| |
Records |
Links |
|
Author |
Chirumamilla, C.S.; Palagani, A.; Kamaraj, B.; Declerck, K.; Verbeek, M.W.C.; Ryabtsova, O.; De Bosscher, K.; Bougarne, N.; Ruttens, B.; Gevaert, K.; Houtman, R.; De Vos, W.H.; Joossens, J.; van der Veken, P.; Augustyns, K.; van Ostade, X.; Bogaerts, A.; De Winter, H.; Vanden Berghe, W. |
|
| |
Title |
Selective glucocorticoid receptor properties of GSK866 analogs with cysteine reactive warheads |
Type |
Administrative Services |
| |
Year  |
2017 |
Publication |
Frontiers in immunology |
Abbreviated Journal |
Front Immunol |
|
| |
Volume |
8 |
Issue |
|
Pages |
1324 |
|
| |
Keywords |
Administrative Services; A1 Journal article; Pharmacology. Therapy; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Medicinal Chemistry (UAMC) |
|
| |
Abstract |
Synthetic glucocorticoids (GC) are the mainstay therapy for treatment of acute and chronic inflammatory disorders. Due to the high adverse effects associated with long-term use, GC pharmacology has focused since the nineties on more selective GC ligand-binding strategies, classified as selective glucocorticoid receptor (GR) agonists (SEGRAs) or selective glucocorticoid receptor modulators (SEGRMs). In the current study, GSK866 analogs with electrophilic covalent-binding warheads were developed with potential SEGRA properties to improve their clinical safety profile for long-lasting topical skin disease applications. Since the off-rate of a covalently binding drug is negligible compared to that of a non-covalent drug, its therapeutic effects can be prolonged and typically, smaller doses of the drug are necessary to reach the same level of therapeutic efficacy, thereby potentially reducing systemic side effects. Different analogs of SEGRA GSK866 coupled to cysteine reactive warheads were characterized for GR potency and selectivity in various biochemical and cellular assays. GR- and NFκB-dependent reporter gene studies show favorable anti-inflammatory properties with reduced GR transactivation of two non-steroidal GSK866 analogs UAMC-1217 and UAMC-1218, whereas UAMC-1158 and UAMC-1159 compounds failed to modulate cellular GR activity. These results were further supported by GR immuno-localization and S211 phospho-GR western analysis, illustrating significant GR phosphoactivation and nuclear translocation upon treatment of GSK866, UAMC-1217, or UAMC-1218, but not in case of UAMC-1158 or UAMC-1159. Furthermore, mass spectrometry analysis of tryptic peptides of recombinant GR ligand-binding domain (LBD) bound to UAMC-1217 or UAMC-1218 confirmed covalent cysteine-dependent GR binding. Finally, molecular dynamics simulations, as well as glucocorticoid receptor ligand-binding domain (GR-LBD) coregulator interaction profiling of the GR-LBD bound to GSK866 or its covalently binding analogs UAMC-1217 or UAMC-1218 revealed subtle conformational differences that might underlie their SEGRA properties. Altogether, GSK866 analogs UAMC-1217 and UAMC-1218 hold promise as a novel class of covalent-binding SEGRA ligands for the treatment of topical inflammatory skin disorders. |
|
| |
Address |
|
|
| |
Corporate Author |
|
Thesis |
|
|
| |
Publisher |
|
Place of Publication |
Place of publication unknown |
Editor |
|
|
| |
Language |
|
Wos |
000414136300001 |
Publication Date |
2017-11-01 |
|
| |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
|
| |
Series Volume |
|
Series Issue |
|
Edition |
|
|
| |
ISSN |
1664-3224 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
| |
Impact Factor |
6.429 |
Times cited |
2 |
Open Access |
OpenAccess |
|
| |
Notes |
|
Approved |
Most recent IF: 6.429 |
|
| |
Call Number |
UA @ lucian @ c:irua:146485 |
Serial |
4750 |
|
| Permanent link to this record |
| |
|
| |
|
Author |
Kamaraj, B.; Purohit, R. |
|
| |
Title |
Mutational Analysis on Membrane Associated Transporter Protein (MATP) and Their Structural Consequences in Oculocutaeous Albinism Type 4 (OCA4)A Molecular Dynamics Approach |
Type |
A1 Journal article |
| |
Year |
2016 |
Publication |
Journal of cellular biochemistry |
Abbreviated Journal |
J Cell Biochem |
|
| |
Volume |
117 |
Issue |
11 |
Pages |
2608-2619 |
|
| |
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
|
| |
Abstract |
|
|
| |
Address |
|
|
| |
Corporate Author |
|
Thesis |
|
|
| |
Publisher |
|
Place of Publication |
New York, N.Y. |
Editor |
|
|
| |
Language |
|
Wos |
000383626800017 |
Publication Date |
2016-03-28 |
|
| |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
|
| |
Series Volume |
|
Series Issue |
|
Edition |
|
|
| |
ISSN |
