Non-GLP Bioanalysis. Introduction. Lab Space and Instrumentation

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1 Non-GLP Bioanalysis Introduction Founded in 2006, WuXi AppTec s non-glp bioanalytical service has established a state-of-the-art LC-MS/MS platform for bioanalysis in the drug discovery field. Over the last decade, WuXi s non-glp bioanalytical team has developed long-term and trusted collaborations with pharmaceutical clients by providing consolidated bioanalytical support for studies ranging from NCE screening through IND filing. A rapid turnaround time and high-quality data are hallmarks of our service which covers in vitro ADME, discovery biology, PK, PD and discovery TK. For in vitro sample analysis, the total runtime per sample can be reduced to 12 seconds using an ADDA (Apricot Designs Dual Arm) direct on-line SPE mode yielding a throughput as high as 72 plates (96-well) per day. For in vivo sample analysis, methodologies for polar, unstable or endogenous compounds such as biomarkers are fully established. Some examples are provided here to demonstrate the breadth of our capabilities: prodrugs, metabolites, oligonucleotides (see Case Study I in the Biologics chapter), peptides (see Case Study II in the Biologics chapter), nucleotide triphosphates, sugar derivatives and neurotransmitters. We also have experience with analytical methods such as dry blood spot and capillary sampling which have been well validated. Lastly, a few cases for protein quantitation and drug carrier bioanalysis such as liposomal, PEGylated or antibody conjugated drugs have been conducted in-house and are under ongoing validation. Due to an optimized experimental workflow, robust training program and a reliance on high throughput technology, WuXi s non-glp bioanalytical group analyzes over 2,000,000 in vitro samples and over 200,000 in vivo samples annually. All our data are thoroughly analyzed as matrix effects, chromatographic peak shapes, specificity, carryover, sensitivity, signal/noise ratios and resolution are all routinely monitored. The average turnaround time is typically within 24 h for in vitro sample analysis and within h for different tiers of in vivo sample analysis. In the future the automation of sample preparation and e-documentation will accommodate further capacity growth and expedite the entire procedure. Lab Space and Instrumentation The non-glp bioanalytical lab in Shanghai is ~8,600 ft 2 which holds four spacious instrument rooms (Figure 1) and one wet lab under yellow light to protect photolabile compounds (Figure 2). In total there are 27 modern LC-MS/MS systems, 11 of which are coupled with various high-throughput autosamplers (Gilson, CTC/DLW, and ADDA) and dedicated for in vitro sample analysis, the remaining 16 mass spectrometers are coupled with Waters UPLCs and are dedicated for in vivo sample analysis. Primarily the mass spectrometers are from AB Sciex: API4000/5500/6500 (Figure 3). Figure 1. One of four LC-MS/MS instrument rooms for non-glp bioanalysis. Figure 2. A wet lab under yellow light to prevent photodegradation. 104 Non-GLP Bioanalysis DMPK LTD.WUXIAPPTEC.COM

2 Waters Acquity AB Sciex API 6500 AB Sciex API 5500 Gilson 215 CTC-DLW Apricot Designs Dual Arm Figure 3. Representative LC-MS/MS systems used in our non-glp bioanalysis. High-throughput Platform ADDA-LC-MS/MS ADDA (Apricot Design Dual Arm) is an autosampler designed for high-throughput bioanalysis. Composed with 2 highspeed robotic arms, 8 independent injection ports and 4 on-board valves (Figure 4), the ADDA is a unique high throughput platform which can be compatible with LC separation in both direct on-line SPE (elute/trap mode) and multiplexing mode (gradient mode). Under the elute/trap mode, one injection can be administered every 12 seconds (refer to Figure 5 for a representative chromatogram) and 7,200 samples can be analyzed within 24 h. Under gradient mode, the ADDA is twice as fast as conventional LC with no loss in separation integrity. The ADDA platform is controlled under a single integrated software called SoundReview which was developed by Sound Analytics Inc. who also developed AB Sciex s DiscoveryQuant software. Consequently, the ADDA platform is fully compatible with the AB Sciex software so data and chromatograms acquired by the ADDA can easily be processed and reviewed by both SoundReview and DiscoveryQuant. An extensive data comparison between the ADDA platform and conventional CTC autosampler has been conducted in our group. For all tested in vitro ADME assays, the ADDA demonstrated good correlation with the CTC system for numerous compounds across myriad chemical structures (Figure 6). Figure 4. Overview of the functional components of the ADDA system. LTD.WUXIAPPTEC.COM DMPK Non-GLP Bioanalysis 105

