Beyond The Rule of 5: Lessons Learned From AbbVie's Drugs and Compound Collection

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Perspective
Beyond the Rule of 5: Lessons Learned from
AbbVie's Drugs and Compound Collection
David A. DeGoey, Hui-Ju Chen, Philip B. Cox, and Michael D. Wendt
J. Med. Chem., Just Accepted Manuscript • DOI: 10.1021/acs.jmedchem.7b00717 • Publication Date (Web): 19 Sep 2017
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Page 1 of 55 Journal of Medicinal Chemistry
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Beyond the Rule of 5: Lessons Learned from
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12 AbbVie's Drugs and Compound Collection
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17 David A. DeGoey,* Hui-Ju Chen, Philip B. Cox, and Michael D. Wendt
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20 Research and Development, AbbVie Inc., 1 North Waukegan Rd., North Chicago, IL 60064,
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United States
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26 KEYWORDS. Beyond Rule of 5, Lipinski’s Rule of 5, drug-like properties, hepatitis C, NS5A,
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28 NS3/4A, Bcl-2, Bcl-xL.
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32 ABSTRACT. Recently, there has been an increasing focus on the pursuit of targets considered
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34 to be less-druggable that offer potential for development of promising new therapeutic agents for
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36 the treatment of diseases with large unmet medical need, particularly in the areas of oncology
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39 and virology. However, conducting drug discovery campaigns in “beyond Rule of 5” (bRo5)
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41 chemical space presents a significant drug design and development challenge to medicinal
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chemists to achieve acceptable oral pharmacokinetics. Retrospective analysis of past successes
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46 and failures in drug discovery bRo5 may shed light on the key principles that contribute to the
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48 oral bioavailability of successful bRo5 compounds and improve the efficiency of drug design for
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51 future projects. We present here highlights and case studies of lessons learned from discovery of
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53 bRo5 compounds. A simple multi-parametric scoring function (AB-MPS) was devised which
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55 correlated preclinical PK results with cLogD, number of rotatable bonds and number of aromatic
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58 rings.
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Introduction
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7 It has been twenty years since the publication of Lipinski’s influential analysis of the
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9 physicochemical property space occupied by Phase II clinical candidates.1 While Lipinski’s Rule
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12 of 5 (Ro5) described the property space with the highest probability of achieving good oral
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14 absorption, today there is an increasing focus on the pursuit of less-druggable targets, such as the
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16 disruption of protein-protein interactions (PPI), that offer high potential for the development of
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19 new therapeutic agents and may require beyond Rule of 5 (bRo5) chemical matter in order to
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21 take advantage of these opportunities. The fact that approximately 6% of oral drugs are outside
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23 of Lipinski space suggests that there are ample opportunities for exploration and exploitation
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26 bRo5. Historically, bRo5 drugs have played a large role in immunosuppression (e.g.,
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28 cyclosporine A, CsA), the treatment of infectious and viral diseases (e.g., antibacterial agents,
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HIV protease inhibitors), and in the areas of oncology (e.g., taxanes) and cardiovascular (e.g.,
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33 digoxin), and that trend has continued in recent years with new approvals of direct-acting
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35 antivirals (DAA) including hepatitis C (HCV) NS5A and NS3/4A protease inhibitors as well as
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38 oncology drugs, such as Bcl-2 inhibitors. In fact, new US FDA drug approvals in the past three
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40 years have yielded 12 new oral bRo5 drugs, accounting for 21% of new oral drug approvals in
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42 that time period, while having a tremendous impact on the treatment of illnesses with high unmet
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45 medical needs such as HCV and cancer (Table 1).