0730-2312 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
| |
Impact Factor |
3.085 |
Times cited |
28 |
Open Access |
|
|
| |
Notes |
|
Approved |
Most recent IF: 3.085 |
|
| |
Call Number |
UA @ lucian @ c:irua:144634 |
Serial |
4671 |
|
| Permanent link to this record |
| |
|
| |
|
Author |
Khosravian, N.; Kamaraj, B.; Neyts, E.C.; Bogaerts, A. |
|
| |
Title |
Structural modification of P-glycoprotein induced by OH radicals: Insights from atomistic simulations |
Type |
A1 Journal article |
| |
Year |
2016 |
Publication |
Scientific reports |
Abbreviated Journal |
Sci Rep-Uk |
|
| |
Volume |
6 |
Issue |
6 |
Pages |
19466 |
|
| |
Keywords |
A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
|
| |
Abstract |
This study reports on the possible effects of OH radical impact on the transmembrane domain 6 of P-glycoprotein, TM6, which plays a crucial role in drug binding in human cells. For the first time, we employ molecular dynamics (MD) simulations based on the self-consistent charge density functional tight binding (SCC-DFTB) method to elucidate the potential sites of fragmentation and mutation in this domain upon impact of OH radicals, and to obtain fundamental information about the underlying reaction mechanisms. Furthermore, we apply non-reactive MD simulations to investigate the long-term effect of this mutation, with possible implications for drug binding. Our simulations indicate that the interaction of OH radicals with TM6 might lead to the breaking of C-C and C-N peptide bonds, which eventually cause fragmentation of TM6. Moreover, according to our simulations, the OH radicals can yield mutation in the aromatic ring of phenylalanine in TM6, which in turn affects its structure. As TM6 plays an important role in the binding of a range of cytotoxic drugs with P-glycoprotein, any changes in its structure are likely to affect the response of the tumor cell in chemotherapy. This is crucial for cancer therapies based on reactive oxygen species, such as plasma treatment. |
|
| |
Address |
Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium |
|
| |
Corporate Author |
|
Thesis |
|
|
| |
Publisher |
|
Place of Publication |
|
Editor |
|
|
| |
Language |
English |
Wos |
000369573900001 |
Publication Date |
2016-02-09 |
|
| |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
|
| |
Series Volume |
|
Series Issue |
|
Edition |
|
|
| |
ISSN |
2045-2322 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
| |
Impact Factor |
4.259 |
Times cited |
7 |
Open Access |
|
|
| |
Notes |
The authors acknowledge financial support from the Fund for Scientific Research (FWO) Flanders, grant number G012413N. The calculations were performed in part using the Turing HPC infrastructure of the CalcUA core facility of the Universiteit Antwerpen, a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the Universiteit Antwerpen.” |
Approved |
Most recent IF: 4.259 |
|
| |
Call Number |
c:irua:131610 |
Serial |
4031 |
|
| Permanent link to this record |
| |
|
| |
|
Author |
Bogaerts, A.; Khosravian, N.; Van der Paal, J.; Verlackt, C.C.W.; Yusupov, M.; Kamaraj, B.; Neyts, E.C. |
|
| |
Title |
Multi-level molecular modelling for plasma medicine |
Type |
A1 Journal article |
| |
Year |
2016 |
Publication |
Journal of physics: D: applied physics |
Abbreviated Journal |
J Phys D Appl Phys |
|
| |
Volume |
49 |
Issue |
49 |
Pages |
054002 |
|
| |
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
|
| |
Abstract |
Modelling at the molecular or atomic scale can be very useful for obtaining a better insight in plasma medicine. This paper gives an overview of different atomic/molecular scale modelling approaches that can be used to study the direct interaction of plasma species with biomolecules or the consequences of these interactions for the biomolecules on a somewhat longer time-scale. These approaches include density functional theory (DFT), density functional based tight binding (DFTB), classical reactive and non-reactive molecular dynamics (MD) and united-atom or coarse-grained MD, as well as hybrid quantum mechanics/molecular mechanics (QM/MM) methods. Specific examples will be given for three important types of biomolecules, present in human cells, i.e. proteins, DNA and phospholipids found in the cell membrane. The results show that each of these modelling approaches has its specific strengths and limitations, and is particularly useful for certain applications. A multi-level approach is therefore most suitable for obtaining a global picture of the plasma–biomolecule interactions. |
