Cancer research experiments

Characterization of partially ordered states in the intrinsically disordered N-terminal domain of p53 using millisecond molecular dynamics simulations.

WU tags:

Description

[Experiment image]

The exploration of intrinsically disordered proteins in isolation is a crucial step to understand their complex dynamical behavior. In particular, the emergence of partially ordered states has not been explored in depth. The experimental characterization of such partially ordered states remains elusive due to their transient nature. Molecular dynamics mitigates this limitation thanks to its capability to explore biologically relevant timescales while retaining atomistic resolution. Here, millisecond unbiased molecular dynamics simulations were performed in the exemplar N-terminal region of p53. In combination with state-of-the-art Markov state models, simulations revealed the existence of several partially ordered states accounting for [Formula: see text] 40% of the equilibrium population. Some of the most relevant states feature helical conformations similar to the bound structure of p53 to Mdm2, as well as novel [Formula: see text]-sheet elements. This highlights the potential complexity underlying the energy surface of intrinsically disordered proteins.

Publications

  • Herrera-Nieto P, Pérez A, De Fabritiis G, Characterization of partially ordered states in the intrinsically disordered N-terminal domain of p53 using millisecond molecular dynamics simulations. Scientific reports 2020. doi:10.1038/s41598-020-69322-2

BadgeRankNameCredit
wat1 GPUGRID Role account109,002,400.00
wat2 Stoneageman103,784,200.00
wat3 RaymondFO*63,510,400.00
wat4 Retvari Zoltan52,315,800.00
wat5 Rick A. Sponholz48,480,200.00
wat6 Herb48,301,800.00
wat7 HA-SOFT, s.r.o.43,462,700.00
wat8 Roald35,546,200.00
wat9 ecafkid30,573,300.00
wat10 Nikke29,168,400.00
Number of contributors: 1450

Computational and experimental characterization of NF023, a candidate anticancer compound inhibiting cIAP2/TRAF2 assembly.

WU tags:

Description

[Experiment image]

Protein-protein interactions are the basis of many important physiological processes, and are currently promising, yet difficult, targets for drug discovery. In this context, inhibitors of apoptosis (IAPs)-mediated interactions are pivotal for cancer cell survival; the interaction of the BIR1 domain of cIAP2 with TRAF2 was shown to lead the recruitment of cIAPs to the TNF-receptor, promoting the activation of NF-κB survival pathway. In this work, using a combined in silico-in vitro approach we identified a drug-like molecule, NF023, able to disrupt cIAP2 interaction with TRAF2. We demonstrated in vitro its ability to interfere with the assembly of the cIAP2-BIR1/TRAF2 complex and performed a thorough characterization of the compound's mode of action through 248 parallel unbiased molecular dynamics simulations of 300 ns (totaling almost 75 µs of all-atom sampling), which identified multiple binding modes to the BIR1 domain of cIAP2 via clustering and ensemble docking. NF023 is, thus, a promising protein-protein interaction disruptor, representing a starting point to develop modulators of NF-κB-mediated cell survival in cancer. This study represents a model-procedure that shows the use of large-scale molecular dynamics methods to typify promiscuous interactors.

Publications

  • Cossu F, Sorrentino L, Fagnani E, Zaffaroni M, Milani M, Giorgino T, Mastrangelo E, Computational and experimental characterization of NF023, a candidate anticancer compound inhibiting cIAP2/TRAF2 assembly. Journal of chemical information and modeling 2020. doi:10.1021/acs.jcim.0c00518

BadgeRankNameCredit
wat1 grcpool.com-3577,500.00
wat2 grcpool.com-2350,625.00
wat3 Stoneageman288,750.00
wat4 melk275,000.00
wat5 grcpool.com247,500.00
wat6 joel247,500.00
wat7 KWSN-SpongeBob SquarePants247,500.00
wat8 Thomas M. Taylor206,250.00
wat9 deepspacecomputing206,250.00
wat10 BelgianEnthousiast206,250.00
Number of contributors: 315

Dopamine D3 receptor antagonist reveals a cryptic pocket in aminergic GPCRs.