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48 Thus, there has been significantly increased interest in the discovery and development of
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bRo5 drugs with a number of excellent reviews and perspectives published in recent years.2-6
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53 However, it is clear that our understanding of the principles that govern success and failure for
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55 designing oral bRo5 drugs is only partial at best. Investigation of bRo5 chemical matter remains
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higher-risk and is fraught with uncertainties that hinder progress. Frequently, bRo5 compounds
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have poor drug metabolism and pharmacokinetic (DMPK) properties, such as low permeability,
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6 low solubility and high metabolic clearance. In addition, poor properties such as low solubility
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8 can limit the utility of in vitro data for establishing in vitro/in vivo correlations (IVIVC) for the
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key drivers of achieving acceptable oral pharmacokinetics (PK), such as correlation of in vitro
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13 permeability with in vivo oral absorption. Some of these compounds may also be substrates for
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15 poorly-understood active transport mechanisms of absorption. As a result of these problems,
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18 advancing projects with bRo5 chemical matter frequently requires empirically-driven PK
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20 campaigns with a high cost in terms of project timelines, compound synthesis and animal
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22 screening.
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26 An emerging area of focus for research on bRo5 drug design is the exploration of
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28 macrocycles,7-9 catalyzed by the observation that several orally bioavailable macrocyclic drugs
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such as CsA are significantly bRo5 and demonstrate chameleon-like conformational flexibility
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33 that may mask polar groups through intramolecular hydrogen bond formation. While
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35 considerable effort is being devoted to the prospective design of orally bioavailable macrocyclic
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38 peptide drugs,10-14 less attention has been paid to the design principles for acyclic bRo5
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40 compounds. In this respect, our present retrospective analysis of AbbVie’s bRo5 projects may
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42 provide valuable insights into acyclic bRo5 compounds due to the larger proportion of acyclic
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45 bRo5 compounds present in AbbVie’s compound collection.
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48 By ascertaining the key learnings from past successes and failures bRo5, it is hoped that
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more rapid progress can be made on the emerging opportunities for medicinal chemists to have
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53 an impact in the treatment of diseases with large unmet medical need. While several excellent
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55 retrospective studies have been published on the analysis of marketed and clinical bRo5
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compound collections,2-6 they provide only a partial picture of potential success in the vast bRo5
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chemical space and little information about bRo5 failures. Although no single organization’s
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6 compounds may be fully representative of the vast bRo5 chemical space, we reasoned that
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8 conducting an analysis of both our clinical and preclinical compound collections with available
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preclinical PK data may provide a better picture of potential success bRo5 by widening the
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13 representation of bRo5 chemical space, while adding information about bRo5 failures. Herein,
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15 we present the result of a retrospective analysis conducted on AbbVie’s preclinical DMPK
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18 database in which we correlated the in vitro and in vivo absorption, distribution, metabolism, and
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20 excretion (ADME) results with in silico physicochemical properties associated with the
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22 compounds. We present a simple multi-parametric scoring function (AB-MPS) which correlated
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25 the preclinical PK results with physicochemical properties. We also present case studies for
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27 projects with bRo5 compounds that advanced to the clinic, including HCV NS5A inhibitors,
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HCV NS3/4A protease inhibitors and Bcl-2 inhibitors.
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33 Table 1. New FDA approvals (2014-present) a of oral bRo5 drugs
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36 Year Therapeutic
37 Drug MW cLogP HBD N+O
Approved Area
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39 velpatasvir 2016 HCV 883.02 2.5 4 16
40 venetoclax 2016 Oncology 868.44 10.4 3 14
41 elbasvir 2016 HCV 882.0 2.6 4 16
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43 grazoprevir 2016 HCV 766.90 -2.0 3 15
44 cobimetinib 2015 Oncology 531.31 5.2 3 5
45 daclatasvir 2015 HCV 738.88 1.3 4 14
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edoxaban 2015 Cardiovascular 548.06 -0.9 3 11
48 ombitasvir 2014 HCV 894.13 1.3 4 15
49 paritaprevir 2014 HCV 765.89 1.1 3 14
50 Nausea from
51 netupitant 2014 578.59 6.8 0 5
52 Chemotherapy
53 ledipasvir 2014 HCV 889.00 0.9 4 14
54 ceritinib 2014 Oncology 558.14 6.5 3 8
55 a
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Source: www.fda.gov/Drugs/DevelopmentApprovalProcess/DrugInnovation/
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Physicochemical Property Analysis of Preclinical DMPK Database
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7 Since the appearance of Lipinski’s rules, a large number of additional pass/fail criteria as
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9 well as multiparametric scoring functions based on physicochemical properties have emerged
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12 and a recent review by Meanwell provides an excellent overview of the strengths and
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14 weaknesses of these approaches.15 In addition, several useful retrospective analyses of the drug-
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16 likeness of compounds prepared by medicinal chemists over the past decades have recently
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19 appeared.16-19 Naturally, the compound datasets employed for older retrospective analyses are
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23 investigated for which compounds were prepared, in contrast to the current focus on less-
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26 druggable targets. In order to more fully understand the effect of physicochemical properties on
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28 compounds bRo5, we sought to focus exclusively on the analysis of bRo5 compounds to
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determine if lessons could be gleaned from an analysis of the physicochemical properties
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33 together with their preclinical PK data.
