant pathogen genome Xanthomonas oryzae pv. o...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2012.698218
更新日期:2013-03-01 00:00:00
abstract::Third generation EGFR inhibitor osimertinib was approved as the first-line treatment for EGFR T790M mutation-positive Non-Small Cell Lung Cancer (NSCLC) patients in 2017. However, EGFR tertiary Cys797 to Ser797 (C797S) point mutation emanate rapidly after treatment of osimertinib, which is undruggable mutation to the ...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2020.1754918
更新日期:2020-04-23 00:00:00
abstract::Inhibition of normal cellular apoptosis or programed cell death is the hallmark of all cancers. Apoptotic dysregulation can result in numerous pathological conditions, such as cancers, autoimmune disorders, and neurodegeneration. Members of the BCL-2 family of proteins regulate the process of apoptosis by its promotio...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2018.1508371
更新日期:2019-08-01 00:00:00
abstract::The deoxydinucleoside triphosphate units d-pCpGp and d-pGpCp were subjected to a rigorous theoretical investigation with a view to describing their distinctive conformational characteristics. For each unit 216 probable three-dimensional forms defined by the backbone-base dihedral angles and sugar pucker modes were con...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1989.10507737
更新日期:1989-02-01 00:00:00
abstract::The sharp spurt in positive cases of novel coronavirus-19 (SARS-CoV-2) worldwide has created a big threat to human. In view to expedite new drug leads for COVID-19, Main Proteases (Mpro) of novel Coronavirus (SARS-CoV-2) has emerged as a crucial target for this virus. Nitric oxide (NO) inhibits the replication cycle o...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2020.1790038
更新日期:2020-07-08 00:00:00
abstract::Cromolyn sodium (CS), an anti-inflammatory drug is used in the treatment of allergic disorders. Bovine serum albumin (BSA) a blood plasma protein is used as a model protein for studying protein folding and ligand binding mechanism as it is the main transporter protein which decides the disposition and pharmacodynamics...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2019.1586588
更新日期:2020-02-01 00:00:00
abstract::Drug resistant mutations have severely restricted the success of HIV therapy. These mutations frequently involve the aspartic protease encoded by the virus. Knowledge of the molecular mechanisms underlying the conformational changes of HIV-1 protease mutants may be useful in developing more effective and longer lastin...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2011.10507379
更新日期:2011-08-01 00:00:00
abstract::Binding affinities of flavonols namely quercetin, myricetin, and kaempferol to human serum albumin (HSA) were determined fluorimetrically and the order was observed to be myricetin > quercetin > kaempferol demonstrating structure-activity relationship. Quercetin-coated silver nanoparticles (AgNPs) show higher binding ...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2018.1462732
更新日期:2019-04-01 00:00:00
abstract::The acute respiratory syndrome caused by the SARS-CoV-2, known as COVID-19, has been ruthlessly tormenting the world population for more than six months. However, so far no effective drug or vaccine against this plague have emerged yet, despite the huge effort in course by researchers and pharmaceutical companies worl...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2020.1869096
更新日期:2021-01-08 00:00:00
abstract::Most fibrous polynucleotides of general sequence exhibit secondary structures that are described adequately by regular helices with a repeated motif of only one nucleotide. Such helices exploit the fact that A:T, T:A, G:C, and C:G pairs are essentially isomorphous and have dyadically-related glycosylic bonds. Polynucl...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1983.10507453
更新日期:1983-10-01 00:00:00
abstract::About one-third of the existing proteins require metal ions as cofactors for their catalytic activities and structural complexities. While many of them bind only to a specific metal, others bind to multiple (different) metal ions. However, the exact mechanism of their metal preference has not been deduced to clarity. ...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2015.1080629
更新日期:2016-07-01 00:00:00
abstract::K562 cells are erythroleukemic cells derived from a chronic myeloid leukemia patient in blast crisis. Comparison of the genome from K562 cells and normal human genome has been very useful strategy, in uncovering eight genes, implicated in acute myeloid leukemia (AML). These genes carry mutations in K562 genome and the...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2012.698190
更新日期:2013-03-01 00:00:00
abstract::Binding interactions of the phenazinium dye Janus green blue (JGB) with human and bovine serum albumins (BSA - and BSA) have been explored for the first time from multi-spectroscopic and calorimetric measurements aided by in silico calculations. The formation of ground state complexes between JGB and the respective se...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2020.1870156
更新日期:2021-01-07 00:00:00
abstract::The pandemic coronavirus disease (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) presents a great threat to public health. Currently, no potent medicine is available to treat COVID-19. Quest for new drugs especially from natural plant sources is an area of immense potential. The curre...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2020.1762743
