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In vitro evolution of an antibody fragment population

In vitro evolution of an antibody fragment population
In vitro evolution of an antibody fragment population

In vitro evolution of an antibody fragment population to?nd high-af?nity hapten binders

Helena Persson1,Henrik Wallmark1,Anne Ljungars2, Johan Hallborn2and Mats Ohlin1,3

1Department of Immunotechnology,Lund University,BMC D13SE-22184, Lund and2BioInvent International AB,So¨lvegatan41SE-22370,Lund, Sweden

3To whom correspondence should be addressed.

E-mail:mats.ohlin@immun.lth.se

Recently,we constructed a focused antibody library tai-lored to interact with haptens.High functionality of this library was demonstrated,as speci?c binders could be retrieved to a range of different haptens.In the current study we have developed a mutagenesis and selection strategy in order to further?ne-tune the hapten binding properties of these antibody fragments.Testosterone was chosen as model antigen for the investigation.A popu-lation,rather than a single clone,originating from this focused library and enriched for testosterone binders, was subjected to random mutagenesis and different phage display selection strategies of various stringencies. These included consecutively lowering the antigen con-centration and having,or not having,soluble hapten present during the phage capture and elution steps.The different selection procedures resulted in a considerable increase in apparent af?nities for several of the selected populations,from which the highest af?nity antibody iso-lated had a K D of2nM,corresponding to an 200-fold af?nity improvement compared with the best clone of the starting population.Importantly,the polyclonal nature of the starting material allowed for the identi?cation of novel unrelated variants that differed in?ne-speci?city, demonstrating that this approach is valuable for explor-ing different parts of structure space.

Keywords:af?nity maturation/antibody library/hapten/phage display/testosterone

Introduction

Besides their importance in the adaptive immune response, antibodies have emerged as an invaluable tool in applications ranging from basic research to disease diagnostics and therapy.The hybridoma technology(Ko¨hler and Milstein, 1975),which relies on animal immunizations,is still the most common way of obtaining antibodies,in particular for diagnostic applications.However,within the past two decades,since the cloning of the?rst antibody repertoires (Huse et al.,1989;Ward et al.,1989)and with the successful production of antibody fragments in bacteria(Skerra and Plu¨ckthun,1988)combined with the functionally display of these on phage(McCafferty et al.,1990;Kang et al.,1991), antibody library technology has gradually become the method of choice for the development of speci?c binders. Over the years numerous antibody libraries have been reported(So¨derlind et al.,2001;Hoogenboom,2002).Various strategies,using natural as well as synthetic diversity,have been utilized,often with the goal to create very large libraries with diversity high enough to provide binding speci?city against any antigen.Although in many cases successful,it has,despite the size of these so called universal or single-pot libraries,been dif?cult to isolate high-af?nity antibodies to some particularly troublesome antigens.In speci?c appli-cations,libraries tailored to interact with a certain antigen or group of antigens,so called focused libraries,have therefore been proposed as an attractive alternative(Collis et al.,2003; Almagro,2004;Almagro et al.,2006;Kehoe et al.,2006; Sidhu and Fellouse,2006).Recently,we successfully con-structed such a focused library with features biased to recog-nize haptens(Persson et al.,2006).

The main principle behind the design of the focused hapten library was based on the fact that the topography of the binding site correlates with the size of its antigen (Webster et al.,1994;MacCallum et al.,1996).As small-molecule antigens almost exclusively interact with cavity-shaped paratopes,a hapten-speci?c antibody,displaying a pronounced binding pocket,was used as structural backbone for library construction.By keeping framework and canoni-cal structure determining residues constant,we reasoned that a large portion of the library would maintain the cavity topo-graphy as seen in the wild-type https://www.doczj.com/doc/2417942271.html,ing site-directed mutagenesis,diversity was mainly restricted to positions and residue types that are commonly involved in hapten contacts (MacCallum et al.,1996;Almagro,2004),resulting in vari-ation of mainly centrally located cavity-lining residues.To possibly allow for the formation of cavities of variable depth (Collis et al.,2003),some variation in loop length was also introduced.Despite the relatively small size of this so-called cavity library(5?107),we were able to identify highly speci?c antibodies to a range of different haptens. Importantly,we could show that the cavity library was a superior source of hapten-binders compared with a consider-ably larger general-purpose repertoire(Persson et al.,2006). In order to be generally applicable,a library has to be able to provide binders of high speci?city as well as of high af?-nity.However,as no particular efforts were made to select for binding strength in the initial study(Persson et al.,2006), the af?nity of the obtained hapten-binders were relatively modest(K D?1026–1027M).Therefore,in the present investigation we set out to further explore the evolution potential of the cavity library to deliver hapten-binding anti-bodies with af?nities required for practical applications. Methods

Construction of libraries

The starting material for library construction was based on a sub-population of the previously described cavity library (Persson et al.,2006).This library had been selected twice on testosterone-biotin(testosterone3-(5-(6-(5-(biotin) pentanamido)hexanamido)pentylcarbamoyl)propanoate) coupled to avidin-coated magnetic beads(Persson