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36 As a first step, we analyzed the property space of all compounds in the AbbVie
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39 preclinical DMPK database, which is a large repository of DMPK data generated in vitro and in
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41 vivo for AbbVie’s compound collection. For the present analysis, we focused primarily on the
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43 large collection of rat oral bioavailability (F) data (n = 8647 at the time of this analysis) which
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46 was accumulated during the course of numerous drug discovery programs where oral low dose
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48 screening of new compounds was utilized to identify promising compounds. While the data was
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curated to remove studies in which PK boosters were utilized which would clearly skew the oral
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53 bioavailability, no attempt was made to account or correct for the effect of formulations on oral
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needed throughout the course of the project. We then calculated the physicochemical properties
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for the compounds in the database, including number of rotatable bonds (NRB), number of
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6 aromatic rings (NAR), number of hydrogen bond donors (HBD), number of hydrogen bond
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8 acceptors (HBA), molecular weight (MW), topological polar surface area (TPSA), number of
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nitrogens and oxygens (N+O), cLogP and cLogD, among others. Using this data, it was then
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13 possible to identify the compounds that violate Lipinski’s Ro5 (n = 1116) by virtue of failing > 1
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15 rule. The compound collection encompassed a wide range of molecular properties, such as MW
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18 = 500-1410, cLogP = -5.8 to 13.9, HBD = 0 to 7, HBA = 2 to 15, N+O = 3 to 20, and NRB = 3
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20 to 26, providing excellent representation of bRo5 chemical matter from 85 projects and 165
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22 chemical series. As part of our preliminary analysis of the data, we examined the properties of
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25 the compounds that demonstrated oral F ≥ 5% in order to estimate the ‘‘possible to be orally
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27 absorbed’’ space. Similar to the observations made by Kihlberg, et al.,2 in their analysis of a set
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of launched and clinical bRo5 compounds, very high MW (≤ 1132) and TPSA (≤ 229), along
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32 with a wide range of cLogP values (-5.5 to 13.3) were tolerated. However, we also observed that
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37 also in close agreement with Kihlberg’s observations.
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40 In order to investigate correlations between molecular properties and oral F, the bRo5
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42 compound set was divided (binned) into quartiles based on their observed F, with the upper
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45 quartile (Q4) defined as acceptable bioavailability (oral F > 27.3), the lower quartile (Q1)
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47 defined as poor bioavailability (oral F ≤ 2.5) and the interquartile range (IQR, Q2 and Q3) (2.5 <
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oral F ≤ 27.3) defined as moderate bioavailability. Box plots of the binned oral F versus the
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52 averages of key physicochemical properties known to effect oral absorption including average
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54 TPSA, NRB, MW, cLogD and NAR appear in Figure 1. From this qualitative analysis, we
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observed that compounds with acceptable oral bioavailability (Q4, F > 27.3) demonstrated lower
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values for these key physicochemical properties, indicative of overall better drug-like properties
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6 than those with moderate and poor oral F. Clearly, bRo5 compounds with acceptable oral
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bioavailability.