3 2.0e5 1.8e5 1.6e e5 Intensity, cps 1.2e5 1.0e5 8.0e4 6.0e4 4.0e4 2.0e Time, min Figure 5. Typical chromatogram of ADDA under elute/trap mode. Figure 6. Representative data comparison between the ADDA platform (ordinates) and conventional CTC system (abscissa) for numerous compounds in human, rat, dog, mouse and cynomolgus monkey liver microsomes. 106 Non-GLP Bioanalysis DMPK LTD.WUXIAPPTEC.COM

4 Gilson LC-MS/MS Like the ADDA, Gilson is another high throughput autosampler that couples direct on-line SPE separation. With a single aspirating/dispensing needle, Gilson is able to complete one injection every 30 seconds. Though longer than the ADDA, this injection rate is much shorter than a conventional CTC autosampler. With a spacious and flat open deck, the Gilson LC-MS/MS can hold up to well or 384-well plates for automated analysis (Figure 7). Figure 7. Representative workflow of the Gilson LC-MS/MS. CTC/DLW LC-MS/MS Equipped with a dynamic motor on a robotic injection arm, the CTC/DLW (Dynamic Load and Wash) has a faster loading and washing cycle compared to conventional CTC autosampling by about 40 s. In addition, the CTC/DLW can pre-load a sample in advance while avoiding sample contamination when the syringe aspirates the holding loop. Carryover is also dramatically reduced during the washing process as compared to the CTC autosampler alone. The CTC/DLW system also has an increased sample capacity holding well or 384-well plates for automated sample analysis. Figure 8. Functional components of the CTC/DLW system. LTD.WUXIAPPTEC.COM DMPK Non-GLP Bioanalysis 107

5 Bioanalytical Capabilities WuXi DMPK s non-glp bioanalytical group has a consolidated expertise in developing assays for diverse analytes. Furthermore our validation process for special sampling and analysis techniques, such as DBS or capillary sampling, is conducted with the demands of sample storage and microsampling. Tables 1 and 2 describe WuXi s experience with the diverse array of analytes we have examined that fall beyond routine NCE analysis. Additionally, Table 3 (also see Table 3 in the Biologics chapter) summarizes our validated sample collection and analysis skills that are different from routine sample collection and analysis. Oligonucleotide Peptide Analyte Challenge Description of Method Antibody-drug conjugate (ADC) 4,000<MW<10,000 Da Low recovery Chromatography MW<5,000 Non-specific binding Low recovery Chromatography Toxin handling Sample processing PEG-conjugated Drug Variable MW Difficult to find Q1 Endogenous Biomarker Highly polar or nonpolar Isomer separation Severe matrix effect Nucleoside Triphosphate Highly polar and ionic Unstable Cassette PK Study Low dose (sensitivity) Interference evaluation Chiral Compounds Chiral column screening Separation Table 1. List of complex analytes with internally developed methods. Mouse Rat Rabbit Pig Dog NHP Human SPE Ion pairing method 10 ng/ml LLOQ in biological matrix Highly acidic mobile phase Additive to solve non-specific binding µelution SPE pg/ml LLOQ in biological matrix More than 100 peptide methods developed Toxin/linker bioanalysis but not for antibody Class II BSC and corresponding safeguard guidance Acidic or basic hydrolysis method Obtain Q1 via ion source fragmentation Dedicated column Surrogate analyte/matrix Stable labeled internal standard SPE HILIC method Ion pairing method pg/ml level LLOQ Collaborate with WuXi Separation Center for rapid chiral column screening Species Matrices Tissue (easy to homogenize) Tissue (difficult to homogenize) Plasma Serum Whole blood CSF Urine Table 2. Various biological tissues and fluids handled in ADME studies for bioanalysis. Brain Liver Spleen Heart Lung Kidney Stomach Uterus Bone marrow Testicle Prostate Skin Muscle Ovary Intestine Fat Bone Eye tissues Technique Challenge Status Dry blood spot Microsampling Validated in both in-life and bioanalytical Microdialysis Limited sample volume Extremely low LLOQ pg/ml level sensitivities obtained Capillary sampling Microsampling Validated in both in-life and bioanalysis Table 3. Summary of micro-sampling and analysis techniques conducted at WuXi. 108 Non-GLP Bioanalysis DMPK LTD.WUXIAPPTEC.COM