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et al .,2006).Plasmid DNA was isolated from this population,from here on designated CT (C for cavity library and T for testosterone),and submitted to one or two rounds of random mutagenesis by error-prone PCR using an excess of guanine and/or thymine (Fig.1).In the ?rst round,the reaction mix (100m l)contained 10mM Tris–HCl (pH 8.3),50mM KCl,9mM MgCl 2,0.75mM MnCl 2,0.001%gelatin (w/v),0.75mM dNTP and an additional 3.2mM dGTP or dTTP,5U AmpliTaq DNA polymerase (Applied Biosystems,Foster City,CA,USA),0.4m M each of the vector-speci?c primers GGCCGATTCATTAATGCAGC and GCCTTTAGCGTCAG ACTGTAG and as template 10ng of the puri?ed vector was used.The DNA was ampli?ed for 26cycles (948C 1min,568C 1min,728C 2min).The two different PCR products,resulting from either an excess in dGTP (denoted CTep1)or dTTP,were pooled and used as a template in the second PCR.The same conditions as for the ?rst round were used,however,only an excess of dGTP was used this time,creat-ing the library CTep2.The mutated gene fragments CTep1and CTep2were gel puri?ed and digested with S?I and Not I (New England Biolabs,Beverly,MA,USA)followed by lig-ation into the corresponding sites of a modi?ed version of the pFab5c.His phagemid (Engberg et al .,1995),shortened to encode only the ?nal C-terminal domain of protein III.The libraries were subsequently transformed into electrocom-petent Top10F’Escherichia coli (Invitrogen,Carlsbad,CA,USA)and random clones sequenced from both libraries.Mutational rates were determined by calculating the percen-tage of mutated residues at the nucleotide or amino acid level,excluding those positions that were targeted for diver-si?cation in the cavity library [38H ,40H ,55H ,57H ,59H ,66H ,107H -109H ,113H ,40L ,105-117L ;the subscript relates to its position in the heavy (H)or light chain (L)](Persson et al .,2006).Throughout this study,residue numbering follows the IMGT nomenclature (Lefranc et al .,2003),inserting gaps at the top of the loops.The three loops of the heavy and light chain are denoted complementarity determining region (CDR)H1-3and CDRL1-3,respectively.

Phage selections

Phage stocks of the two libraries and CT were prepared by VCSM13helper phage infection (Stratagene,La Jolla,CA,USA)as described (Cicortas Gunnarsson et al .,2004).An overview of the selection procedure is illustrated in Fig.1and Table I.Brie?y,three selection rounds were performed,using gradually lower concentration of testosterone-biotin (Sigma-Aldrich Inc.,St Louis,MO,USA)(Fig.2).Also between the rounds,the coating of the paramagnetic beads was alternated between streptavidin (Dynal A/S,Oslo,Norway)and avidin (Spherotech Inc.,Libertyville,IL,USA)to reduce the risk of obtaining carrier-speci?c binders.In the ?rst round,the three different libraries (CT,CTep1and CTep2)were handled separately.The libraries were pre-incubated with testosterone-biotin diluted in selection buffer [0.2%gelatin,0.05%(v/v)Tween 20in phosphate-buffer saline (PBS)]for 2h on rotation at room temperature.Magnetic beads,washed twice in selection buffer,were added and the mixture was allowed to incubate for another 30min.After ?ve washes in selection buffer,followed by two washes in PBS,binding phages were eluted by the addition of trypsin (Invitrogen,Pasley,UK),which cleaves at a site located between the displayed single chain antibody fragment (scFv)and protein III.The cleavage reaction was subsequently inhib-ited by the addition of aprotinin (Invitrogen).Eluted phages were propagated and titers determined as previously described (Cicortas Gunnarsson et al .,2004).Equal amounts of phages from the three selections were pooled and used for the second round of selection,which was carried out essentially as described for the ?rst round but with the following changes;the amount of panning antigen was decreased (from 5?1028to 1?1028M)and the phage capture step was varied,by excluding or including soluble testosterone (1026M,Sigma-Aldrich)as competitor at the time of addition of the magnetic beads.The two resulting populations (C2L and C2H )were treated separately in the third selection round.In addition to varying the antigen concentrations and conditions during the capturing step,the elution method was also altered,yield-ing in total eight different selection strategies (Table I).The strategies were named with three letters;A,C and E,coding for antigen concentration,capture condition and elution method,respectively.The letters were indexed with high (H)or low (L)to denote the selection pressure for each variable.A H for the lower antigen concentration (2?1029M),A L for the higher (1028M),C H if soluble testosterone (1026M)

was

Fig.1.A ?owchart outlining the experimental steps of the study.The starting material of the af?nity maturation process (library CT)was a phage-selected sub-population of the previously described cavity library (Persson et al .,2006).Library CT,which was highly enriched for testosterone binders,was submitted to one or two rounds of random mutagenesis by error-prone PCR,resulting in the two libraries CTep1and CTep2.Different phage display selection strategies were subsequently used on these libraries to ?nd antibody fragments of increased af?nity (for further details on selection parameters see Table I).After a ?rst round of selection,in which the three starting libraries (CT,CTep1and CTep2)had been handled separately,the libraries were pooled and used for a second round of selection.By varying the conditions during the phage capture step,two populations (C2L and C2H )were obtained.These were treated separately in the third selection round,giving in total 8different selection strategies.These were named with three letters;A,C and E,coding for Antigen concentration,Capture condition and Elution method,respectively,and furthermore indexed with H (high)or L (low)to denote selection pressure for each variable.All 16populations depicted were analyzed by competitive phage ELISA and individual scFv obtained from the 10populations of selection rounds two and three were also assayed in soluble format (for further details see Table II).

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present during the capturing step and C L if it was not,E L if the phages were eluted with trypsin or E H if eluted with soluble testosterone (1025M,2h).In all three selection rounds an excess of magnetic beads were used to allow all antigen-bound phages to be captured and to minimize the risk of selecting multivalently displaying phages that otherwise,due to avidity effects,most likely would have a selection advantage.

Phage ELISA and sequencing of selected populations

The unselected libraries (CT,CTep1and CTep2)as well as the different populations from the three selection rounds were analyzed for speci?city using phage ELISA.The popu-lations were tested on testosterone-biotin and FITC-biotin (5(6)-(biotinamidohexanoylamido)pentylthioureidyl?uores-cein)(Sigma-Aldrich),both bound to the plate via streptavi-din,and on bovine serum albumin.Antigen-bound phages were detected by a horseradish peroxidase (HRP)-conjugated anti-M13antibody (GE Healthcare,Uppsala,Sweden)using o -phenylenediamine as chromogen.In addition,six clones,randomly picked from each of the eight strategies of the third selection round,were similarly analyzed for speci?city and subsequently sent for automated DNA sequencing (MWG Biotech,Ebersberg,Germany).