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42 Figure 1. Effect of multiple physicochemical properties on oral bioavailability F. Box
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plot of binned oral bioavailability (red = F ≤ 2.5, blue = 2.5 < F ≤ 27.28, green = F >27.28)
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47 versus average values for physicochemical properties. Comparison circles are shown for alpha
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49 level = 0.05. White line = median value.
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53 One notable exception to trends observed in Figure 1 was the relationship between oral F
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55 and cLogD, one of the most influential physicochemical properties that broadly affects the
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57 DMPK properties of drugs. Previous studies have illustrated the importance of maintaining
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lipophiliciy within a narrow range in order to achieve cell permeability and solubility.5,7 If one
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6 considers the propensity of a compound to have good oral bioavailability, good permeability is a
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8 key pre-requisite, with LogD a key determinant of good passive permeability. It is well known
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that both high hydrophilicity (low LogD<1) and lipophilicity (high LogD>5) have negative
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13 effects on permeability. As an illustration of this, we analyzed 82,000 compounds with available
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15 parallel artificial membrane permeability assay (PAMPA) data and binned by poor (Papp ≤ 2x10-6
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18 cm/sec) and good (Papp >10x10-6 cm/sec) permeability, with moderate permeability between
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20 these two values. The distributions of these three bins is shown in Figure 2, with the compounds
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22 with highest permeability (>10x10-6 cm/sec) showing an almost normal distribution with a peak
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25 at around cLogD=3. As shown in Figure 2, the shape of the cLogD distribution observed for
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compounds with moderate and poor permeability. In contrast to the shape of the distribution
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32 observed for compounds with good permeability, the compounds with poor permeability
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34 exhibited two maxima, one centered at cLogD = 1 and one centered at cLogD = 4. As the curve
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37 for compounds with low permeability demonstrates, having cLogD in the range from 2 to 4 does
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39 not ensure good permeability and other factors must account for their poor permeability. Given
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41 the fact that both high and low cLogD have a negative effect on permeability we reasoned that
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44 deviation from this value of cLogD would have a negative effect on oral absorption and therefore
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46 oral bioavailability. As a result we considered cLogD = 3 to be the sweet spot for optimal
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permeability, and the expression ΔLogD = Abs(cLogD-3) was used as a descriptor for weighting
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51 the effect of cLogD on permeability. As an example, for a compound with cLogD =3, there is a
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ΔLogD demonstrated a clear trend and compounds with acceptable oral F showed lower values
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42 Figure 2. Effect of cLogD on PAMPA permeability.. Red = PAMPA ≤ 2. Yellow = 2 < PAMPA
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44 ≤ 10. Green = PAMPA > 10.
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48 A more quantitative analysis of the average physicochemical properties for compounds in
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50 each quartile set appears in Table 2. In a similar analysis to that conducted by Veber,20 we also
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reported the correlation coefficients r between oral F and the calculated properties. For the bRo5
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55 set, weak negative correlations were observed between oral F and a number of properties
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57 including NRB (r = -0.35), ΔLogD (r = (-0.33), NAR (r = -0.26) and HBD (r = -0.23). While
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weaker negative correlations were also observed for MW (r = (-0.22), TPSA (r = -0.19) and N+O
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6 (r = -0.18), there was no correlation with cLogP or cLogD.
