Realities of high-throughput liquid chromatography/mass spectrometry purification of large combinatorial libraries: a report on overall sample throughput using parallel purification

Just-in-Time Purification: An Effective Solution for Cherry-Picking and Purifying Active Compounds from Large Legacy Libraries

Many companies possess a compound collection consisting of purified compounds and of unpurified products from combinatorial libraries. Using commercial and proprietary compounds as examples, this report provides clear examples of the significant impact purification can have on the activity observed for a compound and highlights the need to retest the purified compounds prior to creating structure-activity relationships. Crude mixtures made with commercial compounds led to an increase in the number of false positives in the SXR-GAL4 assay as compared with their pure and purified counterparts. An examination of proprietary compounds in an HIV assay resulted in the purification of 61 active crude synthetic mixtures. Of these 61 compounds, 32 were 5-fold less active and 2 were 5-fold more active after purification. This report details a semiautomated process developed and implemented for cherry-picking, tracking, and selectively purifying compounds found active in high-throughput screening campaigns.

Greener Solvent Usage for Discovery Chemistry Analysis and Purification

The concept of green chemistry has been implemented in chemical manufacturing and process chemistry over the past 15 years. Only recently has the concept been introduced to smaller volume activities such as medicinal and analytical chemistry. This chapter discusses green chemistry approaches suitable for discovery chemistry analysis and purification. Topics covered include use of supercritical fluid chromatography (SFC) for analysis and purification to reduce solvent usage, optimizing analytical LC methods to minimize solvent usage, optimization of reverse phase purifications, use of greener solvents for flash purification, and an evaluation of flash SFC for discovery chemistry purifications. Approaches that have been successful in numerous pharmaceutical medicinal chemistry laboratories will be presented.

Preparative two-dimensional liquid chromatography/mass spectrometry for the purification of complex pharmaceutical samples

A new preparative two-dimensional liquid chromatography/mass spectrometry system (2D LC-LC/MS) has been designed and implemented to enhance capability and resolving power for the separation and purification of pharmaceutical samples. The system was constructed by modifications of a conventional preparative LC/MS instrument with the addition of a set of switching valves and a sample loop, as well as interfacing a custom software program with MassLynx. The system integrates two chromatographic separations from the first and second dimensions into a single automated run to perform the purification of a target compound from a complex mixture without intermediate steps of sample preparation. The chromatography in the first dimension, operated in the heart-cutting mode, separates the target compound from the impurities by mass-triggered fractionation based on its molecular weight. This purified fraction from the first dimension is stored in the sample loop, and then gets transferred to the second column by using at-column dilution. A control software program, coined Prep 2D LCMS, was designed to integrate with MassLynx to retrieve data acquisition status. All of the chromatographic hardware components used in this preparative 2D LC-LC/MS system are from the original open access preparative LC/MS system, which has high level of robustness and affords easy and user-friendly operation. The new system is very versatile and capable of collecting multiple fractions with different masses under various purification modes as configured in the methods, such as conventional one-dimensional (1D) purification and/or 2D purification. This new preparative 2D LC-LC/MS system is therefore the ideal tool for medicinal chemistry lab in drug discovery environment.

High-throughput purification platform in support of drug discovery

The application of parallel synthesis is an efficient approach to explore the chemical space and to rapidly develop meaningful structure activity relationship (SAR) data for drug discovery programs. However, the effectiveness of the parallel synthesis requires a high throughput purification workflow that can process a large number of crude samples within a meaningful time frame. This paper describes a high throughput purification platform that has been adopted at Merck's Rahway research site. The platform includes the evaluation of crude samples, mass-directed HPLC purification, fraction analysis, compound registration, final compound purity assessment and assay distribution. Assisting with the sample tracking and the data management is the internally designed laboratory information management system, Light Automation Framework (LAF). Using this process and the tools described herein, the group has successfully achieved purities of 95% or greater for 90% of samples.

Mass spectrometry analysis of new chemical entities for pharmaceutical discovery

In this Section, we review the applications of mass spectrometry for the analysis and purification of new chemical entities (NCEs) for pharmaceutical discovery. Since the speed of synthesis of NCEs has dramatically increased over the last few years, new high throughput analytical techniques have been developed to keep pace with the synthetic developments. In this Section, we review both novel, as well as modifications of commonly used mass spectrometry techniques that have helped increase the speed of the analytical process. Part of the review is devoted to the purification of NCEs, which has undergone significant development in recent years, and the close integral association between characterization and purification to drive high throughput operations. At the end of the Section, we review potential future directions based on promising and exciting new developments.