To estimate the binding af?nity for soluble testosterone,the different populations were further analyzed in a competi-tive phage ELISA format.Testosterone was used to compete with testosterone-biotin immobilized on streptavidin as described (Persson et al .,2006).This allowed for the deter-mination of IC 50values,i.e.the concentration of competing hapten that inhibited 50%of phages binding to the immobi-lized antigen.IC 50values were similarly determined for estradiol (Sigma-Aldrich),?uorescein (Sigma-Aldrich)and testosterone-biotin.Before the addition of the phage solution containing the inhibiting antigen (1–20000ng/ml),care was taken to saturate the biotin-binding sites of streptavidin by adding an excess of testosterone-biotin,a crucial step when inhibiting with biotinylated substances as in the case of testosterone-biotin.For comparison studies,two testosterone-speci?c clones (TC-5and TC-20,GenBank accession numbers DQ250208and DQ250223,respectively),which previously had been isolated from the cavity library (Persson et al .,2006),were also

analyzed.

Fig.2.Molecular structures of testosterone-biotin (A),the derivative used for the phage display selections and the subsequent ELISA and BIAcore assays,and testosterone (B).

T a b l e I .O v e r v i e w o f t h e s e l e c t i o n s t r a t e g i e s

S e l e c t i o n 1

S e l e c t i o n 2

S e l e c t i o n 3

I n p u t A n t i g e n

C a t c h i n g E l u t i o n

O u t p u t

I n p u t

A n t i g e n C a t c h i n g

E l u t i o n

O u t p u t

I n p u t A n t i g e n

C a t c h i n g E l u t i o n O u t p u t

C T

5*1028M T B

S A T r y p s i n C T *

C T *C T e p 1*C T e p 2*p o o l e d t o g e t h e r

1028M T B

A v i d i n

T r y p s i n

C 2L

C 2L

2*1029M T B S A T r y p s i n A H C L E L

C 2L

2*1029M T B S A 1025M T A H C L E H

C T e p 1

5*1028M T B

S A

T r y p s i n C T e p 1*

C 2L

1028M T B S A T r y p s i n A L C L E L

C 2L

1028M T B S A 1025M T A L C L E H

C T *C T e p 1*C T e p 2*p o o l e d t o g e t h e r 1028M T B

A v i d i n t1026M T

T r y p s i n

C 2H

C 2H

2*1029M T B S A t1026M T T r y p s i n A H C H E L

C 2H

2*1029M T B S A t1026M T 1025M T A H C H E H

C T e p 25*1028M T B S A

T r y p s i n C T e p 2*

C 2H

1028M T B S A t1026M T T r y p s i n A L C H E L

C 2H

1028M T B

S A t1026M T 1025M T

A L C H E H T

B ,t e s t o s t e r o n e -b i o t i n .S A ,s t r e p t a v i d i n .T ,t e s t o s t e r o n e .

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High-throughput ELISA screening

For the subsequent analysis steps,an automated ELISA screening procedure was performed using integrated robotic workstations as reviewed by Hallborn and Carlsson(2002). For this purpose a change to a compatible vector,that allows the production of soluble scFv,was needed.Phagemide DNA from the ten populations of selection rounds two and three as well as from the control clones TC-5and TC-20was isolated and digested with the restriction enzymes S?I and Avr II(New England Biolabs).The fragment encoding the scFv was gel-puri?ed and subsequently inserted into a vector that provides the secreted scFv with three FLAG-epitopes and a hexahistidine tag at their C-termini(BioInvent International AB,Lund,Sweden).The constructs were trans-formed into chemically competent Top10E.coli using stan-dard heat chock treatment.

A total of1152clones from each strategy were picked, transferred to384-well plates containing media supplemented with isopropyl thiogalactoside and scFv were produced over-night at378C with vigorous shaking.After sedimentation of the bacteria,the supernatants containing the scFv were screened for binding to biotinylated testosterone in a primary and a secondary assay.Brie?y,the produced scFv were cap-tured by anti-FLAG antibodies(M2,Sigma-Aldrich)that had been adsorbed on the surface of microtiter plates.By limiting the anti-FLAG antibody,differences in scFv production levels should minimally affect the assay,making any observed differences in signal dependent on binding ability. Following a washing-step,testosterone-biotin was added (40nM).After1h of incubation,unbound antigen was removed and HRP-labeled streptavidin(Dako Cytomation, Glostrup,Denmark)added.After a last washing-step,lumi-nescent substrate(Pierce supersignal,Pierce,Rockford,IL, USA)was added and the plates were read in a Tecan Ultra instrument(Tecan AG,Ma¨nnedorf,Switzerland).To get a value of the binding properties of the scFv,a threshold was set using the clones TC-5and TC-20with known af?nity (Persson et al.,2006).FITC-biotin was used as a negative reference to assess the speci?city of the interaction.The48 clones from each strategy that gave the highest speci?c signals in the primary assay were selected for a secondary analysis.The basic set-up of both screenings was the same; however,the secondary assay was much more stringent, using lower testosterone-biotin concentration(10nM)and an increased number of washes.From the secondary screen-ing twelve clones were picked for sequencing from each selection strategy,the?ve clones that gave the highest signal and seven clones picked at random.Of the96sequenced clones,nine unique clones were identi?ed(designated TM-1–9).

Competitive immunoassays of soluble scFv

To investigate the binding af?nity of the nine unique clones for testosterone and testosterone-biotin,competitive ELISA on crude expression supernatants was performed,essentially as described for the phage-displayed scFv but with the following changes:scFv fragments were detected using the HRP-labeled anti-FLAG M2antibody(Sigma-Aldrich)and the reaction developed using luminescent substrate.The binding to estradiol and?uorescein was also accessed.The concentration range used for the inhibiting antigens were0.05–20000ng/ml.

The ELISA IC50values were subsequently veri?ed in a competitive BIAcore assay using a BIAcore3000instrument (BIAcore AB,Uppsala,Sweden).Streptavidin was covalently coupled to a CM5sensor chip using amine coupling accord-ing to the manufacturer’s instructions and an excess of testosterone-biotin,enough to cover all available biotin-binding sites,was added.A second?ow cell was treated with the same chemical procedure but without the addition of antigen and used as reference.A?xed concentration of scFv (TM-2,TM-5,TM-7,TC-5and TC-20),puri?ed from the periplasmic space using af?nity chromatography on Ni-NTA agarose(Qiagen,Hilden,Germany),was mixed with a range of concentrations(0–20000ng/ml)of the inhibiting antigens (testosterone,testosterone-biotin,estradiol and?uorescein), allowed to reach equilibrium and subsequently injected onto the chip at a?ow rate of20m l/min.All experiments were performed at258C and the chip was regenerated in20mM HCl,150mM NaCl.Response curves were generated by sub-tracting the signal obtained from the control?ow cell and IC50values determined.Of note,none of the analyzed scFv showed any signs of reactivity with streptavidin.