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9 Table 2. Physicochemical Property Averages by Rat Oral Bioavailability Quartile
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13 F range
Quartile AB-MPS NRB ΔLogD NAR HBD MW TPSA N+O cLogP cLogD
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15 bRo5 Set (n = 1116)
16 4 >27.3 14.0 8.6 1.9 3.6 2.0 655.1 123.2 9.9 5.3 4.2
17 2,3 >2.5-≤27.3 18.8 11.5 3.0 4.2 2.4 754.6 137.2 11.2 6.9 5.5
18 1 ≤2.5 19.8 12.1 3.4 4.4 2.9 723.2 148.3 11.5 5.2 4.1
19 All (averages) 18.8 17.9 10.9 2.8 4.1 2.4 721.9 136.5 10.9 6.1 4.8
20 r with F -0.41 -0.35 -0.33 -0.26 -0.23 -0.22 -0.19 -0.18 -0.09 -0.08
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22 b
Tier 7 Set (n = 2643)
23 4 >34.8 11.0 6.6 1.5 2.9 1.7 521.1 92.8 7.4 4.8 3.8
24 2,3 >3.8-≤34.8 13.8 8.3 2.1 3.3 1.8 583.6 99.1 8.1 5.7 4.7
25 1 ≤3.8 15.3 9.1 2.6 3.6 2.3 594.8 115.8 9.0 4.8 3.9
26 All (averages) 23.1 13.4 8.0 2.1 3.3 1.9 571.0 101.7 8.2 5.4 4.3
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r with F -0.28 -0.24 -0.25 -0.18 -0.12 -0.17 -0.13 -0.13 -0.09 -0.10
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30 Molecular Weight >500 Set (n = 1662)
31 4 >31.2 12.5 7.7 1.6 3.2 1.8 600.6 112.2 9.0 4.4 3.9
32 2,3 >2.9-≤31.2 16.4 10.2 2.4 3.8 2.1 687.1 124.3 10.0 5.7 4.8
33 1 ≤2.9 17.5 10.7 2.9 4.0 2.6 669.4 137.0 10.6 4.6 3.8
34 All (averages) 21.2 15.7 9.7 2.32 3.7 2.2 661.7 124.5 9.9 5.2 4.3
35 r with F -0.35 -0.30 -0.28 -0.26 -0.22 -0.22 -0.19 -0.18 -0.12 -0.08
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37 Fail > 1 Lipinski rule. b Fail ≥ 1 Lipinski rule. c Fail Lipinski rule MW > 500.
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Based on the observed correlations in Table 2, we sought to evaluate simple multi-
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43 parametric functions that might provide a higher correlation with oral F and provide the potential
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45 to be used prospectively to evaluate bRo5 compounds. Toward this goal, we selected the three
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48 properties with the highest correlation coefficients with oral F and combined them as shown
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50 below in Equation 1 to arrive at a simple scoring function, which we called AbbVie Multi-
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52 Parametric Score (AB-MPS). We found that AB-MPS provided a higher negative correlation
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55 coefficient with oral F (r = -0.41) (Table 2), wherein lower AB-MPS values were correlated with
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57 higher oral F. The distributions of AB-MPS as a function of binned oral F rat was also visualized
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using a box plot for the bRo5 set, as shown in Figure 3. We observed that compounds with
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6 acceptable oral bioavailability (F > 27.3 %) demonstrated a lower average AB-MPS values of 14
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8 with a much narrower distribution (IQR= 5.4) than compounds with poor (IQR=9.4) and
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moderate (IQR=10.2) oral bioavailability. The narrower IQR for AB-MPS for compounds with
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13 acceptable oral F resulted from correspondingly narrower IQR values for NRB and ∆logD, while
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15 the IQR for NAR was similar across the oral F bins. We also observed that an individual
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18 compound that deviates from drug-likeness in one property (∆LogD, NAR or NRB) can achieve
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20 a low AB-MPS value by having more drug-like values for the remaining properties, a principle
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22 also captured in other multi-parametric scoring function such as the simple property forecast
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25 index (PFI)21,22 and the more sophisticated quantitative estimate of drug-likeness (QED).23
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27 However, we found that PFI provided a poorer correlation (r = -0.15) with the oral F dataset than
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AB-MPS, while QED provided a similar correlation (r = 0.34) with the oral F dataset to AB-
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32 MPS. By virtue of its simple calculation, AB-MPS may offer a simple mnemonic for medicinal
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34 chemists to evaluate bRo5 chemical matter, with AB-MPS values ≤ 14 predicting a higher
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37 probability of success. Unlike pass/fail metrics, AB-MPS also provides for a continuum of scores
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39 for medicinal chemists to evaluate drug-likeness, rather than relying on cutoff values.