A systematic investigation of recovery in preparative reverse phase high performance liquid chromatography/mass spectrometry

In this paper we report a systematic recovery study based on reversed phase high performance liquid chromatography (RP-HPLC) separation and mass spectrometric (MS) based fractionation. Factors including a compound's physicochemical properties, column mass loading and presence of impurities were investigated through commercially available compounds. Results suggest that the delay time between MS peak detection and fraction collection, fraction detector's signal-to-noise ratio and compound's base peak width in the chromatogram have the biggest impacts on purification recovery. In an effort to assess sample recovery within our high throughput purification process, re-purification was performed on four compound libraries that were synthesized in-house. Reproducible recoveries (>80%) were achieved in all tests.

Principles and applications of LC-MS in new drug discovery

The use of high-performance liquid chromatography combined with mass spectrometry (HPLC-MS) or tandem mass spectrometry (HPLC-MS-MS) has proven to be the analytical technique of choice for most assays used in various stages of new drug discovery. A summary of the key components of HPLC-MS systems, as well as an overview of major application areas that use this technique as part of the drug discovery process, will be described here. This review will also provide an introduction into the various types of mass spectrometers that can be selected for the multiple tasks that can be performed using LC-MS as the analytical tool. The strategies for optimizing the use of this technique and also the potential problems and how to avoid them will be highlighted.

Purifying the masses: integrating prepurification quality control, high-throughput LC/MS purification, and compound plating to feed high-throughput screening

In this paper we report using a parallel, four-channel HPLC/MUX/MS purification system, the Purification Factory, to purify thousands of compounds destined for high-throughput screening in a single month. The maximum sample throughput during this 20-workday month was 704 samples/day. Since this purification throughput exceeded the postpurification sample and data handling capabilities provided by commercial solutions, a custom-integrated solution was designed to address these shortcomings. In this paper we detail the key improvements in automation, solvent handling, and sample handling logistics implemented to sustain a mean throughput of 528 samples/day over a multimonth time period.

A novel method for immediate post-purification purity determination of fractions collected during high-throughput purification

Following purification, the fractions of purified samples typically are analyzed to determine the relative purities of each fraction. We report a novel technique for performing post-purification analysis immediately after each preparative LC/MS run. The Single Pass Compound Purification and Analysis System (SPACPASS) samples and stores a representative aliquot from the fraction while it is being collected. Demonstrated for '1:1' fraction collections, this method of fraction purity assessment streamlined sample processing by reducing post-purification sample handling. For 97% of the collected fractions, this technique provided relative purities to within +/-5% when compared with more traditional post-purification analysis.

Maximizing Automation in LC/MS High-Throughput Analysis and Purification

Here, we describe a system for LC/MS-based analysis and purification of compounds aiming at the minimization of manual interference in the overall process. Key elements of the concept are automated identification of the target compounds, automated assignment of optimized preparative gradients for purification of the target compounds, and automated purity assessment of fractions with subsequent pooling of validated product fractions. Additional support is provided by an automated solvent and waste management system. One person can easily process 100-200 compounds on a 150-mg scale per day on that system, while still the maximization of purity and yield after purification is guaranteed. Reduced demands with respect to purity or yield can lead to significantly higher throughput numbers.

Application of main component fraction collection method for purification of compound libraries

In order to support high-throughput library purification, a novel UV triggered fraction collection method was developed in which a maximum-seeking-algorithm-driven, six-port valve collects the largest chromatographic peak. This straightforward strategy achieves the one sample-one fraction approach, thus resulting in a simpler and less error prone workup procedure. The effectiveness of this main component fraction collection method will be illustrated here by the results of the purification of compound libraries (altogether 6086 compounds, having an averaged success rate of 79.4%). Advanced applications, where the desired component differs from the main component, will also be discussed.

High-Throughput Purification of Single Compounds and Libraries

The need for increasing productivity in medicinal chemistry and associated improvements in automated synthesis technologies for compound library production during the past few years have resulted in a major challenge for compound purification technology and its organization. To meet this challenge, we have recently set up three full-service chromatography units with the aid of in-house engineers, different HPLC suppliers, and several companies specializing in custom laboratory automation technologies. Our goal was to combine high-throughput purification with the high attention to detail which would be afforded by a dedicated purification service. The resulting final purification laboratory can purify up to 1000 compounds/week in amounts ranging from 5 to 300 mg, whereas the two service intermediate purification units take 100 samples per week from 0.3 to 100 g. The technologies consist of normal-phase and reversed-phase chromatography, robotic fraction pooling and reformatting, a bottling system, an automated external solvent supply and removal system, and a customized, high-capacity freeze-dryer. All work processes are linked by an electronic sample registration and tracking system.