Results

Library construction and analysis

The aim of the study was to develop a mutagenesis and selection system(Fig.1)to?nd high-af?nity binders for haptens,in this study exempli?ed by testosterone.The CT library,a sub-population of the previously described cavity library(Persson et al.,2006),was chosen as our initial source of diversity.The cavity library had been designed to include binders of high frequency and functionality against a broad range of different haptens.This library had been sub-jected to two rounds of phage selections on testosterone, yielding the CT library.Analysis of individual members of this pool by ELISA showed that$90%of these were testos-terone speci?c.Also,sequencing revealed a high diversity among those residues targeted for modi?cation(Persson et al.,2006),providing a polyclonal nature of the starting material used for evolution.

Additional diversity was introduced randomly by error-prone PCR(Fig.1).In this way the two libraries CTep1and CTep2were created,each having an estimated size of3–4?107clones of which89%had an insert and80%were in-frame(data not shown).If excluding those positions tar-geted in the design of the cavity library,the random nucleo-tide substitution frequencies of CTep1and CTep2were0.77 and0.87%,respectively,giving an average of3.8(range1–6)and3.9(range2–7)amino acid substitutions per scFv (data not shown).This procedure resulted in$6–8times higher mutation frequencies compared with the CT library (0.12%).Importantly,the extensive diversity found in the cavity-lining residues of the CT library was maintained in both error-prone evolved libraries.

Binding characteristics of the selected populations

We used different selection strategies of various stringencies to select clones with increased testosterone binding activity. Differences were related to the amount of antigen

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(testosterone-biotin)used,whether or not soluble antigen (testosterone)was present during the phage capturing step and choice of elution method.The different approaches are summarized in Table I.

In order to follow the contributions of the different selec-tion parameters,the initial libraries(CT,CTep1and CTep2) and the various pools obtained after each round of selection were analyzed for binding speci?city using phage ELISA. All populations were highly speci?c for testosterone-biotin (data not shown),suggesting that the selection procedures preserved the original speci?city of the starting material. None of the populations showed reactivity to?uorescein,the speci?city of clone FITC8,which was used as diversity-carrying scaffold when constructing the cavity library,nor to estradiol,a steroid highly similar to testosterone.

A competitive ELISA analysis to assess the apparent af?-nities to testosterone-biotin and to soluble testosterone was also performed(Table II).In the?rst selection round,a rela-tively low selection pressure was applied,allowing the removal of non-functional clones formed by the mutagenesis process and also allowing the ampli?cation of rare and poorly expressed scFv.Consequently,this round did not alter the obtained IC50values.In the two following rounds the selection pressure was increased considerably.As one might expect,there was a correlation between binding af?nity for the biotinylated target antigen and the number of selections, with the best result obtained for strategy A H C H E L(IC50?4?1028M)of the third round(Table II).Thus,resulting in at least a500-fold increase in apparent af?nity for testosterone-biotin compared with the starting material.The most prominent increase in binding strength was obtained by decreasing the antigen concentration.The presence of soluble testosterone(C H)during the catching step also seemed to promote lower IC50values;however,no obvious positive effect of the elution method could be observed. Whereas the af?nity for testosterone-biotin showed a peak after the third selection round,it is apparent that the binding to the soluble hapten did not follow the same trend.An initial decrease in IC50values was seen when going from the ?rst to the second selection round.This was especially appar-ent for population C2L.The subsequent selection of these clones,including higher stringency with respect to both antigen concentration and elution method,did not signi?-cantly change the af?nity of the bulk population for testoster-one.In contrast,as illustrated by the differences in IC50 values of the two populations C2H and C2L(33-fold),the presence of soluble testosterone during the phage-catching phase had a major deleterious effect on the binding to free testosterone of the recovered population.This effect was further observed in selection round three,where half of the populations no longer had a detectable testosterone reactivity, suggesting that the addition of soluble testosterone comple-tely drained the populations of testosterone binders. Nevertheless,C2L of the second round of selection and four of the eight populations of the third round showed an $100-fold increase in apparent af?nity for the native antigen compared with the starting populations.

Screening of individual clones

A total of1152clones were picked from each of the total10 strategies from selection round two and three and their scFv were produced in soluble form.In a high-throughput ELISA the clones were assessed for binding to testosterone-biotin.A primary screening assay identi?ed numerous clones that gave signals10–50-fold higher than the control clones TC-5and TC-20,which had previously been isolated from the CT

T able II.Characteristics of the initial libraries and the different selected populations

Population Competitive phage ELISA on

populations of binders High-throughput ELISA screening of individual

soluble scFv

Number of

unique scFv c

Number of scFv

binding to the

soluble hapten d

IC50(TB,nM)IC50(T,nM)Primary screening a(%)Secondary screening b(%)

Unselected CT.2000050000--

CTep1.2000030000––

CTep2.2000070000––

Selection1CT*.2000050000––

CTep1*.2000070000––

CTep2*.2000040000––

Selection2C2L100030040

C2H10001000016

Selection3A H C L E L50060033923/121/3

A H C L E H20060018943/121/3

A L C L E L70040056315/123/5

A L C L E H70040028465/123/5

A H C H E L40.7000033981/120/1

A H C H E H200.70000441002/120/2

A L C H E L2007000041923/121/3

A L C H E H200.7000033903/120/3

TB,testosterone-biotin.

T,testosterone.

a Percentage of clones having a signal greater than5000.1152clones from each strategy were analyzed in this assay.In this assay,the control antibody fragments TC-5and TC-20,which had previously been isolated from the CT library,had signals in the range of500to700.

b Percentage of clones having a signal greater than10000.48clones from each strategy were analyzed in this assay.TC-5and TC-20did not result in any detectable signal in this assay.

c The number of unique scFv was determine

d by sequencing of positiv

e scFv as de?ned by the secondary ELISA screening.

d Th

e number o

f scFv bindin

g the soluble hapten was assessed by competitive ELISA.