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42 AB-MPS = Abs(cLogD-3) + NAR + NRB (Equation 1)
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Figure 3. Box plot of binned oral F versus AB-MPS value. Red = F ≤ 2.5, blue = 2.5 < F ≤
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41 27.28, green = F >27.28. Comparison circles are shown for alpha level = 0.05. White solid line =
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43 median, white dashed line = average.
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We next conducted a similar analysis of compounds regarded to be in poor drug-like
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49 space by virtue of failing at least one of Lipiniski’s rules, which coincides with Tier 7
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51 physicochemical property space as defined by Cox, et al.24 The Tier 7 set (n = 2643) provided
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54 additional chemical diversity with compounds from 184 projects and 382 chemical series. As
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56 shown in Table 2 for the Tier 7 set, we observed weak negative correlations between oral F and a
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number of properties including NRB (r = -0.24), ΔLogD ( r = -0.25) and NAR (r = -0.18), similar
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6 to the results observed with the bRo5 set. In this case as well, AB-MPS provided the highest
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8 correlation (r = -0.28). As many bRo5 projects target large molecules to achieve adequate
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11 potency, we also analyzed the set of compounds with MW > 500 (n = 1662). Like the previous
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13 bRo5 and Tier 7 sets, we observed weak negative correlations between oral F and AB-MPS (r = -
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0.35), NRB (r = -0.30), ΔLogD ( r = -0.28) and NAR (r = -0.26). Interestingly, we observed
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18 higher negative correlation between AB-MPS and oral F as the MW increased (r = -0.41 for MW
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20 > 600 and r = -0.46 for MW > 700), indicating an increased usefulness of the metric in less-
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23 desirable compound space.
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26 Oral bioavailability is defined by the equation F = FaFgFh, where Fa = fraction
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28 absorbed, Fg = fraction escaping intestinal metabolism and Fh = fraction escaping hepatic
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31 metabolism. Given that oral bioavailability can be influenced by many factors such as
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33 formulation, dose, solubility, intestinal metabolism and hepatic metabolism, in addition to
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permeability, we also looked at absorption in the context of FaFg, which is a measure of
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38 intestinal absorption without the complexity of considering hepatic metabolism.25,26 Assuming
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40 primarily hepatic clearance for large bRo5 drugs, we used the equation FaFg = F/(1-Clp/Qh),
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43 where Clp is the total clearance and Qh is hepatic blood flow. Again, the thresholds for binning
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45 acceptable, moderate and poor FaFg were defined by the overall distribution, with acceptable
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47 FaFg >0.39 (Q3) and poor FaFg ≤ 0.06 (Q1). When we examined the distribution of AB-MPS
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50 values relative to binned FaFg (Figure 4), we again observed a lower average AB-MPS value
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52 (13.5) with a narrower distribution (IQR = 4.7) for compounds with acceptable FaFg compared
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54
to compounds with moderate and low FaFg.
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40 Figure 4. Box plot of binned oral FaFg versus AB-MPS value. Red = FaFg ≤ 0.06, blue = 0.06
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42 < FaFg ≤ 0.39, green = FaFg > 0.39. Comparison circles are shown for alpha level = 0.05.
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45 White solid line = median, white dashed line = average.
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47
48 Permeability is an important factor that contributes to the likelihood of good oral
49
50
51
absorption. While this is not the only factor influencing oral absorption, high intrinsic
52
53 permeability will significantly improve the odds of achieving good oral absorption, and therefore
54
55 bioavailability. With this in mind, we revisited the PAMPA permeability data that was available
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58 for the bRo5 set (n = 7,345) and analyzed the relationship between AB-MPS and PAMPA
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14
1
2
3
permeability. As shown in the box plot of AB-MPS versus binned PAMPA (Figure 5), we
4
5
6 observed that compounds with good PAMPA permeability (Papp >10x10-6 cm/sec) demonstrated
7
8 lower AB-MPS values (average = 11) with a narrower distribution (IQR = 2.6) compared to
9
10
11
compounds with moderate or low PAMPA permeability. In addition, we observed a weak
12
13 negative correlation (r = -0.28) between PAMPA and AB-MPS for this bRo5 compound set.
