Improved molecular recognition of Carbonic Anhydrase IX by polypeptide conjugation to acetazolamide

Yang, Jie; Koruza, Katarina; Fisher, Zoë; Knecht, Wolfgang; Baltzer, Lars

doi:10.1016/j.bmc.2017.09.017

Cited by 8 publications

(9 citation statements)

References 35 publications

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“…The resulting peptide bundles T-4 and T-16 promote aldimine to ketamine conversion, emulating biosynthetic transamination reactions (Allert and Baltzer, 2003). Finally, the graded reactivity of KO-42 has been used to allow the site-directed assembly of auxiliary binding groups, to create binders of protein surfaces with sub-nanomolar affinity for the proteins of interest (Baltzer, 2011; Yang et al ., 2017 a , 2017 b ).…”

Section: Computational Design Guided By Fundamental Physicochemical Pmentioning

confidence: 99%

De novoprotein design, a retrospective

Korendovych

DeGrado

2020

Quart. Rev. Biophys.

175

179

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Proteins are molecular machines whose function depends on their ability to achieve complex folds with precisely defined structural and dynamic properties. The rational design of proteins from first-principles, or de novo, was once considered to be impossible, but today proteins with a variety of folds and functions have been realized. We review the evolution of the field from its earliest days, placing particular emphasis on how this endeavor has illuminated our understanding of the principles underlying the folding and function of natural proteins, and is informing the design of macromolecules with unprecedented structures and properties. An initial set of milestones in de novo protein design focused on the construction of sequences that folded in water and membranes to adopt folded conformations. The first proteins were designed from first-principles using very simple physical models. As computers became more powerful, the use of the rotamer approximation allowed one to discover amino acid sequences that stabilize the desired fold. As the crystallographic database of protein structures expanded in subsequent years, it became possible to construct proteins by assembling short backbone fragments that frequently recur in Nature. The second set of milestones in de novo design involves the discovery of complex functions. Proteins have been designed to bind a variety of metals, porphyrins, and other cofactors. The design of proteins that catalyze hydrolysis and oxygen-dependent reactions has progressed significantly. However, de novo design of catalysts for energetically demanding reactions, or even proteins that bind with high affinity and specificity to highly functionalized complex polar molecules remains an importnant challenge that is now being achieved. Finally, the protein design contributed significantly to our understanding of membrane protein folding and transport of ions across membranes. The area of membrane protein design, or more generally of biomimetic polymers that function in mixed or non-aqueous environments, is now becoming increasingly possible.

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Section: Computational Design Guided By Fundamental Physicochemical Pmentioning

confidence: 99%

De novoprotein design, a retrospective

Korendovych

DeGrado

2020

Quart. Rev. Biophys.

175

179

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“…Inspired with drug repurposing strategy, here, we exploit the new power of traditional CA inhibitor with its self-assembled nanostructure. This work presents an excellent example that uses several amino acids to facilitate the therapeutic efficacy of traditional drugs ( 34 , 35 ), which should be relatively easy to approach for drug manufacture. It enables the existing traditional drugs to afford nanostructures through simple and cost-effective amino acid modifications, thereby achieving an innovative drug treatment mechanism, which consequently improve the existing clinical drug treatment.…”

Section: Discussionmentioning

confidence: 99%

New power of self-assembling carbonic anhydrase inhibitor: Short peptide–constructed nanofibers inspire hypoxic cancer therapy

et al. 2019

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Carbonic anhydrase (CA) IX overexpresses exclusively on cell membranes of hypoxic tumors, regulating the acidic tumor microenvironment. Small molecules of CA inhibitor modified with short peptide successfully achieve CA IX–targeted self-assembly that localizes CA inhibitors on hypoxic cancer cell surfaces and enhances their inhibition efficacy and selectivity. CA IX–related endocytosis also promotes selective intracellular uptake of these nanofibers under hypoxia, in which nanofiber structures increase in size with decreasing pH. This effect subsequently causes intracellular acid vesicle damage and blocks protective autophagy. The versatility of tunable nanostructures responding to cell milieu impressively provokes selective toxicities and provides strategic therapy for hypoxic tumors. Moreover, in vivo tests demonstrate considerable antimetastatic and antiangiogenesis effects in breast tumors, and particularly remarkable enhancement of antitumor efficacy in doxorubicin administration. With its biocompatible components and distinctive hypoxia therapies, this nanomaterial advances current chemotherapy, providing a new direction for hypoxic cancer therapy.

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“…The wild-type cDNA construct (referred to here as Construct 1) was synthesized by GeneArt (ThermoFisher, Waltham, MA, USA) and subcloned into pVL1393 (BD Bioscience, Franklin Lakes, NJ, USA) [47]. Construct 2 containing the Cys174Ser mutation was a generous gift from Claudiu T. Supuran (University of Florence, Italy) and Seppo Parkkila (University of Tampere, Finland).…”

Section: Expression and Purification Of Ecd Of Ca IXmentioning

confidence: 99%

“…Details of protein production for Construct 1 has been described previously [47]. Briefly, the protein was produced using BEVS and expression was done in Sf9 cells (Invitrogen, Carlsbad, CA, USA).…”

Section: Construct 1 Protein Expression and Purificationmentioning

confidence: 99%

Biophysical Characterization of Cancer-Related Carbonic Anhydrase IX

Koruza

Murray

Mahon

et al. 2020

IJMS

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Upregulation of carbonic anhydrase IX (CA IX) is associated with several aggressive forms of cancer and promotes metastasis. CA IX is normally constitutively expressed at low levels in selective tissues associated with the gastrointestinal tract, but is significantly upregulated upon hypoxia in cancer. CA IX is a multi-domain protein, consisting of a cytoplasmic region, a single-spanning transmembrane helix, an extracellular CA catalytic domain, and a proteoglycan-like (PG) domain. Considering the important role of CA IX in cancer progression and the presence of the unique PG domain, little information about the PG domain is known. Here, we report biophysical characterization studies to further our knowledge of CA IX. We report the 1.5 Å resolution crystal structure of the wild-type catalytic domain of CA IX as well as small angle X-ray scattering and mass spectrometry of the entire extracellular region. We used matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry to characterize the spontaneous degradation of the CA IX PG domain and confirm that it is only the CA IX catalytic domain that forms crystals. Small angle X-ray scattering analysis of the intact protein indicates that the PG domain is not randomly distributed and adopts a compact distribution of shapes in solution. The observed dynamics of the extracellular domain of CA IX could have physiological relevance, including observed cleavage and shedding of the PG domain.

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Improved molecular recognition of Carbonic Anhydrase IX by polypeptide conjugation to acetazolamide

Cited by 8 publications

References 35 publications

De novoprotein design, a retrospective

De novoprotein design, a retrospective

New power of self-assembling carbonic anhydrase inhibitor: Short peptide–constructed nanofibers inspire hypoxic cancer therapy

Biophysical Characterization of Cancer-Related Carbonic Anhydrase IX

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