Structural hot spots for the solubility of globular proteins

Ganesan, Ashok; Siekierska, Aleksandra; Beerten, Jacinte; Brams, Marijke; Durme, Joost Van; Baets, Greet De; Kant, Rob van der; Gallardo, Rodrigo; Ramakers, Meine; Langenberg, Tobias; Wilkinson, Hannah; Smet, Frederik De; Ulens, Chris; Rousseau, Frédéric; Schymkowitz, Joost

doi:10.1038/ncomms10816

Cited by 64 publications

(70 citation statements)

References 52 publications

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“…Although this would not eliminate the intrinsic aggregation potential of the molecules, it would at least increase their colloidal stability and hence reduce the initial association required to initiate protein aggregation [36]. In addition, APR disruption could display an interplay with the net charge, as was observed in the engineering of protective antigen [16], where we noticed that the gatekeeper that increased the net charge of the protein also performed best at reducing aggregation. Moreover, for green fluorescent protein, it was previously shown that extreme supercharging is effective at suppressing aggregation, but this is probably not an option for therapeutic molecules due to immunogenicity considerations [36].…”

Section: Resultsmentioning

confidence: 86%

Prediction and Reduction of the Aggregation of Monoclonal Antibodies

Kant

Karow-Zwick

Durme

et al. 2017

Journal of Molecular Biology

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121

112

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Protein aggregation remains a major area of focus in the production of monoclonal antibodies. Improving the intrinsic properties of antibodies can improve manufacturability, attrition rates, safety, formulation, titers, immunogenicity, and solubility. Here, we explore the potential of predicting and reducing the aggregation propensity of monoclonal antibodies, based on the identification of aggregation-prone regions and their contribution to the thermodynamic stability of the protein. Although aggregation-prone regions are thought to occur in the antigen binding region to drive hydrophobic binding with antigen, we were able to rationally design variants that display a marked decrease in aggregation propensity while retaining antigen binding through the introduction of artificial aggregation gatekeeper residues. The reduction in aggregation propensity was accompanied by an increase in expression titer, showing that reducing protein aggregation is beneficial throughout the development process. The data presented show that this approach can significantly reduce liabilities in novel therapeutic antibodies and proteins, leading to a more efficient path to clinical studies.

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Section: Resultsmentioning

confidence: 86%

Prediction and Reduction of the Aggregation of Monoclonal Antibodies

Kant

Karow-Zwick

Durme

et al. 2017

Journal of Molecular Biology

Self Cite

121

112

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“…4). By selectively mutating amino acids at the protein surface, it is possible to tune their solubility while preserving their structure and function (66). This provides a potential means to condense enzymes and thereby elevate their catalytic capability.…”

Section: Discussionmentioning

confidence: 99%

“…For instance, the relationship between protein surface domains and the binding affinity of molecules of a drug, protein, or DNA/RNA could aid the design of new molecules to condense enzymes for advanced catalytic performance, and of new therapeutic peptides for selectively targeting certain types of proteins (70). Moreover, protein solubility could be elevated or suppressed by mutating amino acids while preserving bioactivity (66).…”

Section: Discussionmentioning

confidence: 99%

Water follows polar and nonpolar protein surface domains

Qiao

Jiménez-Ángeles

Nguyen

et al. 2019

Proc. Natl. Acad. Sci. U.S.A.

100

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The conformation of water around proteins is of paramount importance, as it determines protein interactions. Although the average water properties around the surface of proteins have been provided experimentally and computationally, protein surfaces are highly heterogeneous. Therefore, it is crucial to determine the correlations of water to the local distributions of polar and nonpolar protein surface domains to understand functions such as aggregation, mutations, and delivery. By using atomistic simulations, we investigate the orientation and dynamics of water molecules next to 4 types of protein surface domains: negatively charged, positively charged, and charge-neutral polar and nonpolar amino acids. The negatively charged amino acids orient around 98% of the neighboring water dipoles toward the protein surface, and such correlation persists up to around 16 Å from the protein surface. The positively charged amino acids orient around 94% of the nearest water dipoles against the protein surface, and the correlation persists up to around 12 Å. The charge-neutral polar and nonpolar amino acids are also orienting the water neighbors in a quantitatively weaker manner. A similar trend was observed in the residence time of the nearest water neighbors. These findings hold true for 3 technically important enzymes (PETase, cytochrome P450, and organophosphorus hydrolase). Our results demonstrate that the water−amino acid degree of correlation follows the same trend as the amino acid contribution in proteins solubility, namely, the negatively charged amino acids are the most beneficial for protein solubility, then the positively charged amino acids, and finally the charge-neutral amino acids.

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“…Grafting APRs of known amyloidogenic proteins onto proteins that do not aggregate by themselves creates chimeras that recapitulate both the aggregation propensity and aggregate morphology of the donor protein (Ventura et al, 2004;Teng and Eisenberg, 2009). Conversely, it has also been shown that the introduction of point mutations that abolish the aggregation propensity of an APR is sufficient to reduce the aggregation propensity of the entire protein (Ganesan et al, 2016;Marshall et al, 2016). Finally, short peptides solely coding for such APRs are able to induce the aggregation of a full-length protein comprising that APR Khodaparast et al, 2018;Betti et al, 2016).…”

Section: Introductionmentioning

confidence: 99%