14
15 While the trend between good PAMPA and superior drug-like properties is clear, one caveat
16
17
18 with the interpretation is that we observed a higher percentage of invalid data (14%) for the bRo5
19
20 set compared to the Ro5 compliant set (8%). Thus, the poor physicochemical properties of bRo5
21
22 compounds such as low solubility may result in poor recovery and a higher invalid data rate,
23
24
25 confounding the prediction of in vivo oral bioavailability based on in vitro PAMPA. Lokey et al.
26
27 recently reported on the challenges of interpreting PAMPA permeability for a series of
28
29
macrocyclic peptides, noting that low Papp values in PAMPA may result from higher membrane
30
31
32 retention and observing a steep drop-off in permeability for compounds with MW > 1000.7
33
34
35 While the PAMPA assay provides a measure of passive permeability without the
36
37
38 influence of transporters, one must consider the potential role of active transport in the efflux and
39
40 uptake of bRo5 compounds.2,6 In our dataset, we found that the median efflux ratio for bRo5
41
42 compounds (MDCK MDR1 efflux ratio = 17.2) to be significantly higher (p < 0.001 by one-way
43
44
45 ANOVA) than that for Ro5 compliant (MDCK MDR1 efflux ratio = 2.4). While the effect of
46
47 efflux transport on oral absorption and tissue distribution has been widely studied, the effect of
48
49
uptake transporters is significantly less well understood. Although there are many suggestions
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52 for the contribution of uptake transporters in intestinal absorption of drugs, information on the
53
54 potential transporter molecules responsible for the intestinal absorptive process is limited, with
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peptide transporter PEPT1 and organic anion transporting polypeptide (OATP) transporters such
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15
1
2
3
as OATP1A2 and OATP2B1 among the most studied.27 While the scope PEPT1 substrate
4
5
6 specificity may be too narrow to accommodate bRo5 drugs, OATP1A2 and OATP2B1 have been
7
8 proposed to play a role in the intestinal absorption of several bRo5 drugs, such as montelucast,
9
10
11
clarithromycin and HIV protease inhibitors, with broader substrate selectivity.28 The co-
12
13 expression of OATPs in the liver leading to potential increased hepatic clearance may confound
14
15 understanding the role of intestinal uptake by these transporters on the disposition of oral drugs.
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Figure 5. Box plot of binned PAMPA versus AB-MPS value for bRo5 compounds. Red =
4
5
6 PAMPA ≤ 2, blue = 2 < PAMPA ≤ 10, green = PAMPA > 10. Comparison circles are shown for
7
8 alpha level = 0.05. White solid line = median, white dashed line = average.
9
10
11
12 As molecular structures get progressively larger, the probability of having an opportunity
13
14 to undergo a form of self-organization, be it internal hydrogen bonding, salt bridge formation, pi-
15
16 stacking or hydrophobic collapse, increases and eventually goes to unity. Such self-organization
17
18
19 processes may lead to chameleon-like behavior where molecules may achieve both an active and
20
21 a permeable conformation by masking both lipophilic and polar residues as required for binding
22
23 to a protein target and crossing a lipid bilayer.6,11,29-31 This means that two-dimensional proxies
24
25
26 for physicochemical properties such as TPSA, cLogD and molecular volume calculated from 2D
27
28 structures, which cannot consider self-organization, will come to overestimate these parameters
29
30
31
progressively as those molecules get larger. Several measures to quantify the degree of three-
32
33 dimensionality of molecules have been proposed including fraction of sp3 carbons (Fsp3),
34
35 normalized principal moments of inertia ratio (NPR), and plane of best fit (PBF).32 While similar
36
37
38 average Fsp3 (0.35) and NPR1 + NPR2 (1.07) values were observed for the bRo5 and Ro5
39
40 compound sets, the PBF observed for the bRo5 set (1.38) was significantly higher (p < 0.001 by
41
42 one-way ANOVA) than for the Ro5 set (0.83), consistent with a high degree of three-
43
44
45 dimensionality for the bRo5 set. A recent study of the effects of 3D shape on permeability for
46
47 bRo5 compounds employed radius of gyration (R-gyr) and 3D-PSA as surrogates for
48
49
hydrodynamic radius, although such methods require approximations and assumptions to be
50
51
52 made about the molecular conformations of a molecule including selecting a single low energy
53
54 conformation.33 With the large structural diversity and molecular complexity found in the
55
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57
current bRo5 dataset, we reasoned that selecting a single conformation was an unreasonable
58
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60
17
1
2
3
simplification due to the myriad of potential conformations and focused our analysis on 2D
4
5
6 molecular descriptors, despite the limitations.
