Structure–Activity Relationship Studies To Probe the Phosphoprotein Binding Site on the Carboxy Terminal Domains of the Breast Cancer Susceptibility Gene 1

Yuan, Zhengrong; Kumar, Eric A.; Kizhake, Smitha; Natarajan, Amarnath

doi:10.1021/jm1016413

Cited by 16 publications

(28 citation statements)

References 26 publications

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“…14,15,60 The highest affinity peptide from this screen had an affinity of 162 nM. Further optimization by Natarajan and coworkers has led to a tetrapeptide with a 40 nM binding affinity 51,61,62 (Fig. 3).…”

Section: Development Of Therapeutic Peptides and Small Molecule Inhibmentioning

confidence: 84%

BRCA1-directed, enhanced and aberrant homologous recombination

et al. 2012

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Despite intense studies, questions still remain regarding the molecular mechanisms leading to the development of hereditary breast and ovarian cancers. Research focused on elucidating the role of the breast cancer susceptibility gene 1 (BRCA1) in the DNA damage response may be of the most critical importance to understanding these processes. The BRCA1 protein has an N-terminal RING domain possessing E3 ubiquitinligase activity and a C-terminal BRCT domain involved in binding specific phosphoproteins. These domains are involved directly or indirectly in DNA double-strand break (DSB) repair. As the two terminal domains of BRCA1 represent two separate entities, understanding how these domains communicate and are functionally altered in regards to DSB repair is critical for understanding the development of BRCA1-related breast and ovarian cancers and for developing novel therapeutics. Herein, we review recent findings of how altered functions of these domains might lead to cancer through a mechanism of increased aberrant homologous recombination and possible implications for the development of BRCA1 inhibitors.

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Section: Development Of Therapeutic Peptides and Small Molecule Inhibmentioning

confidence: 84%

BRCA1-directed, enhanced and aberrant homologous recombination

et al. 2012

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“…The relative binding free energy for ligand X ( X = P2–P14, C1, N1) to ligand P1 is approximated using the half maximal inhibitory concentration IC50 as ΔΔG exp = RT ln IC50( X )/IC50(P1) based on equation Δ G = RT ln K d = RT ln(IC50 + 0.5 C enzyme ) ≈ RT ln IC50 [44, 45]. Binding free energies for L1–L4 are calculated through equation ΔG exp = RT ln ( K d ). a IC50 values of P1–P14 were taken from ref [24]. IC50 values of C1 was taken from ref [27].…”

Section: Methodsmentioning

confidence: 99%

Characterization of Promiscuous Binding of Phosphor Ligands to Breast-Cancer-Gene 1 (BRCA1) C-Terminal (BRCT): Molecular Dynamics, Free Energy, Entropy and Inhibitor Design

et al. 2016

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Inhibition of the protein-protein interaction (PPI) mediated by breast-cancer-gene 1 C-terminal (BRCT) is an attractive strategy to sensitize breast and ovarian cancers to chemotherapeutic agents that induce DNA damage. Such inhibitors could also be used for studies to understand the role of this PPI in DNA damage response. However, design of BRCT inhibitors is challenging because of the inherent flexibility associated with this domain. Several studies identified short phosphopeptides as tight BRCT binders. Here we investigated the thermodynamic properties of 18 phosphopeptides or peptide with phosphate mimic and three compounds with phosphate groups binding to BRCT to understand promiscuous molecular recognition and guide inhibitor design. We performed molecular dynamics (MD) simulations to investigate the interactions between inhibitors and BRCT and their dynamic behavior in the free and bound states. MD simulations revealed the key role of loops in altering the shape and size of the binding site to fit various ligands. The mining minima (M2) method was used for calculating binding free energy to explore the driving forces and the fine balance between configuration entropy loss and enthalpy gain. We designed a rigidified ligand, which showed unfavorable experimental binding affinity due to weakened enthalpy. This was because it lacked the ability to rearrange itself upon binding. Investigation of another phosphate group containing compound, C1, suggested that the entropy loss can be reduced by preventing significant narrowing of the energy well and introducing multiple new compound conformations in the bound states. From our computations, we designed an analog of C1 that introduced new intermolecular interactions to strengthen attractions while maintaining small entropic penalty. This study shows that flexible compounds do not always encounter larger entropy penalty, compared with other more rigid binders, and highlights a new strategy for inhibitor design.

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“…These protein–protein interactions play a critical role in the DNA damage response pathway (Cantor et al, 2001; Kim et al, 2007; Liu et al, 2007; Sobhian et al, 2007; Wang et al, 2007). It was shown that tetrapeptides bind BRCT-BRCA1 with nanomolar affinities (Joseph et al, 2010; Yuan et al, 2011a,b). A poly-arginine-tagged tetrapeptide inhibitor blocked the BRCA1–phospho-protein interaction and sensitized cells to PARP inhibition (Pessetto et al, 2012).…”

Section: Introductionmentioning

confidence: 99%

Irreversible binding of an anticancer compound (BI-94) to plasma proteins

et al. 2015

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1. We investigated the mechanisms responsible for the in vivo instability of a benzofurazan compound BI-94 (NSC228148) with potent anti-cancer activity. 2. BI-94 was stable in MeOH, water, and in various buffers at pHs 2.5–5, regardless of the buffer composition. In contrast, BI-94 was unstable in NaOH and at pHs 7–9, regardless of the buffer composition. BI-94 disappeared immediately after spiking into mice, rat, monkey, and human plasma. BI-94 stability in plasma can be only partially restored by acidifying it, which indicated other mechanisms in addition to pH for BI-94 instability in plasma. 3. BI-94 formed adducts with the trapping agents, glutathione (GSH) and N-acetylcysteine (NAC), in vivo and in vitro via nucleophilic aromatic substitution reaction. The kinetics of adduct formation showed that neutral or physiological pHs enhanced and accelerated GSH and NAC adduct formation with BI-94, whereas acidic pHs prevented it. Therefore, physiological pHs not only altered BI-94 chemical stability but also enhanced adduct formation with endogenous nucleophiles. In addition, adduct formation with human serum albumin-peptide 3 (HSA-T3) at the Cys34 position was demonstrated. 4. In conclusion, BI-94 was unstable at physiological conditions due to chemical instability and irreversible binding to plasma proteins.

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Structure–Activity Relationship Studies To Probe the Phosphoprotein Binding Site on the Carboxy Terminal Domains of the Breast Cancer Susceptibility Gene 1

Cited by 16 publications

References 26 publications

BRCA1-directed, enhanced and aberrant homologous recombination

BRCA1-directed, enhanced and aberrant homologous recombination

Characterization of Promiscuous Binding of Phosphor Ligands to Breast-Cancer-Gene 1 (BRCA1) C-Terminal (BRCT): Molecular Dynamics, Free Energy, Entropy and Inhibitor Design

Irreversible binding of an anticancer compound (BI-94) to plasma proteins

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