2018
DOI: 10.1021/acs.molpharmaceut.8b00186
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Computational Design To Reduce Conformational Flexibility and Aggregation Rates of an Antibody Fab Fragment

Abstract: Computationally guided semirational design has significant potential for improving the aggregation kinetics of protein biopharmaceuticals. While improvement in the global conformational stability can stabilize proteins to aggregation under some conditions, previous studies suggest that such an approach is limited, because thermal transition temperatures ( T) and the fraction of protein unfolded ( f) tend to only correlate with aggregation kinetics where the protein is incubated at temperatures approaching the … Show more

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Cited by 30 publications
(72 citation statements)
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“…Zhang et al 124 performed a computational design calculation to explore relationships between conformational and colloidal stabilities of the Fab region of an antibody, the T m of which was 71.8 C, based on measurements made with the UNit instrument (Unchained Laboratories, UK). In their strategy, potentially flexible regions were first identified based on MD simulations of a homology model of the antibody and B-factors derived from crystal structures of the homologous antibodies (53%-90% sequence identities).…”
Section: Predicted Ddg As a Selection Criterionmentioning
confidence: 99%
“…Zhang et al 124 performed a computational design calculation to explore relationships between conformational and colloidal stabilities of the Fab region of an antibody, the T m of which was 71.8 C, based on measurements made with the UNit instrument (Unchained Laboratories, UK). In their strategy, potentially flexible regions were first identified based on MD simulations of a homology model of the antibody and B-factors derived from crystal structures of the homologous antibodies (53%-90% sequence identities).…”
Section: Predicted Ddg As a Selection Criterionmentioning
confidence: 99%
“…Antibody bivalency would then facilitate formation of HMWS. Partial unfolding of proteins is generally considered as a risk factor for formation of oligomers via non-specific interactions, including in antibody solutions44 . This is not to say that the CDRs are predominantly unfolded, rather that partial unfolding in a sub-population would lead to self-association.The second feature (in addition to CDRs length) used in the linear fit ofFigure 2bis the maximum surface (non-interfacial) NPP ratio of a Fab.…”
mentioning
confidence: 99%
“…The C226S heavy-chain variant was used to avoid the formation of linked Fab dimers. We used the Rosetta method “minirosetta”, as detailed in previous works [48].…”
Section: Methodsmentioning
confidence: 99%
“…Next, the “BuildModel” command was used to introduce the point mutations, optimize the structure of the new protein variant, and calculate the stability change upon mutation. The Rosetta “ddg_monomer” method was used, where an example of mutation and option files, listing the parameters of the executable, can be seen in previous work [48]. Jobs were submitted to the UCL Legion High-Performance Computing Facility.…”
Section: Methodsmentioning
confidence: 99%