|
| |
Address |
|
|
| |
Corporate Author |
|
Thesis |
|
|
| |
Publisher |
|
Place of Publication |
|
Editor |
|
|
| |
Language |
|
Wos |
000368944100003 |
Publication Date |
2015-12-16 |
|
| |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
|
| |
Series Volume |
|
Series Issue |
|
Edition |
|
|
| |
ISSN |
0022-3727 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
| |
Impact Factor |
2.588 |
Times cited |
11 |
Open Access |
|
|
| |
Notes |
This work is financially supported by the Fund for Scientific Research Flanders (FWO) and the Francqui Foundation. The calculations were carried out in part using the Turing HPC infrastructure of the CalcUA core facility of the Universiteit Antwerpen, a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the Universiteit Antwerpen. |
Approved |
Most recent IF: 2.588 |
|
| |
Call Number |
c:irua:131571 |
Serial |
3985 |
|
| Permanent link to this record |
| |
|
| |
|
Author |
Bogaerts, A.; Khosravian, N.; Van der Paal, J.; Verlackt, C.C.W.; Yusupov, M.; Kamaraj, B.; Neyts, E.C. |
|
| |
Title |
Multi-level molecular modelling for plasma medicine |
Type |
A1 Journal article |
| |
Year |
2016 |
Publication |
Journal Of Physics D-Applied Physics |
Abbreviated Journal |
J Phys D Appl Phys |
|
| |
Volume |
49 |
Issue |
5 |
Pages |
054002-54019 |
|
| |
Keywords |
A1 Journal article; Plasma, laser ablation and surface modeling – Antwerp (PLASMANT) |
|
| |
Abstract |
|
|
| |
Address |
|
|
| |
Corporate Author |
|
Thesis |
|
|
| |
Publisher |
|
Place of Publication |
London |
Editor |
|
|
| |
Language |
|
Wos |
|
Publication Date |
0000-00-00 |
|
| |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
|
| |
Series Volume |
|
Series Issue |
|
Edition |
|
|
| |
ISSN |
0022-3727 |
ISBN |
|
Additional Links |
UA library record |
|
| |
Impact Factor |
2.588 |
Times cited |
|
Open Access |
|
|
| |
Notes |
|
Approved |
Most recent IF: 2.588 |
|
| |
Call Number |
UA @ lucian @ c:irua:129798 |
Serial |
4467 |
|
| Permanent link to this record |
| |
|
| |
|
Author |
Kamaraj, B.; Bogaerts, A. |
|
| |
Title |
Structure and function of p53-DNA complexes with inactivation and rescue mutations : a molecular dynamics simulation study |
Type |
A1 Journal article |
| |
Year |
2015 |
Publication |
PLoS ONE |
Abbreviated Journal |
Plos One |
|
| |
Volume |
10 |
Issue |
10 |
Pages |
e0134638 |
|
| |
Keywords |
A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
|
| |
Abstract |
The tumor suppressor protein p53 can lose its function upon DNA-contact mutations (R273C and R273H) in the core DNA-binding domain. The activity can be restored by second-site suppressor or rescue mutations (R273CT284R, R273HT284R, and R273HS240R). In this paper, we elucidate the structural and functional consequence of p53 proteins upon DNA-contact mutations and rescue mutations and the underlying mechanisms at the atomic level by means of molecular dynamics simulations. Furthermore, we also apply the docking approach to investigate the binding phenomena between the p53 protein and DNA upon DNA-contact mutations and rescue mutations. This study clearly illustrates that, due to DNA-contact mutants, the p53 structure loses its stability and becomes more rigid than the native protein. This structural loss might affect the p53-DNA interaction and leads to inhibition of the cancer suppression. Rescue mutants (R273CT284R, R273HT284R and R273HS240R) can restore the functional activity of the p53 protein upon DNA-contact mutations and show a good interaction between the p53 protein and a DNA molecule, which may lead to reactivate the cancer suppression function. Understanding the effects of p53 cancer and rescue mutations at the molecular level will be helpful for designing drugs for p53 associated cancer diseases. These drugs should be designed so that they can help to inhibit the abnormal function of the p53 protein and to reactivate the p53 function (cell apoptosis) to treat human cancer. |
|
| |
Address |
|
|
| |
Corporate Author |
|
Thesis |
|
|
| |
Publisher |
|
Place of Publication |
|
Editor |
|
|
| |
Language |
|
Wos |
000359061400096 |
Publication Date |
2015-08-05 |
|
| |
Series Editor |
|
Series Title |
|
Abbreviated Series Title |
|
|
| |
Series Volume |
|
Series Issue |
|
Edition |
|
|
| |
ISSN |
1932-6203; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
| |
Impact Factor |
2.806 |
Times cited |
|
Open Access |
|
|
| |
Notes |
|
Approved |
Most recent IF: 2.806; 2015 IF: 3.234 |
|
| |
Call Number |
c:irua:126779 |
Serial |
3278 |
|
| Permanent link to this record |
