De-immunization results for mutation loads of <i>k</i> = 1,2,3.

<p>De-immunization results for mutation loads of <i>k</i> = 1,2,3.</p

Population-specific design of de-immunized protein biotherapeutics - Fig 5

<p>(A) Correlation of experimental and predicted immunogenicity of each peptide. The experimental immunogenicity score of a peptide is defined as the linear combination of the individual experimentally determined relative HLA binding affinity of each HLA allele h ∈ H weighted by the HLA allele frequency. (B) Correlation of experimental and predicted immunogenicity of the whole redesigned region. The summarized immunogenicity score of the whole region is the linear combination of the overlapping peptides used to reconstruct the region, normalized by total number of peptides used. The predicted immunogenicity scores per peptide were computed according to our immunogenicity objective function. The red lines are a fitted linear regression and the red tubes represent their 95-confidence interval.</p

Depiction of the parallel two-phase rectangle splitting approach.

<p>(A) First, the boundaries of the Pareto front are identified. (B) Then, the space between the boundaries is evenly divided and searched in parallel for nondominated points using the ε-constraint method. (C) The identified nondominated points are used to initiate rectangle search spaces which can be processed in parallel using the standard rectangle-splitting approach, by splitting the rectangle in half and searching independently the bottom and top half (D). If the corner points of the rectangles are found during the search, it is proofs, that no further nondominated point resides within the search space and all points have been identified.</p

Evolutionary couplings-based model and FoldX prediction correlations.

<p>The red line is a fitted linear regression, and the red tube represents its 95-confidence interval. The orange-circled dots are the two mutational designs with the highest discrepancy. FoldX predicted these two mutations less deleterious compared maximum entropy model, although both designs introduced a mutation at a membrane-binding site.</p

Bi-objective integer linear program formulation of the de-immunization problem.

<p>Bi-objective integer linear program formulation of the de-immunization problem.</p

Use of an Additional Hydrophobic Binding Site, the Z Site, in the Rational Drug Design of a New Class of Stronger Trypanothione Reductase Inhibitor, Quaternary Alkylammonium Phenothiazines^§

Improved rationally designed lead drug structures against African trypanosomiasis, Chagas disease, and leishmaniasis were obtained against trypanothione reductase from Trypanosoma cruzi. Substituted-benzyl [3-(2-chloro-4a,10a-dihydrophenothiazin-10-yl)propyl]dimethylammonium salts, synthesized by Menschutkin quaternization of the tertiary alkylamine ω-nitrogen atom of chlorpromazine, were linear, competitive inhibitors of recombinant trypanothione reductase from T. cruzi, with either trypanothione disulfide or N-benzyloxycarbonyl-l-cysteinylglycyl 3-dimethylaminopropylamide disulfide as substrate. The permanent positive charge on the distal nitrogen atom of the tricyclic side chain contribution to binding was estimated as ≥5.6 kcal·mol-1 by comparison with the analogue with the cationic nitrogen atom of the quaternary replaced by an ether oxygen atom. A further major contribution to improving Ki values and inhibition strength was the hydrophobic natures and structures of the N-benzyl substituents. The strongest inhibitor, the [3-(2-chloro-4a,10a-dihydrophenothiazin-10-yl)propyl](3,4-dichlorobenzyl)dimethylammonium derivative (Ki 0.12 μM), was ∼2 orders of magnitude more inhibitory than the parent chlorpromazine. Several of these quaternary phenothiazines completely inhibited T. brucei parasite growth in vitro at <1 μM. Antiparasite activity was not solely determined by inhibition strength against trypanothione reductase, there being a strong contribution from hydrophobicity (for example, benzhydryl-quaternized chlorpromazime had ED50 Leishmania donovani, none of the analogues showed major improvement in this activity relative to chlorpromazine or other nonquaternized phenothiazines. The p-tert-butylbenzyl-quaternized analogue very strongly inhibited (ED50 < 1 μM) growth of the amastigote stage of T. cruzi