WU tags:

Description

[Experiment image]

The recent increase in the number of X-ray crystal structures of G-protein coupled receptors (GPCRs) has been enabling for structure-based drug design (SBDD) efforts. These structures have revealed that GPCRs are highly dynamic macromolecules whose function is dependent on their intrinsic flexibility. Unfortunately, the use of static structures to understand ligand binding can potentially be misleading, especially in systems with an inherently high degree of conformational flexibility. Here, we show that docking a set of dopamine D3 receptor compounds into the existing eticlopride-bound dopamine D3 receptor (D3R) X-ray crystal structure resulted in poses that were not consistent with results obtained from site-directed mutagenesis experiments. We overcame the limitations of static docking by using large-scale high-throughput molecular dynamics (MD) simulations and Markov state models (MSMs) to determine an alternative pose consistent with the mutation data. The new pose maintains critical interactions observed in the D3R/eticlopride X-ray crystal structure and suggests that a cryptic pocket forms due to the shift of a highly conserved residue, F

Publications

  • Ferruz N, Doerr S, Vanase-Frawley MA, Zou Y, Chen X, Marr ES, Nelson RT, Kormos BL, Wager TT, Hou X, Villalobos A, Sciabola S, De Fabritiis G, Dopamine D3 receptor antagonist reveals a cryptic pocket in aminergic GPCRs. Scientific reports 2018. doi:10.1038/s41598-018-19345-7

BadgeRankNameCredit
wat1 Stoneageman83,460,000.00
wat2 Roald69,270,000.00
wat3 RaymondFO*63,660,000.00
wat4 jjch62,400,000.00
wat5 Retvari Zoltan59,310,000.00
wat6 caffeineyellow552,680,000.00
wat7 Rion Family45,450,000.00
wat8 Orange_105040,860,000.00
wat9 Acey Pilot36,360,000.00
wat10 neilp6232,700,000.00
Number of contributors: 1885

The pathway of ligand entry from the membrane bilayer to a lipid G protein-coupled receptor.

WU tags:

Description

[Experiment image]

The binding process through the membrane bilayer of lipid-like ligands to a protein target is an important but poorly explored recognition process at the atomic level. In this work we succeeded in resolving the binding of the lipid inhibitor ML056 to the sphingosine-1-phosphate receptor 1 (S1P1R) using unbiased molecular dynamics simulations with an aggregate sampling of over 800 μs. The binding pathway is a multi-stage process consisting of the ligand diffusing in the bilayer leaflet to contact a "membrane vestibule" at the top of TM 7, subsequently moving from this lipid-facing vestibule to the orthosteric binding cavity through a channel formed by TMs 1 and 7 and the N-terminal of the receptor. Unfolding of the N-terminal alpha-helix increases the volume of the channel upon ligand entry, helping to reach the crystallographic pose that also corresponds to the predicted favorable pose. The relaxation timescales of the binding process show that the binding of the ligand to the "membrane vestibule" is the rate-limiting step in the multi microseconds timescale. We comment on the significance and parallels of the binding process in the context of other binding studies.

Publications

  • Stanley N, Pardo L, Fabritiis GD, The pathway of ligand entry from the membrane bilayer to a lipid G protein-coupled receptor. Scientific reports 2016. doi:10.1038/srep22639

BadgeRankNameCredit
wat1 Stoneageman632,093,025.00
wat2 Retvari Zoltan421,258,500.00
wat3 Erik Postnieks255,971,550.00
wat4 HA-SOFT, s.r.o.213,276,600.00
wat5 Venec188,482,000.00
wat6 Grzegorz Roman Granowski170,047,850.00
wat7 GPUGRID158,681,025.00
wat8 5pot158,478,400.00
wat9 Ken Florian152,314,200.00
wat10 Herb138,056,400.00
Number of contributors: 4815

Kinetic modulation of a disordered protein domain by phosphorylation

WU tags: KIDc22

Description

[Experiment image]

Not all proteins are naturally structured, and those that aren't are called intrinsically disordered proteins (IDPs). While they don't have structure, they do have many important roles in cell biology that are still being fully understood. They are often found mutated in many cancers at places that control the expression of genes and intra-cellular communication. In this work we show that a common chemical modification to IDPs known as phosphorylation can cause one IDP know as KID to change it's behavior. We further show that this could have important consequences for protein interactions, which affects all kinds of things like what genes are expressed and how signals are passed inside the cell.

Publications

  • N. Stanley. et al. Kinetic modulation of a disordered protein domain by phosphorylation. Nat. Commun. 5:5272 (2014)

BadgeRankNameCredit
wat1 Stoneageman432,230,350.00
wat2 RaymondFO*209,571,425.00
wat3 GPUGRID195,325,675.00
wat4 flashawk169,940,000.00
wat5 Retvari Zoltan168,413,875.00
wat6 Venec123,876,950.00
wat7 Rick A. Sponholz109,582,625.00
wat8 Grzegorz Roman Granowski103,799,025.00
wat9 Bedrich Hajek102,075,950.00
wat10 werdwerdus93,249,525.00
Number of contributors: 2838

Visualizing the Induced Binding of SH2-Phosphopeptide.