6 Bioanalytical Assays WuXi DMPK s non-glp bioanalytical team provides bioanalytcial support for studies ranging from discovery screening through definitive studies for an IND package. Table 4 details the current assay types which are stratified by different bioanalytical criteria during method development and sample analysis. Assay Description Deliverables Acceptance Criteria TAT (working days) Bioanalysis for Screening Studies Single or cassette analyte quantitation All biological matrices All preclinical species and human samples Analytical method Dose vehicle evaluation Specificity Carryover Stability (on request) Sample analysis Standard curve and LLOQ QC samples (low, middle, high) accounting for 5% of total sample number Dose vehicle variation within ±25% Specificity less than 1/2 of LLOQ Linearity exhibited for 75% of standards within ± 20% ( ± 25% LLOQ) for biofluids, and ± 25% for tissue and feces samples Accuracy 67% for all QC samples within ±20% for biofluid and ±25% for tissue or feces sample LLOQ as low as 1~3 ng/ml Carryover preferentially LLOQ 2-3 Bioanalysis for INDenabling Studies All biological matrices All preclinical species and human samples Available for CFDA, FDA and EMA IND/CTA filing Word report in English or Chinese Full data qualification Must be below 9 items Linear regression Within-run and between-run precision and accuracy Specificity and interference Matrix effect Extraction recovery Dilution integrity Carryover System suitability Batch size Partial data qualification Less than 9 validation items is flexible Linear regression Within-run and between-run precision and accuracy Specificity and interference Matrix effect Extraction recovery Dilution integrity Carryover System suitability Batch size 75% standards within ±15% ( ±20% LLOQ), at least 6 levels for each curve 67% of all QCs within ± 15% (within ± 20% for LLOQ), 50% at each level pass Specificity: double blank response 20% LLOQ, from 6 lots of matrix and % CV 20% LLOQ, from 6 lots of matrix Interference: double blank response 20% of analyte LLOQ and single blank response 5% of IS Sensitivity: depends on client s request and at least S/N> 5 Carryover: 20% of LLOQ Matrix effect: 6 lots at 2 concentrations, %CV within ± 15% Extraction recovery: triplicate and 3 concentrations, %recovery %CV 15% Accuracy within ±10% and %CV 10% for stability studies (based on the level of method qualification) Stability evaluation Option of below 7 items Stock solution Working solution Room temperature -80 C (two time points) Freeze-thaw Autosampler Stock and working stability: accuracy within ±10% and %CV 10% Other stability: triplicate at 2 concentrations, accuracy within ±15% Based on stability period Table 4. Summary of WuXi Non-GLP bioanalytical assay types. LTD.WUXIAPPTEC.COM DMPK Non-GLP Bioanalysis 109

7 Case Studies Case study I: determination of serine in cellular assay under ADDA gradient mode The amino acid serine can be used as a biomarker for certain biological pathways. Utilizing the ADDA platform in gradient mode instead of a CTC autosampler, the run time of each cellular sample was reduced from 1.2 min/per injection to 0.67 min/per injection without compromising the data quality. LC-MS/MS Method for Serine LC System Column Mobile Phase A Mobile Phase B Flow Rate LC Condition MS/MS Condition Table 5. LC-MS/MS conditions for 13 C3-serine. Shimadzu 20-AD Amide column 0.5% formic acid in water 0.5% formic acid in ACN 1.0 ml/min Gradient SRM 109.0/62.2, positive ESI 13 C 3 -Serine Internal standard Figure 9. Representative chromatogram of 13 C 3 -serine obtained using the ADDA platform. Case study II: bioanalysis of a PEGylated peptide using LC-MS/MS PEGylation can be used to increase the half-life, solubility and safety of protein or peptide drugs. However, PEGylation of peptides creates several challenges in terms of bioanalysis due to its large, polydispersed MW, proclivity toward nonspecific binding and co-precipitation during typical protein precipitation workups. The following is an example on the quantitation of a PEGylated peptide via ion-source fragmentation. The method was validated for linearity, sensitivity, accuracy, precision, carryover and selectivity over the range of 10-10,000 ng/ml in support of a PK study in mice. LC-MS/MS Method for a PEGylated Peptide LC System Waters Acquity UPLC Column C18 Mobile Phase A Water with formic acid Mobile Phase B ACN with formic acid Flow Rate 0.55 ml/min LC Condition Gradient MS/MS Condition MW ~ 5,300 Da, ion-source fragmentation, positive ESI Table 6. LC-MS/MS conditions for a PEGylated-peptide of MW ~5,300 Da. 110 Non-GLP Bioanalysis DMPK LTD.WUXIAPPTEC.COM

