Peter Iliades

Triabodies: single chain Fv fragments without a linker form trivalent trimers

A single chain Fv fragment (scFv) of the murine monoclonal antibody 11‐1G10 was constructed by directly joining the C‐terminal residue of the VH domain to the N‐terminal residue of VL. 11‐1G10 is an anti‐idiotype and competes with the antigen, influenza virus neuraminidase (NA), for binding to the NC41 antibody. The scFv formed stable trimers with three active antigen combining sites for NC41 Fab fragments. We propose that trimeric scFvs may be the preferred conformation for directly linked VH‐VL molecules, which contrasts the formation of scFv dimers (diabodies) when the VH and VL domains are joined by short flexible linkers of between 5–10 residues. BIAcore biosensor binding experiments showed that the trimeric scFv showed an expected increase in binding affinity, due to avidity, compared to the monomeric 15‐residue linked scFv. The increase in avidity of scFv trimers offers advantages for imaging and immunotherapy.

Orientation of antigen binding sites in dimeric and trimeric single chain Fv antibody fragments

Electron microscopy of dimeric and trimeric single chain antibody Fv fragments (scFvs) complexed with anti‐idiotype Fab fragments was used to reveal the orientation of antigen binding sites. This is the first structural analysis that discloses the multivalent binding orientation of scFv trimers (triabodies). Three different scFv molecules were used for the imaging analysis; NC10 scFv‐5 and scFv‐0, with five‐ and zero‐residue linkers respectively between the VH and VL domains, were complexed with 3‐2G12 anti‐idiotype Fab fragments and 11‐1G10 scFv‐0 was complexed with NC41 anti‐idiotype Fab fragments. The scFv‐5 molecules formed bivalent dimers (diabodies) and the zero‐linker scFv‐0 molecules formed trivalent trimers (triabodies). The images of the NC10 diabody‐Fab complex appear as boomerangs, not as a linear molecule, with a variable angle between the two Fab arms and the triabody‐Fab complexes appear as tripods.

Dihydropteroate Synthase Mutations in Pneumocystis jiroveci Can Affect Sulfamethoxazole Resistance in a Saccharomyces cerevisiae Model

ABSTRACT Dihydropteroate synthase (DHPS) mutations in Pneumocystis jiroveci have been associated epidemiologically with resistance to sulfamethoxazole (SMX). Since P. jiroveci cannot be cultured, inherent drug resistance cannot be measured. This study explores the effects of these mutations in a tractable model organism, Saccharomyces cerevisiae. Based on the sequence conservation between the DHPS enzymes of P. jiroveci and S. cerevisiae, together with the structural conservation of the three known DHPS structures, DHPS substitutions commonly observed in P. jiroveci were reverse engineered into the S. cerevisiae DHPS. Those mutations, T597A and P599S, can occur singly but are most commonly found together and are associated with SMX treatment failure. Mutations encoding the corresponding changes in the S. cerevisiae dhps were made in a yeast centromere vector, p414FYC, which encodes the native yeast DHPS as part of a trifunctional protein that also includes the two enzymes upstream of DHPS in the folic acid synthesis pathway, dihydroneopterin aldolase and 2-amino-4-hydroxymethyl dihydropteridine pyrophosphokinase. A yeast strain with dhps deleted was employed as the host strain, and transformants having DHPS activity were recovered. Mutants having both T597 and P599 substitutions had a requirement for p-aminobenzoic acid (PABA), consistent with resistance being associated with altered substrate binding. These mutants could be adapted for growth in the absence of PABA, which coincided with increased sulfa drug resistance. Upregulated PABA synthesis was thus implicated as a mechanism for sulfa drug resistance for mutants having two DHPS substitutions.

Mutations in the Pneumocystis jirovecii DHPS Gene Confer Cross-Resistance to Sulfa Drugs

ABSTRACT Pneumocystis jirovecii is a major opportunistic pathogen that causes Pneumocystis pneumonia (PCP) and results in a high degree of mortality in immunocompromised individuals. The drug of choice for PCP is typically sulfamethoxazole (SMX) or dapsone in conjunction with trimethoprim. Drug treatment failure and sulfa drug resistance have been implicated epidemiologically with point mutations in dihydropteroate synthase (DHPS) of P. jirovecii. P. jirovecii cannot be cultured in vitro; however, heterologous complementation of the P. jirovecii trifunctional folic acid synthesis (PjFAS) genes with an E. coli DHPS-disrupted strain was recently achieved. This enabled the evaluation of SMX resistance conferred by DHPS mutations. In this study, we sought to determine whether DHPS mutations conferred sulfa drug cross-resistance to 15 commonly available sulfa drugs. It was established that the presence of amino acid substitutions (T517A or P519S) in the DHPS domain of PjFAS led to cross-resistance against most sulfa drugs evaluated. The presence of both mutations led to increased sulfa drug resistance, suggesting cooperativity and the incremental evolution of sulfa drug resistance. Two sulfa drugs (sulfachloropyridazine [SCP] and sulfamethoxypyridazine [SMP]) that had a higher inhibitory potential than SMX were identified. In addition, SCP, SMP, and sulfadiazine (SDZ) were found to be capable of inhibiting the clinically observed drug-resistant mutants. We propose that SCP, SMP, and SDZ should be considered for clinical evaluation against PCP or for future development of novel sulfa drug compounds.