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population,prior to the error-prone evolution and the strin-gent selections (Table II).Forty-eight of the clones display-ing the highest signal from each strategy were subjected to a secondary screening assay of higher stringency,as evidenced by the fact that neither of the two control scFv showed any detectable signal in this assay.In both the primary and sec-ondary screening assays,the frequency of clones displaying high signals were considerably lower for the populations of the second selection round compared with the third.

Based on the result of the secondary screening,twelve clones from each of the strategies in selection round three were sequenced.Out of 96sequenced scFv,nine different variants were found (denoted TM-1–9,Fig.3).Notably,one of the sequences,TM-7,was found in all strategies and rep-resented 75%of all sequenced clones.In contrast,some of the sequence variants were only found in one or a few of the populations,thus suggesting that the selection strategies were different enough to tap different parts of the available sequence space.It can also be seen that higher stringency selections,with respect to antigen concentration and catching conditions,had an adverse effect on the diversity of the selected population (Table II).

The nine unique scFv were further analyzed in a competi-tive ELISA to assess the binding af?nity to testosterone and testosterone-biotin.As shown in Table III,?ve of the nine clones (TM-1–5)had similar binding af?nities to testosterone and testosterone-biotin,whereas four of the scFv (TM-6–9)only recognized the biotinylated form of the antigen.These data were later con?rmed by competitive BIAcore analysis (Table III).The best clone,TM-4,had an IC 50value of 2?1029M for soluble testosterone (Fig.4),corresponding to a 200-fold increase in apparent af?nity compared with TC-5.

Sequence and structure of selected scFv

Based on sequence similarity,the nine isolated scFv could be grouped into two groups (Fig.3).Interestingly,this division correlates with the observed reactivity pattern (Table III).Whereas the ?ve clones that bound soluble tes-tosterone had a CDRL3length of 11,the remaining four scFv had a nine amino acids long CDRL3loop.This ?ne-speci?city could further be coupled to highly conserved resi-dues within each of the two groups,in particular residues 40H ,55H and 107L .The preferred combination of these CDRL3lengths and these three residues was also evident among the 48random sequenced clones picked from the 8strategies of selection round three,before the high-throughput ELISA analyses (data not shown).

The random mutagenesis process introduced in total 32amino acid changes among the nine sequence variants.As shown in Fig.3,each clone has between 1and 8amino

acid

Fig.3.Alignment of sequence variants (TM-1-9)identi?ed after three cycles of phage display and 2rounds of high-throughput ELISA screening.The wild-type sequence is a ?uorescein-speci?c scFv whose gene served as diversity carrying scaffold.Mutated regions include those targeted by site-directed mutagenesis,introduced in a previous study (Persson et al .,2006),and those randomly introduced in the current study through an error-prone PCR process.Our previous design strategy (Persson et al .,2006)also allowed for the observed length variations in CDRH2and CDRL3.The scFv TC-5and TC-20that were isolated directly from the CT library (Persson et al .,2006)before the error-prone evolution,are also included in the ?gure.Residues identical with the wild-type sequence are shown with dots while absent residues are indicated with gaps.Residues of the heavy and light chains are numbered according to IMGT (Lefranc et al .,2003)and the linker region ((G 4-S)3)from 1to 15.Amino acids are abbreviated according to their one letter https://www.doczj.com/doc/2417942271.html,plete gene sequences are available in GenBank,accession numbers EU095633-41.

T able III.Binding characteristics of the nine isolated scFv (TM-1-9)as determined by competitive BIAcore and ELISA measurements scFv

ELISA (IC 50)BIAcore (IC 50)TB (nM)

T (nM)TB (nM)T (nM)TM-15030ND ND TM-220305030TM-340200ND ND TM-442ND ND TM-550207050TM-640.70000ND ND TM-720.7000030.70000

TM-870.70000ND ND TM-940.70000

ND ND TC-5ND ND 500400TC-20

ND

ND

600

700

For comparisons,scFv TC-5and TC-20,previously isolated from the CT library (Persson et al .,2006),are also included.TB,testosterone-biotin.T,testosterone.

ND,not determined.

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changes (average 3.6)distributed over the variable domain of the heavy chain (V H ),the light chain (V L )and the linker.This number is similar to the level of diversi?cation found in CTep1and CTep2,but considerable higher than the number of substitutions found in the unmutated population (CT)or among the randomly picked clones after three rounds of selection,which had an average of 0.26and 1.4amino acid substitutions per scFv,respectively.No hot spots of mutations could be observed,as the locations of the substi-tutions were all unique.Also,none of the positions targeted for diversi?cation in the cavity library were changed into residues not intended by the design.Some accumulation of mutations was observed in the CDRs (amino acid frequency change: 1.7%)compared with framework regions (1.3%).Also,an increased mutational frequency was observed in the linker region (3.7%).

Discussion

Anti-hapten antibodies are often of lower af?nity than those of high molecular weight antigens like proteins (Chappey et al .,1994).Being small and hydrophobic,haptens generally contain few functional groups that can provide speci?c inter-action with the antibody-binding site.Furthermore,owing to their non-immunogenic nature,haptens need to be covalently attached to a larger carrier molecule,such as a protein,in order to be used as an immunogen.Consequently,the anti-bodies,whether raised in vivo or in vitro ,typically show higher af?nities for the immunogen than for the free hapten (Franek,1987;Charlton et al .,2001;Moghaddam et al .,2001).However,there are not any inherent restrictions in the structure of antibodies that prevent them from binding small molecules strongly and several recombinant antibody libraries have been reported to contain antibodies against soluble haptens (Grif?ths et al .,1994;Vaughan et al .,1996;So

¨derlind et al .,2000).In a study by Boder et al .(2000),the af?nity of a ?uorescein-speci?c antibody was evolved to a K D of 48fM,to our knowledge the highest monovalent ligand-binding so far reported for an antibody.Nevertheless,

haptens remain challenging targets that often require opti-mized mutagenesis and selection strategies in order to ?nd high-af?nity binders (Charlton et al .,2001;Moghaddam et al .,2001;Sheedy et al .,2007).