更新日期:2020-05-12 00:00:00
abstract::Elicitins, produced by most of the phytopathogenic fungi of the genus Phytophthora, provoke in the tobacco plant both remote leaf necrosis and the induction of a resistance against subsequent attack by various micro-organisms. The crystal structure of b-cryptogein (CRY), secreted by Phytophthora cryptogea, was previou...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2000.10506680
更新日期:2000-12-01 00:00:00
abstract::COVID-19 and its causative organism SARS-CoV2 that emerged from Wuhan city, China have paralyzed the world. With no clinically approved drugs, the global health system is struggling to find an effective treatment measure. At this crucial juncture, screening of plant-derived compounds may be an effective strategy to co...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2020.1835729
更新日期:2020-10-22 00:00:00
abstract::Human major histocompatibility complex class I (MHC I) - or human leukocyte antigen (HLA) - proteins present intracellularly processed peptides to cytotoxic T lymphocytes in the adaptive immune response to pathogens. A high level of polymorphism in human MHC I proteins defines the peptide-binding specificity of thousa...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2017.1295884
更新日期:2018-02-01 00:00:00
abstract::The model of spatial structure for the principal neutralizing determinant (PND) of the HIV-1 envelope protein gp120 is proposed in terms of two-dimensional nuclear Overhauser effect (NOE) spectroscopy data. To build the model, the NMR-based theoretical conformational analysis of synthetic PND peptides of length 40, 24...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1999.10508303
更新日期:1999-02-01 00:00:00
abstract::The knowledge of the relationship between the three-dimensional structure of a protein and its biological and stability is one of the most challenging problem in protein chemistry, since offers the possibility of changing both the specific action of a protein and its stability. In this work, we have approached the pro...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1998.10508259
更新日期:1998-10-01 00:00:00
abstract::Enzymes involved in the pyrimidine biosynthesis pathway have become an important target for the pharmacological intervention. One among those enzymes, Aspartate Trans Carbamoylase (ATCase), catalyses the condensation of aspartate and carbamoyl phosphate to form N-carbamoyl-l-aspartate and inorganic phosphate. The pres...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2013.782825
更新日期:2014-04-01 00:00:00
abstract::The interaction of 6-Thioguanine molecule, an antitumor drug with carbon nanotube and boron nitride nanotube (BNNT) is investigated using molecular dynamics simulations. Based on the obtained results, the strongest negative van der Waals interaction is found between 6-TG and BNNT among the studied nanotubes, which ind...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2019.1585951
更新日期:2020-02-01 00:00:00
abstract::A computer simulation of guanine (G), cytosine (C), the G-C base pair, protonated C (CH+), acetic acid in neutral (AcOH) and deprotonated (AcO-) forms, G-AcO-, C-AcOH, and CH(+)-AcO- complexes, solvated in DMSO was carried out by the Monte Carlo method. It is shown that the G-C base pair formation in DMSO is energetic...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1997.10508197
更新日期:1997-10-01 00:00:00
abstract::A procedure is described for the complete resolution of concentration profiles of oligonucleotide triplexes as a function of pH and temperature. The pH and temperature ranges at which triplexes are present and the relative concentrations of all the species involved in acid-base and conformational equilibria are succes...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2003.10506922
更新日期:2003-10-01 00:00:00
abstract::The eIF2α kinase activity of the heme-regulated inhibitor (HRI) is regulated by heme which makes it a unique member of the family of eIF2α kinases. Since heme concentrations create an equilibrium for the kinase to be active/inactive, it becomes important to study the heme binding effects upon the kinase and understand...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2017.1368417
更新日期:2018-08-01 00:00:00
abstract::Cytochrome bcc complex is important for ATP synthesis and cellular activity, as a crucial step in the terminal reduction of oxygen in aerobic electron transport chains. The b subunit of cytochrome bcc complex (QcrB) has been reported as a promising anti-tuberculosis target, with many novel anti-tuberculosis scaffolds ...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2019.1688196
更新日期:2020-10-01 00:00:00
abstract::Breast cancer (BC) is the second most prevalent cancer worldwide. Estrogen receptor beta (ERβ) is an essential protein of breast cells to suppress estrogen-induced uncontrolled proliferation. Thus, small molecules that can modulate and enhance ERβ expression would be an effective agent to suppress BC development. Stud...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2020.1737233
更新日期:2020-03-11 00:00:00
abstract::Inspection of stereochemical models suggests a possible correlation between the proportion (Yg-/Yt) of the g- and t rotamers and the S pucker populations irrespective of the anti-syn conformational composition of the base. Interpretation of the NMR vicinal coupling constants in terms of conformational populations show...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1984.10507558
更新日期:1984-08-01 00:00:00