WU tags:

Description

[Experiment image]

Approximately 100 proteins in the human genome contain an SH2 domain recognizing small flexible phosphopeptides. It is therefore important to understand in atomistic detail the way these peptides bind and the conformational changes that take place upon binding. Here, we obtained several spontaneous binding events between the p56 lck SH2 domain and the pYEEI peptide within 2 Å RMSD from the crystal structure and with kinetic rates compatible with experiments using high-throughput molecular dynamics simulations. Binding is achieved in two phases, fast contacts of the charged phospho-tyrosine and then rearrangement of the ligand involving the stabilization of two important loops in the SH2 domain. These observations provide insights into the binding pathways and induced conformations of the SH2-phosphopeptide complex which, due to the characteristics of SH2 domains, should be relevant for other SH2 recognition peptides.

Publications

  • Giorgino T, Buch I, De Fabritiis G, Visualizing the Induced Binding of SH2-Phosphopeptide. Journal of chemical theory and computation 2012. doi:10.1021/ct300003f

BadgeRankNameCredit
wat1 Retvari Zoltan70,087,760.00
wat2 Venec66,760,584.00
wat3 comfortw49,023,649.00
wat4 WirelessDude46,764,909.00
wat5 Stoneageman46,347,778.00
wat6 CTAPbIi26,015,698.00
wat7 Helmholdt24,759,551.00
wat8 Nikke24,262,322.00
wat9 CNT - IQE23,991,650.00
wat10 Ketzer723,985,157.00
Number of contributors: 3113

Computational modeling of an EGFR single-mutation resistance to cetuximab in colorectal cancer treatment

WU tags: EGFR

Description

[Experiment image]

Extracellular S468R mutation of the epidermal growth factor receptor (EGFR) was recently identified as the cause of resistance to cetuximab, a widely used drug in colorectal cancer treatment. Here, we have determined the binding free energies of cetuximab's Fab V(H)-V(L) domains and endogenous EGF ligand to wild type and S468R EGFR by high-throughput molecular dynamics. This work provides a possible mechanism of resistance in terms of increased competition, an hypothesis that can be further validated experimentally.

Publications

  • I. Buch, N. Ferruz and G. De Fabritiis, Computational modeling of an EGFR single-mutation resistance to cetuximab in colorectal cancer treatment, J. Chem. Inf. Model., 2013, 53 (12), pp 3123–3126

BadgeRankNameCredit
wat1 Stoneageman77,231,380.00
wat2 Retvari Zoltan76,352,566.00
wat3 comfortw64,158,341.00
wat4 Venec47,340,586.00
wat5 Bikermatt34,035,023.00
wat6 escape31,904,255.00
wat7 mclaver31,857,293.00
wat8 ftpd27,038,309.00
wat9 netwraith24,550,849.00
wat10 WirelessDude23,912,620.00
Number of contributors: 3349

Molecular simulations of the SH2 and ligand peptide binding affinity

WU tags: pYEEI, SH2

Description

The SH2 is a protein domain involved in protein-protein interactions. This particular domain plays a major role in cell communication on the sigalling processes for cell growth and development. However, the end goal for running such simulations is not to expand the knowldege on this particular system, but to use it as a model for developing methods to calculate protein-protein binding affinities.
Such methods will be very useful, for example, in the study of why certain wrong forms of proteins stop interacting with other partner proteins, as a way to give explanation to diseases in which these sort of mechanisms occur.

Publications

  • I. Buch, S. K. Sadiq and G. De Fabritiis, Optimized potential of mean force calculations of standard binding free energy, J. Chem. Theory Comput., 7, 1765–1772 (2011)
  • I. Buch, M. J. Harvey, T. Giorgino, D. P. Anderson and G. De Fabritiis, High-throughput all-atom molecular dynamics simulations using distributed computing, J. Chem. Inf. and Mod. 50, 397 (2010)

BadgeRankNameCredit
wat1 Stoneageman76,590,546.00
wat2 dak164036,161,500.00
wat3 Grzegorz Roman Granowski31,711,633.00
wat4 whizbang25,439,249.00
wat5 comfortw21,920,469.00
wat6 123bob20,694,903.00
wat7 tng*20,332,716.00
wat8 dajeepster20,182,204.00
wat9 CNT - IQE19,654,731.00
wat10 Oleg Tchij18,806,232.00
Number of contributors: 9662