The aim of the current study was to explore the potential of a focused antibody library for the development of high-af?nity hapten binders.Based on known structure–function relation-ships of antibodies,a focused library,designated the cavity library,had previously been designed to have an improved rec-ognition for hapten targets (Persson et al .,2006).Highly speci?c binders were retrieved to a range of different haptens and importantly these could not only bind the hapten bound to its carrier but also the free,soluble hapten.It appeared that by focusing the diversity solely to those residues that commonly interact with the hapten,unwanted interactions (e.g.with the linker or the carrier)that skew the selection process could be minimized (Persson et al .,2006).The selection pressure was in the previous study kept relatively low and as a consequence the retrieved binders were of moderate af?nity (106–107M 21).However,the high diversity of the obtained binders suggested that the standardized selection procedure did not utilize the full capacity of the library and that there was considerable room for improvement.It is also likely that the introduction of additional diversity would help to increase the af?nity even further.Several studies have shown a lack of correspondence between the residues in contact with the antigen and those modi?ed in af?nity maturation processes (Tomlinson et al .,1996;Daugherty et al .,2000;Ramirez-Benitez and Almagro,2001).Mutations of buried or peripherally located residues have been shown,through long-range effects,to provide ?ne-tuning of the antigen-binding site and an increase in af?nity.Therefore,to increase the likelihood of isolating high-af?nity binders,additional diversity was introduced to include more peripheral positions of the paratope that were not included in the original diversity design.Furthermore,by comparing the

antibody repertoires of na?

¨ve and secondary responses in vivo it has been demonstrated that not all clones are suitable for effective maturation.Several studies have described dominat-ing clones in the initial repertoire that are absent or rarely found in secondary responses.It has therefore been suggested that some clones will,due to the VDJ recombination,be allo-cated to a part of structural space that make them non-competitive in the subsequent hypermutation process (Alzari et al .,1990;Furukawa et al .,1999;George and Gray,1999).However,the molecular mechanisms governing the maturation pathway of antibodies are still poorly understood and thus dif?-cult to predict.Rather than utilizing a single clone as starting material for diversi?cation,which is standard procedure when performing af?nity maturation experiments,we therefore based the new library on an entire pool of clones that had been enriched by phage display for variants speci?c for testosterone,the hapten chosen as model antigen for this investigation.

The various selection procedures resulted in a signi?cant improvement of the obtained IC 50values for several of the selected populations,an improvement that was mainly achieved by the reduction in antigen concentration between each round.By using a high concentration of competing soluble antigen during the period when antigen-bound phages are caught onto the magnetic beads,the recovery of scFv with fast off-rates,including those that are displayed multivalently,should ef?ciently be prevented (Hawkins et al .,1992).Although having some positive effect on the binding

af?nity

Fig.4.Dose-dependent binding of scFv TM-4to testosterone (squares)and testosterone-biotin (circles)as determined by competitive ELISA.The mean binding signal,average of duplicates,at each antigen concentration was divided by the antibody binding response obtained in the absence of inhibiting antigen to give percentage binding.The IC 50values,being equal to the antigen concentration at which the binding response is half-maximum (50%),are 2and 4nM for testosterone and testosterone-biotin,respectively,thus making this antibody fragment suitable for measuring testosterone within the clinically relevant range (0.7–70nM)(Fitzgerald and Herold,1996).

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to testosterone-biotin,this procedure adversely affected the binding to free testosterone.It appears that this process selected for variants that had matured by making contacts with the biotinylated conjugate compared with the naked mol-ecule,an evolution facilitated by the small size of the antigen, suggesting that this step was too stringent with respect to the kinetics of the population.The use of soluble antigen to com-petitively elute phages rather than using non-speci?c elution methods have in several studies been utilized to enhance the selection of binders with higher af?nity for the free hapten (Sheedy et al.,2007).However,in the current study this approach had no detectable effect on the quality of the selected populations as assessed by binding to soluble testos-terone.Despite the fact that the presence of soluble testoster-one during the catching or elution steps did not have the intended effect,our diversi?cation and selection strategy still allowed us to successfully evolve several of the populations to at least a100-fold increase in mean af?nity for the biotiny-lated as well as for the unmodi?ed hapten.

Importantly,the best clone showed an$200-fold af?nity improvement for soluble testosterone compared with the best clone obtained from the original population,corresponding to an af?nity useful for analyses of clinically relevant levels of testosterone(Fitzgerald and Herold,1996).The nine isolated clones could,based on sequence similarity,be clustered into two distinct groups.The most obvious feature differing between these were CDRL3length(9or11residues)and type of residue found in40H,55H and107L.Interestingly,there was a striking correlation between these groups and their?ne speci-?city.Only antibody fragments harboring the longer CDRL3 loop could bind soluble testosterone,whereas clones of the other group were highly linker-dependent.Among the total34 sequenced clones of the starting material(CT,CTep1and CTep2),75%contained the longer CDRL3version(data not shown).In contrast,none of these randomly picked sequences were found to have a CDRL3of length9,suggesting that there was a substantial selection advantage for clones having this loop length.These results clearly imply that some of the selec-tion parameters as well as the subsequent screening process preferentially‘selected’clones that recognized the conjugated form of the hapten over antibodies that speci?cally recognized the free hapten.It is therefore likely that the introduction of a method early in the screening program that also assesses for recognition of the free hapten should substantially improve the chances of yielding even better soluble hapten-binders.