Folate biosynthesis - Reappraisal of old and novel targets in the search for new antimicrobials

Folate biosynthesis remains a key target for antimicrobial therapy. Folate is an essential vitamin (vitamin B9) that is required for many one-carbon transfer reactions and is a critical precursor for the biosynthesis of purines, pyrimidi- nes, and amino acids. Unlike higher eukaryotes that scavenge preformed folates, prokaryotic and lower eukaryotic micro- organisms are dependent on several enzymes for the de novo biosynthesis of folate. One of these enzymes, dihydropte- roate synthase (DHPS), is the target of the first chemically-synthesized antimicrobial agents, the sulfadrugs, which date back to the 1940s. Others are essential enzymes that remain to be explored as drug targets. Resistance to the sulfadrugs rapidly emerges due to the ability of the microbe to alter its susceptibility to the drug by various means. Recently a num- ber of new structures of the enzymes in the pathway has become available. We review the recent literature relating to these targets (the enzymes: GTP cyclohydrolase (GTP-CH); 7,8-dihydroneopterin aldolase (DHNA), 6-hydroxymethyl- 7,8-dihydropterin pyrophosphokinase (HPPK), dihydropteroate synthase (DHPS), dihydrofolate synthase (DHFS)), their mode of action and how current drugs may modulate this on a structural level. Furthermore, these data advance our un- derstanding of the emergence of drug resistance and may aid efforts and play a major role in the design of new, more ef- fective compounds as antimicrobial agents. To this end we also review the recent literature in the development of inhibi- tors of these enzymes. Future progress in this key area has the potential to benefit the war against devastating organisms such as drug-resistant Staphylococcus aureus and Plasmodium falciparum.

Promoter strength of folic acid synthesis genes affects sulfa drug resistance in Saccharomyces cerevisiae

The enzyme dihydropteroate synthase (DHPS) is an important target for sulfa drugs in both prokaryotic and eukaryotic microbes. However, the understanding of DHPS function and the action of antifolates in eukaryotes has been limited due to technical difficulties and the complexity of DHPS being a part of a bifunctional or trifunctional protein that comprises the upstream enzymes involved in folic acid synthesis (FAS). Here, yeast strains have been constructed to study the effects of FOL1 expression on growth and sulfa drug resistance. A DHPS knockout yeast strain was complemented by yeast vectors expressing the FOL1 gene under the control of promoters of different strengths. An inverse relationship was observed between the growth rate of the strains and FOL1 expression levels. The use of stronger promoters to drive FOL1 expression led to increased sulfamethoxazole resistance when para-aminobenzoic acid (pABA) levels were elevated. However, high FOL1 expression levels resulted in increased susceptibility to sulfamethoxazole in pABA free media. These data suggest that up-regulation of FOL1 expression can lead to sulfa drug resistance in Saccharomyces cerevisiae.

Single-Chain Fv of Anti-idiotype 11-1G10 Antibody Interacts with Antibody NC41 Single-Chain Fv with a Higher Affinity than the Affinity for the Interaction of the Parent Fab Fragments

A single-chain Fv (scFv) fragment of anti-idiotype antibody 11-1G10, which recognizes an idiotope of anti-neuraminidase antibody NC41, was constructed by joining VH and VL domains with a (Gly4Ser)3 linker, with a pelB leader sequence, and two C-terminal FLAG™ tag sequences, and expressed in E. coli (10 mg/L). The 11-1G10 scFv was isolated by affinity chromatography on an anti-FLAG M2 antibody column as a 2:1 mixture of monomer and dimer forms which were separated by Superdex 75 chromatography; monomer (at 100 μg/ml) was stable for 7 days at 21°C and 30 days at 4°C, whereas the dimer slowly dissociated to monomer to yield a 2:1 monomer–dimer equilibrium mixture after 30 days at 4°C. The dimer was bivalent, with each combining site binding an NC41 Fab to yield a stable complex of Mr ≍ 156,000. Binding affinities, determined in solution using a BIAcore™ biosensor, showed that the affinity for the interaction of 11-1G10 scFv monomer with NC41 scFv monomer was five- to six-fold higher than the interaction of the parent Fab pair. This is the first example of an scFv derived from a monoclonal antibody with a higher affinity than its parent Fab.