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Introducing weak affinity chromatography to drug discovery with focus on fragment screening
Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
2013 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Fragment-based drug discovery is an emerging process that has gained popularity in recent years. The process starts from small molecules called fragments. One major step in fragment-based drug discovery is fragment screening, which is a strategy to screen libraries of small molecules to find hits. The strategy in theory is more efficient than traditional high-throughput screening that works with larger molecules. As fragments intrinsically possess weak affinity to a target, detection techniques of high sensitivity to affinity are required for fragment screening. Furthermore, the use of different screening methods is necessary to improve the likelihood of success in finding suitable fragments. Since no single method can work for all types of screening, there is a demand for new techniques. The aim of this thesis is to introduce weak affinity chromatography (WAC) as a novel technique for fragment screening.

WAC is, as the name suggests, an affinity-based liquid chromatographic technique that separates compounds based on their different weak affinities to an immobilized target. The higher affinity a compound has towards the target, the longer it remains in the separation unit, and this will be expressed as a longer retention time. The affinity measure and ranking of affinity can be achieved by processing the obtained retention times of analyzed compounds.

In this thesis, WAC is studied for fragment screening on two platforms. The first system comprised a 24-channel affinity cartridge that works in cooperation with an eight-needle autosampler and 24 parallel UV detector units. The second system was a standard analytical LC-MS platform that is connected to an affinity column, generally called WAC-MS or affinity LC-MS. The evaluation criteria in studying WAC for fragment screening using these platforms were throughput, affinity determination and ranking, specificity, operational platform characteristics and consumption of target protein and sample. The model target proteins were bovine serum albumin for the first platform, thrombin and trypsin for the latter. Screened fragments were either small molecule drugs, a thrombin-directed collection of compounds, or a general-purpose fragment library. To evaluate WAC for early stages of fragment elaboration, diastereomeric mixtures from a thrombin-directed synthesis project were screened.

Although both analytical platforms can be used for fragment screening, WAC-MS shows more useful features due to easy access to the screening platform, higher throughput and ability to analyze mixtures. Affinity data from WAC are in good correlation with IC50 values from enzyme assay experiments. The possibility to distinguish specific from non- specific interactions plays an important role in the interpretation of WAC results. In this thesis, this was achieved by inhibiting the active site of the target protein to measure off-site interactions. WAC proves to be a sensitive, robust, moderate in cost and easy to access technique for fragment screening, and can also be useful in the early stages of fragment evolution.

In conclusion, this thesis has demonstrated the proof of principle of using WAC as a new tool to monitor affinity and to select hits in fragment-based drug discovery. This thesis has indicated the primary possibilities, advantages as well as the limitations of WAC in fragment screening procedures.  In the future, WAC should be evaluated on other targets and fragment libraries in order to realize more fully the potential of the technology.

Place, publisher, year, edition, pages
Växjö: Linnaeus University Press, 2013.
Series
Linnaeus University Dissertations, 124/2013
Keyword [en]
affinity LC-MS, fragment-based drug discovery, fragment screening, high throughput, mass spectrometry, stereoisomer, enantiomer, thrombin, weak affinity chromatography, WAC, WAC-MS.
National Category
Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
Research subject
Natural Science, Biomedical Sciences; Natural Science, Biochemistry
Identifiers
URN: urn:nbn:se:lnu:diva-24642OAI: oai:DiVA.org:lnu-24642DiVA: diva2:608862
Public defence
2013-04-05, N2007, Smålandsgatan 26E, Kalmar, 09:30 (English)
Opponent
Supervisors
Available from: 2013-03-11 Created: 2013-03-01 Last updated: 2013-04-29Bibliographically approved
List of papers
1. Toward high-throughput drug screening on a chip-based parallell affinity separation platform
Open this publication in new window or tab >>Toward high-throughput drug screening on a chip-based parallell affinity separation platform
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2010 (English)In: Journal of Separation Science, ISSN 1615-9306, E-ISSN 1615-9314, Vol. 33, no 17-18, 2575-2581 p.Article in journal (Refereed) Published
Abstract [en]

High-throughput screening of compound libraries, including the study of fragments, has become one of the cornerstones in modern drug discovery research. During this process hits are defined that may be developed into valuable leads and eventually into possible drug candidates. In this paper, we have demonstrated that parallel zonal weak affinity chromatography in microcolumns on a chip offers a possible screening format for weakly binding ligands toward a protein target. We used albumin as a model system because this transport protein is well established as a binder (both weak and strong) for drug substances. Bovine serum albumin was immobilized on microparticulate diolsilica particles and then packed into a 24-channel cartridge, which served as the separation platform. Analysis of the obtained chromatograms yielded information about affinity even in the millimolar range. Employing this approach, thousands of substances can be screened in just a day. We feel confident that zonal affinity chromatography will provide a useful technology in the future for performing high-throughput screening.