The observed change in antibody repertoire is not surpris-ing since an increased selection pressure put higher demands on the antigen–antibody interaction and accordingly new ways have to be found to increase the af?nity.As outlined above,repertoire shifts have frequently been observed during immune responses such as those to hapten conjugates(Berek and Milstein,1987)and to some extent also to protein anti-gens(Newman et al.,1992;Kalinke et al.,1996).Related to these?ndings,Brown et al.(2000)noted that antibodies of the late phase of an immune response were better suited for interacting with the hapten in context of the carrier in com-parison to clones of the initial response.This was structurally explained by a widening of the original deep pocket,result-ing in an elongated shallow groove that more ef?ciently accommodated parts of the carrier or the linker in addition to the hapten itself.Whether a similar structural change resulted in the observed speci?city change of clones TM-6-9is conceivable but unclear.The polyclonal starting population allowed for the observed repertoire shift.Although it did not, for the purpose of this study,provide any additional ben-e?cial binding characteristics,the results demonstrate, together with a recent study by Groves et al.(2006),the potential of using polyclonal populations to more ef?ciently exploit structural space.

Whereas a clear connection existed between the obtained reactivity pattern and residues targeted in the original design, no such correlation could be attributed to any of the ran-domly introduced mutations.No consensus mutations were found among these,and at a?rst glance they could easily be disregarded as neutral mutations accumulated during the ran-domization process.However,the considerably higher mutation frequency found among the nine clones isolated after the high-throughput screening assay compared with the number of mutations found after the three rounds of phage selections indicates the importance of these additional substi-tutions in creating novel binders of higher af?nity.The lack of consensus mutations suggests that there are numerous paths to improved?tness.Although,some accumulation of mutations was seen in the CDRs,none of the substituted amino acids were among those proposed to line the antigen-binding cavity(Persson et al.,2006),supporting the notion that af?nity maturation of antibodies can effectively be achieved through peripheral or‘second-sphere’changes (Tomlinson et al.,1996;Ramirez-Benitez and Almagro, 2001).An increased mutational frequency was found in the scFv linker,which might possibly in?uence the stability of the scFv or the orientation of its two domains and thereby the af?nity of the antigen–antibody interaction.

In conclusion,we have demonstrated that the process of in vitro af?nity maturation can successfully be applied on a population of molecules in order to?ne-tune the binding activity and speci?city of hapten-binders originating from the cavity library.Similar to the natural system,we started out with an anti-body repertoire having diversity mainly focused to the central parts of the paratope.An initial enrichment allowed for the retrieval of a population of binders having an effective imprint of the ligand in their binding pockets.In analogy with the somatic hypermutation process,additional diversity was intro-duced to include more peripherally located regions.This allowed adjustments of the initially obtained imprints,resulting in the retrieval of antibody fragments with signi?cantly improved binding af?nities for the hapten target of investigation. Acknowledgements

We gratefully acknowledge?nancial support from BioInvent International AB and the Swedish Research Council.

Funding

BioInvent International AB;the Swedish Research Council (grant number2006-5446).

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Edited by Carl Borrebaeck

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常用化疗药分类

1.细胞周期非特异性药物(CCNSC)和细胞周期特异性药物(CCSC )的区别 CCSC是周期特异性药物,特异性地杀伤处于特定时相的肿瘤细胞,需等肿瘤细胞处于对应时相才有效,故应慢滴。 2.化疗药物给药剂量按体表面积计算(文生氏公式) 体表面积(m2)=0.0061×身高(cm)+0.128×体重(kg)-0.1529 工作中计算体表面积:以身高1.6m,体重60公斤,体表面积为1.6m2,做调整 3.肿瘤病人治疗后,无复发,生存率≥5年,算治愈 4.联合化疗方案药物成原则 a.两种以上作用机制不同的药物组成 b.周期非特异性药物和不同时相的周期特异性药物配合 c.各药的毒性不相重复 d.一般3~4个药物最好,临床上一般2-3个药合用,4个药合用一般用于复发的肿瘤患者或者难治性的血液病患者, 5.化疗药物的器官毒性 ADR(多柔比星,阿霉素):心脏毒性 BLM(博来霉素):肺纤维化 DDP(顺铂):肾毒性 L-OHP(奥沙利铂)、VCR(长春新碱)、PTX(紫杉醇):神经毒性 BCNU(卡莫司汀):肝毒性 6.化疗分为 a.诱导化疗:又称新辅助化疗,实施局部治疗方法(如手术或放疗)前所做的全身化疗,目的是使肿块缩小、及早杀灭看不见的转移细胞,以利于后续的手术、放疗等治疗。对于早期和晚期肿瘤患者不采用新辅助化疗的方法。 b.辅助化疗:手术治疗和放疗的后,杀灭手术无法清除的微小病灶,减少复发,提高生存率。

c.姑息化疗:对于手术后复发、转移或就诊时不能切除的肿瘤病人,目的并不是彻底地消灭肿瘤,而在于能够平稳地控制肿瘤的进展,缓解患者的痛苦,延长其生命。这时的化疗称作“姑息化疗”。 7.常用细胞周期特异性药物 S 期特异性药物: 抗叶酸类:甲氨蝶呤(MTX ,胸腺嘧啶、嘌呤)、培美曲塞(PEM ,胸腺 嘧啶、嘌呤,)、雷替曲塞(胸腺嘧啶)、六甲蜜胺(嘧啶) 抗嘧啶类:氟尿嘧啶(5-FU )、卡培他滨(CAPE ,希罗达,5-FU 前体药)、 替加氟(FT207,5-FU 衍生物)、替吉奥(替加氟+吉美嘧啶 +奥替拉西钾)、优福定(替加氟+尿嘧啶)、卡莫氟(HCFU , 5-FU 衍生物)、 阿糖胞苷(Ara-c )、吉西他滨(GEM ,作用机制同Ara-c)、 安西他滨(Ara-c 衍生物) 抗嘌呤类:6-巯嘌呤(6-MP )、硫唑嘌呤(体内转化6-巯嘌呤起作用)、 氟达拉滨(Ara-A ,阿糖腺苷类似物,抗病毒类)、硫鸟嘌呤 (6-TG )、喷他司丁(DCF ,新的抗代谢药,本品是从链霉素 菌中分离得的抗生素) 干扰嘌呤和嘧啶合成 :羟基脲(HU) 拓扑异构酶I :喜树碱类,羟喜树碱(HCPT ),伊立替康(CPT-11)、 拓扑替康 拓扑异构酶II :依托泊苷(VP-16)、替尼泊苷(VM-26) M 期特异性药物:长春碱类:长春碱(VLB )、长春新碱(VCR )、长春瑞滨(NVB )、 长春地辛(VDS ) 紫杉类:紫杉醇(PTX )、多西他赛(DOC ) G 1期特异性药物:L-ASP (L-门冬酰胺酶),肾上腺皮质类固醇 G 2期特异性药物:博来霉素(BLM ,国外)、平阳霉素 (PYM ,国内,与BLM 成 分相近) 影响蛋白质功能与合成的药 门冬酰胺酶、培门冬酶、高三尖杉酯碱 抗代谢类 拓扑异构酶抑制剂