8 C 2 H 4 O (44) C 3 H 6 O (58) Figure 10. Q1 mass spectrum of a ~5,300 Da PEGylated peptide via in-source fragmentation. Case study III: LC-MS/MS analysis of an ADC with unknown toxicity (small molecule: toxin/toxin plus linker) Antibody drug conjugates (ADCs) are a class of therapeutic agents that are generally defined as the conjugation of an antibody with a toxin (e.g. cytotoxic drug). These conjugates are believed to be more efficacious in the treatment of tumors as they combine the site selectivity of an antibody with the cytotoxic potency of the toxin. Our group has worked with several ADCs including one where the conjugated toxins have never been fully investigated, and thus their specific toxicological profiles unknown. For instances such as this, WuXi Apptec s DMPK and Bioanalysis groups have implemented specific safeguards so we are fully capable to work with these compounds in a safe and efficient manner. As shown in Figure 11, we operate a BSL2 lab to protect the staff while working with the toxin. Figure 11. A picture of WuXi s in-house scientists working in a BSL2 environment during sample preparation of an ADC with unknown toxicity. LTD.WUXIAPPTEC.COM DMPK Non-GLP Bioanalysis 111

9 Case study IV: capillary sampling Capillary sampling can greatly improve the efficiency of sample collection after dosing and has been validated for both in-life studies and the subsequent bioanalysis. Parallel data were obtained through samples collected using the general sampling method and capillary sampling following intravenous administration of diclofenac to male CD-1 mice. Figure 12 shows good correlation between these two sets of data demonstrating the accuracy of the capillary sampling method. Concentration (ng/ml) Mean Blood Concentration of Diclofenac after IV Dosing at 1 mg/kg (Group 1 & 2) Time (h) Mean Group 1 Mean Group 2 Figure 11. Overlay of mean blood concentrations of diclofenac after routine (Group 1) and capillary (Group 2) sample collection. Recent Poster Presentations at International Conferences 1. Guo L. et al. Determination of Homocysteine, Cysteine, Cystathionine, S-Adenosyl methionine and S-Adenosyl homocysteine in Biological Samples Using Ultra Performance Liquid Chromatography with Tandem Mass Spectrometry. 62nd ASMS Conference, Baltimore, Jun Hong H. et al. Determination of Ribavirin Triphosphate in Rat Red Blood Cells and Liver by Liquid Chromatography/High- Resolution Accurate Mass Spectrometry. 62nd ASMS Conference, Baltimore, Jun Zhou Y. et al. Alternative Choice Besides Immunoassays - Development and Validation of a Highly Sensitive UPLC-MS/MS Method for Exendin-4 in Monkey Plasma. CPSA Conference, Shanghai, Tao Y. et al. Development and Validation of a UPLC-MS/MS Method for PHOTOCYANINE in Human Plasma to Support In Vitro Plasma Protein Binding Assay. CPSA Conference, Shanghai, Tao Y. et al. Evaluation of a High-Throughput Autosampler (Apricot Design Dual Arm ADDA) for Discovery ADME Sample Analysis. CPSA Conference, Shanghai, Han Y. et al. Development and Validation of an LC-MS/MS Method for Determination of Suramin in Monkey Plasma. CPSA Conference, Shanghai, Cao WQ. et al. Determination of Minodronate in Rat Plasma by Liquid Chromatography/Tandem Mass Spectrometry (LC- MS/MS). 63rd ASMS Conference, St. Louis, Jun Yu ZR. et al. Liquid Chromatography/In-source Fragmentation and Tandem Mass Spectrometry for the Quantitation of a PEGylated Peptide in Mouse Plasma. 63rd ASMS Conference, St. Louis, Jun Lu JL. et al. Optimization of Detection Sensitivity for Derivatized and Underivatized Neurotransmitters on Different Triple Quadrupole Mass Spectrometer Platform. 63rd ASMS Conference, St. Louis, Jun Non-GLP Bioanalysis DMPK LTD.WUXIAPPTEC.COM

10 References 1. Li W. et al. Handbook of LC-MS Bioanalysis: Best Practices, Experimental Protocols, and Regulations (WILEY, 2013). 2. Jemal M. et al. LC-MS development strategies for quantitative bioanalysis. Curr Drug Metab (2006). 3. Shou W. et al. Recent development in software and automation tools for high-throughput discovery bioanalysis. Bioanalysis (2012). 4. Janiszewski J. et al. Development of a high-speed, multiplexed sample-delivery instrument for LC-MS/MS bioanalysis Bioanalysis (2012). 5. US FDA Guidance for Industry, Bioanalytical Method Validation (2001). 6. CFDA Good Laboratory Practice for Nonclinical Laboratory Studies, Appendix VI (2013). 7. EMA Guideline on Bioanalytical Method Validation (2011). 8. No. 1, OECD Principles of Good Laboratory Practice (1997). LTD.WUXIAPPTEC.COM DMPK Non-GLP Bioanalysis 113