High-throughput characterization and quality control of small-molecule combinatorial libraries

To fully realize the potential of combinatorial synthesis and high-throughput screening for increasing the efficiency of the drug discovery and development process, issues related to compound purity must be addressed. Impurities, often present after synthesis, can lead to ambiguous screening results and inhibit the development of quality structure-activity relationships. The demand for high-throughput analytical characterization of combinatorial libraries has prompted the development of more rapid methods to keep pace with compound production. Recent progress has focused upon the development of parallel separation methods, multiplexed detector interfaces, and synergistic combinations of different detectors possessing complementary selectivities.

Natural products and combinatorial chemistry: back to the future

The introduction of high-throughput synthesis and combinatorial chemistry has precipitated a global decline in the screening of natural products by the pharmaceutical industry. Some companies terminated their natural products program, despite the unproven success of the new technologies. This was a premature decision, as natural products have a long history of providing important medicinal agents. Furthermore, they occupy a complementary region of chemical space compared with the typical synthetic compound library. For these reasons, the interest in natural products has been rekindled. Various approaches have evolved that combine the power of natural products and organic chemistry, ranging from the combinatorial total synthesis of analogues to the exploration of natural product scaffolds and the design of completely unnatural molecules that resemble natural products in their molecular characteristics.

UV-Triggered Main-Component Fraction Collection Method and Its Application for High-Throughput Chromatographic Purification of Combinatorial Libraries

A maximum-seeking, algorithm-driven fraction collection method was developed to support high-throughput chromatographic purification, which provides new possibilities for off-line high-performance liquid chromatography mass spectroscopy (HPLC/MS) quality control experiments. The method is based on manipulation of a six-port valve that is installed downstream from the UV detector and equipped with a fraction collector loop. The detector signal is monitored by a programmable microcontroller that controls the state of the fraction collector valve. After detecting a chromatographic peak, the appropriate fraction is stored in the collector loop. The height of the next peak is compared to the previous one (using a maximum-seeking algorithm) and, depending on the result, the collected fraction is or is not exchanged with the new one. At the end of the run, the stored UV main component is pumped into the external fraction vial. This configuration was used for chromatographic purification of large compound libraries (the results of the purification of 5324 compounds are reported here), as well as for high-throughput off-line HPLC quality control experiments, where the collected main component fractions of an analytical-scale separation were subjected to further mass spectrometric molecular weight verification.

Preparative LC−MS Purification: Improved Compound-Specific Method Optimization

One of the remaining challenges in providing effective preparative LC-MS purification is balancing throughput and compound purity. We describe here an approach to optimizing preparative LC-MS methods that provides significantly better chromatographic resolution and, hence, better compound purity than generic preparative LC methods consuming the same amount of time. This approach is easier to implement, is more rugged, and permits significantly greater flexibility than previously reported approaches. The instrument configurations and protocols presented here are specifically tailored for open access support, but the basic approach is equally suitable and effective in high-throughput situations.

High-throughput preparative process utilizing three complementary chromatographic purification technologies

A high-throughput process was developed in which wells in plates generated from parallel synthesis are automatically channeled to an appropriate purification technique using analytical data as a guide. Samples are directed to either of three fundamentally different preparative techniques: HPLC with UV-triggered fraction collection, supercritical fluid chromatography (SFC) with UV-triggered fraction collection, or HPLC with MS-triggered fraction collection. Automated analysis of the analytical data identifies the product compound mass and creates work lists based on chromatographic properties exhibited in the data so that each preparative instrument cherry picks the appropriate list of samples to purify when a preparative-scale plate is loaded.

Normal-phase high-performance liquid chromatographic separations using ethoxynonafluorobutane as hexane alternative

We have reported recently that high-speed normal-phase (NP) HPLC separations of a broad range of organic compounds can be performed on cyano columns using gradients of methanol in hexane-like solvent-ethoxynonafluorobutane (ENFB), available commercially. In this communication, we demonstrate that atmospheric pressure chemical ionization (APCI) in combination with mass spectrometry (MS) can be effectively used for detection in such separations. The efficiency of APCI under conditions studied has also been compared to the efficiency of traditional electrospray ionization (ESI) in combination with MS for reversed-phase (RP) HPLC of the same compounds. The compounds included in this study were steroids, benzodiazepines, and other central nervous system-active substances, nonsteroidal anti-inflammatory drugs, tricyclic antidepressants, and beta-adrenergic blocking agents. Non-polar compounds were found to respond stronger when APCI-MS technique was used, whereas APCI and ESI ionization efficiencies were comparable when polar substances were studied. The combination of normal-phase HPLC separation conditions with mass spectral detection may expand the range of LC-MS applications traditionally associated with reversed-phase HPLC and ESI-MS detection.