National Category
Natural Sciences
Research subject
Natural Science, Biotechnology
Identifiers
urn:nbn:se:lnu:diva-7628 (URN)10.1002/jssc.201000314 (DOI)2-s2.0-77956896903 (Scopus ID)
Available from: 2010-08-22 Created: 2010-08-22 Last updated: 2017-12-12Bibliographically approved
2. Weak affinity chromatography as a new approach for fragment screening in drug discovery
Open this publication in new window or tab >>Weak affinity chromatography as a new approach for fragment screening in drug discovery
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2011 (English)In: Analytical Biochemistry, ISSN 0003-2697, E-ISSN 1096-0309, Vol. 414, no 1, 138-146 p.Article in journal (Refereed) Published
Abstract [en]

Fragment-based drug design (FBDD) is currently being implemented in drug discovery, creating a demand for developing efficient techniques for fragment screening. Due to the intrinsic weak or transient binding of fragments (mM–uM in dissociation constant (KD)) to targets, methods must be sensitive enough to accurately detect and quantify an interaction. This study presents weak affinity chromatography (WAC) as an alternative tool for screening of small fragments. The technology was demonstrated by screening of a selected 23 compound fragment collection of documented binders, mostly amidines, using trypsin and thrombin as model target protease proteins. WAC was proven to be a sensitive, robust, and reproducible technique that also provides information about affinity of a fragment in the range of 1 mM–10uM. Furthermore, it has potential for high throughput as was evidenced by analyzing mixtures in the range of 10 substances by WAC–MS. The accessibility and flexibility of the technology were shown as fragment screening can be performed on standard HPLC equipment. The technology can further be miniaturized and adapted to the requirements of affinity ranges of the fragment library. All these features of WAC make it a potential method in drug discovery for fragment screening.

Place, publisher, year, edition, pages
Elsevier, 2011
National Category
Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy) Analytical Chemistry
Research subject
Natural Science, Biochemistry; Natural Science, Biomedical Sciences
Identifiers
urn:nbn:se:lnu:diva-24639 (URN)10.1016/j.ab.2011.02.022 (DOI)2-s2.0-79955686355 (Scopus ID)
Available from: 2013-03-01 Created: 2013-03-01 Last updated: 2017-12-06Bibliographically approved
3. High-Throughput Fragment Screening by Affinity LC-MS
Open this publication in new window or tab >>High-Throughput Fragment Screening by Affinity LC-MS
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2013 (English)In: Journal of Biomolecular Screening, ISSN 1087-0571, E-ISSN 1552-454X, Vol. 18, no 2, 160-171 p.Article in journal (Refereed) Published
Abstract [en]

Fragment screening, an emerging approach for hit finding in drug discovery, has recently been proven effective by its first approved drug, vemurafenib, for cancer treatment. Techniques such as nuclear magnetic resonance, surface plasmon resonance, and isothemal titration calorimetry, with their own pros and cons, have been employed for screening fragment libraries. As an alternative approach, screening based on high-performance liquid chromatography separation has been developed. In this work, we present weak affinity LC/MS as a method to screen fragments under high-throughput conditions. Affinity-based capillary columns with immobilized thrombin were used to screen a collection of 590 compounds from a fragment library. The collection was divided into 11 mixtures (each containing 35 to 65 fragments) and screened by MS detection. The primary screening was performed in < 4 h (corresponding to > 3500 fragments per day). Thirty hits were defined, which subsequently entered a secondary screening using an active site-blocked thrombin column for confirmation of specificity. One hit showed selective binding to thrombin with an estimated dissociation constant (K-D) in the 0.1 mM range. This study shows that affinity LC/MS is characterized by high throughput, ease of operation, and low consumption of target and fragments, and therefore it promises to be a valuable method for fragment screening.

Keyword
drug discovery, fragment screening, mass spectrometry, thrombin, weak affinity chromatography
National Category
Biochemistry and Molecular Biology
Research subject
Chemistry, Biochemistry; Natural Science, Biomedical Sciences
Identifiers
urn:nbn:se:lnu:diva-24535 (URN)10.1177/1087057112459271 (DOI)000313661900002 ()2-s2.0-84872546422 (Scopus ID)
Available from: 2013-02-25 Created: 2013-02-25 Last updated: 2017-12-06Bibliographically approved
4. Weak Affinity Chromatography for Evaluation of Stereoisomers in Early Drug Discovery
Open this publication in new window or tab >>Weak Affinity Chromatography for Evaluation of Stereoisomers in Early Drug Discovery
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2013 (English)In: Journal of Biomolecular Screening, ISSN 1087-0571, E-ISSN 1552-454X, Vol. 18, no 6, 748-755 p.Article in journal (Refereed) Published
Abstract [en]

In early drug discovery (e.g. in fragment screening), recognition of stereoisomeric structures is valuable and guides medicinal chemists to focus only on useful configurations. In this work, we concurrently screened mixtures of stereoisomers and estimated their affinities to a protein target (thrombin) using weak affinity chromatography-mass spectrometry (WAC-MS). Affinity determinations by WAC showed that minor changes in stereoisomeric configuration could have major impact on affinity. The ability of WAC-MS to provide instant information about stereoselectivity and binding affinities directly from analyte mixtures is a great advantage in fragment library screening and drug lead development.

Place, publisher, year, edition, pages
Sage Publications, 2013
Keyword
fragment-based drug discovery, mixture screening, stereoisomers, thrombin, weak affinity chromatography
National Category
Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
Research subject
Natural Science, Biomedical Sciences; Natural Science, Biochemistry
Identifiers
urn:nbn:se:lnu:diva-24641 (URN)10.1177/1087057113480391 (DOI)000320888100013 ()2-s2.0-84879476954 (Scopus ID)
Available from: 2013-03-01 Created: 2013-03-01 Last updated: 2017-12-06Bibliographically approved

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