单克隆抗体在肿瘤治疗中的应用

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因子等加强ADCC作用。此外,一些偶联抗体通过连接细胞毒化合物或放射性物质来杀伤肿瘤细胞,如TDM1(trastuzumab emtansine)、Zevalin等。1997-2013年FDA 和CFDA批准的抗肿瘤单抗类药物列表如图15。图15:1997-2013年FDA和CFDA批准的抗肿瘤单抗类药物(点开大图观看更清晰?)截至目前,全球上市的单克隆抗体共51个,其中鼠源单克隆4个、嵌合抗体7个、人源化单克隆抗体23个、全人单克隆抗体17个。单抗药物中,抗肿瘤药物占了一半左右。截至目前,中国上市的抗肿瘤单抗类药物共有7个,其中进口4个,国产3个,国内自主研发的第一个单克隆抗体类抗肿瘤药物为百泰药业治疗鼻咽癌的药物尼妥珠单抗(泰欣生)2008年4月被正式批准联合放疗治疗EGFR表达阳性的Ⅲ/Ⅳ期鼻咽癌(比埃克替尼早了3年),这是全球第一个以EGFR为靶点的人源化单抗药物。2015年,中国国内单抗药物销售额约为72亿元人民币,其中肿瘤药占了80%,约为57亿元,同比约占全球抗药市场的1.13%。对比小分子靶向药物,2014年国内22重点城市样本医院靶向小分子抗肿瘤药物市场为13.21亿元,根据2015年样本医院全年靶向小分子药物购入金额为14.92亿元,占全球市场的1.34%。 从全球市场上看,2015年靶向抗肿瘤药物TOP10中有6个是单抗,前3名全是单抗,且销售额差距明显,前3名2015

铂类化疗药区别

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骨细胞相关因子在骨重建中的作用

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阿霉素、柔红霉素、平阳霉素等长春碱类衍生物。 单抗药物对肿瘤相关靶点的特异性作用:特定受体或特定的基因表达蛋白可能作为单抗药物的靶点。 单抗药物对抗药性肿瘤细胞的杀伤作用:单抗偶联物对于抗药性肿瘤细胞仍显示较强的杀伤活性。例如长期服用氨甲喋呤而出现抗药性的成骨肉瘤细胞,单抗氨甲喋呤偶联物仍显示较强的杀伤作用。 存在的问题与解决途径 单抗药物的临床研究结果已为其应用于治疗肿瘤展现出良好的前景,但仍存在涉及免疫学和药理学两方面的问题。免疫学方面的问题主要是人抗鼠抗体(HAMA)反应。药理学方面的问题主要是到达肿瘤的药量不足,由于单抗药物是异体蛋白,会被网状内皮系统摄取,有相当数量将积聚于肝、脾和骨髓。单抗药物是大分子物质,通过毛细血管内皮层以及穿透肿瘤细胞外间隙均受到限制,解决途径主要包括: 降低单抗药物的免疫原性:使用人源化单抗仍不能解决“弹头”(毒素)的免疫原性问题,使用化疗药物为“弹头”则可避免此部分的抗体反应。 提高单抗药物在肿瘤组织的浓度:单抗药物在体内的运送过程与肿瘤局部的供血状况有关,动物实验表明,血管丰富、血流量较大的肿瘤,用单抗药物治疗的效果也比较好。 加强单抗药物对肿瘤细胞的杀伤作用:单抗能特异性结合到相关的肿瘤靶细胞,但通常难以杀伤靶细胞。单抗治疗剂一般须调动体内的免疫系统,包括细胞免疫和体液免疫效以达到治疗肿瘤的效果。如上所述,单抗药物实际到达肿瘤细胞的数量有限,为取得良好的结果,单抗药物需要高效化,仅有微量的偶联物到达靶部位即可杀伤肿瘤细胞。 进一步提高药物作用的选择性:将单抗偶联的活化酶与前体药物联合使用,在靶肿瘤进行酶性活化。前体药物是指该药无治疗活性或仅有较低活性,需在体内经过代谢转化为活性型才显示药物活性。其优越性是可能降低毒性和延长药物体内作用的时间。

抗肿瘤药分类

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1995年,世界卫生组织对世界上近百种抗癌药物进行评价,顺铂的疗效、市场等综合评价得分名列前茅,排在第2位。另据统计,在我国医院抗癌化疗治疗方案中,以顺铂为主或有顺铂参加配伍的方案占所有化疗方案的70%~ 80%(3)。通过这些数据表明,铂类药物在化疗治疗中占有举足轻重的地位。下面本文就对一些临床上常用的各类铂类抗肿瘤药物做一下简单的介绍。 1.第一代铂类抗癌药 1.1.顺铂 顺铂的化学名为顺式二氨基二氯络铂,又名顺氯氨铂,英文缩写为DDP。1967年,美国密执安州立大学教授Rosenberg等人发现,其顺式异构体有抗癌作用,而反式异构体无此作用。1969年,顺铂开始应用于临床(4)。 在血液中氯离子浓度相对高(100mM )的环境中,顺铂以完整分子形态和血浆蛋白相结合。在胞内氯离子浓度相对较低(4~20mM)的环境中发生水化,其中的双氯配体全部或其中一个解离,这样顺铂才能和靶标DNA相结合。它作用于鸟嘌呤的N7位,部分通过共价键与腺嘌呤结合,当结合上第2个DNA键时形成一个闭合的环状复合物,扭转了DNA 分子构象,从而阻止复制和转录,最终致细胞凋亡。

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