Optimization strategies for the analysis and purification of drug discovery compounds by reversed-phase high-performance liquid chromatography with high-pH mobile phases

Careful selection of both high-pH mobile phase as well as organic modifier, was performed in order to develop and optimize HPLC conditions for the separation of drug discovery compounds. High-pH mobile phases provide excellent chromatographic resolution and increased mass loading of basic compounds. The analytical methods so defined have been successfully transferred to preparative automated UV-directed purification, an important fact due to the increasing number of samples requiring purification. It should be noted that, the single prerequisite for this approach is an analytical LC-UV-MS run, therefore the system has the ability to collect only fractions likely to contain the target product. A cost-effective strategy for maximizing the purification of drug discovery compounds is proposed.

Optimal Fraction Collecting in Preparative LC/MS

In this paper, we discuss various methods for fraction collection in high-throughput chromatography. UV-triggered fractionation allows precise cutting of peaks. However, valuable fraction collector space is wasted, because many undesired compounds are collected. In mass-triggered fraction collection, the collector space is used more efficiently, because only peaks containing the desired products are collected. Unfortunately, mass peaks are broader than UV peaks, and therefore, fractions contaminated by a closely following peak are often collected. This can be avoided if the collection in preparative LC/MS occurs by a logical AND combination of UV- and mass-triggered collection. The success of this optimal collection mode is shown for three examples.

Comparison of Preparative HPLC/MS and Preparative SFC Techniques for the High-Throughput Purification of Compound Libraries

A diverse set of 16 high-throughput organic synthesis libraries, consisting of 48 samples per library, has been purified by both preparative supercritical fluid chromatography (SFC) and preparative high-performance liquid chromatography (HPLC). This paper details the relative effectiveness of these two purification techniques in terms of success, yield, and purity of final product.

Application of Visual Basic in High-Throughput Mass Spectrometry-Directed Purification of Combinatorial Libraries

We present an approach to customize the sample submission process for high-throughput purification (HTP) of combinatorial parallel libraries using preparative liquid chromatography electrospray ionization mass spectrometry. In this study, Visual Basic and Visual Basic for Applications programs were developed using Microsoft Visual Basic 6 and Microsoft Excel 2000, respectively. These programs are subsequently applied for the seamless electronic submission and handling of data for HTP. Functions were incorporated into these programs where medicinal chemists can perform on-line verification of the purification status and on-line retrieval of postpurification data. The application of these user friendly and cost effective programs in our HTP technology has greatly increased our work efficiency by reducing paper work and manual manipulation of data.

Quality control in combinatorial chemistry: determination of the quantity, purity, and quantitative purity of compounds in combinatorial libraries

The quality of combinatorial libraries determines the success of biological screening in drug discovery programs. In this paper, we evaluate and compare various methods for measuring identity, purity, and quantity (yield) of combinatorial libraries. Determination of quantitative purity reveals the true library quality and often indicates potential quality problems before full-scale library production. The relative purity can be determined for every member in a large library in a high-throughput mode, but must be cautiously interpreted. In particular, many impurities are not observable by relative purity measurements using detectors such as UV(214), UV(254), and evaporative light-scattering detection. These "invisible" impurities may constitute a significant portion of the sample weight. We found that TFA, plastic extracts, inorganic compounds, and resin washout are among these impurities. With compelling evidence, we reach a conclusion that purification is the only way to remove "invisible" impurities and improve the quantitative purity of any compound even though some compounds may have a high relative purity before purification.

Development of a custom high-throughput preparative liquid chromatography/mass spectrometer platform for the preparative purification and analytical analysis of compound libraries

Solution-phase parallel synthesis has had a profound impact on the speed of compound synthesis delivering relatively pure compounds (>80%) in short order. However, to develop structure activity relationships (SAR) for a compound series, each library member should preferably be >95% pure. Historically, achieving and quantifying such high-purity criteria for each library member proved to be the slow step for most lead discovery groups. To address this issue, significant modifications have been made to a commercial Agilent preparative LC/MS system to allow for the general mass-guided purification of diverse compound libraries. The custom modifications include (1) the "DMSO slug" approach for the purification of samples with poor solubility; (2) an active splitter to reduce system back-pressure, reduce the delay volume, and allow for a variable split ratio; (3) a sample loading pump for the quick purification of large, dilute samples; (4) a preparative column-selection valve to quickly change column selectivity or sample loading; and (5) an analytical injector with a separate flow path for crude reaction or fraction analyses.