7
8
9 Given the relationship between low AB-MPS and acceptable oral absorption for bRo5
10
11
12 compounds, we analyzed a set of drugs delivered orally in humans (n = 852) which was culled
13
14 from a collection of 1211 marketed drugs. As originally noted by Veber,20 one must use caution
15
16 in the analysis of drug databases due to “a need to assume that all orally administered drugs are
17
18
19 intended to be absorbed.” Therefore, the route of administration for marketed compounds was
20
21 confirmed, removing compounds that are administered orally but display no or sub-therapeutic
22
23 systemic exposures, act locally in the GI tract or oral cavity, or are prodrugs that are metabolized
24
25
26 before absorption of the parent molecule. Prodrugs that are largely absorbed prior to metabolism
27
28 to the parent were included in set. After calculating the physicochemical properties, we identified
29
30
31
138 bRo5 drugs in the collection, including 69 orally administered and 69 parenterally
32
33 administered drugs. As shown in Figure 6, the average AB-MPS value for the oral bRo5 set was
34
35 14.9, while the parenterally administered drugs demonstrated a higher average AB-MPS value.
36
37
38 The average AB-MPS value for the oral bRo5 set (15) was comparable to the average AB-MPS
39
40 value (14) for the internal bRo5 compounds with acceptable oral bioavailability. This suggests
41
42 that from a prospective design perspective, bRo5 compounds targeted to occupy property space
43
44
45 defined by AB-MPS ≤ 15 will have enhanced odds of achieving reasonable levels of oral
46
47 absorption. Interestingly, analysis of the Ro5 compliant orally administered marketed drugs in
48
49
the set (n = 768) revealed a low average AB-MPS value of 8.9 with an IQR of 5.2, suggesting
50
51
52 that AB-MPS value, as a key indicator of acceptable oral absorption of compounds, transcends
53
54 compounds both within and outside of the Ro5.
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33
34 Figure 6. Box plot of binned Route of Administration versus AB-MPS value for bRo5
35
36
compounds. Comparison circles are shown for alpha level = 0.05. White solid line = median,
37
38
39 white dashed line = average.
40
41
42 Case Studies
43
44
45
46 It is now becoming recognized that compounds bRo5 appear to be particularly well-
47
48 suited for drugging important but less-druggable targets in oncology, virology and infectious
49
50 diseases and a number of excellent reviews on the topic have recently appeared.3 In the case
51
52
53 studies included here, we’ve selected some of our recent drug discovery research programs in
54
55 HCV and oncology that highlight some of the benefits and challenges of conducting medicinal
56
57
chemistry with bRo5 chemical matter. In each case study, we’ve highlighted the obstacles to
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19
1
2
3
successful drug discovery for the particular targets, while focusing on the properties of both
4
5
6 successful as well as failed compounds.
7
8
9 Discovery HCV NS5A Inhibitors
10
11
12
13 Today, highly potent HCV NS5A inhibitors, together with HCV NS5B polymerase or
14
15 HCV NS3 protease inhibitors, form the backbone of the highly efficacious and well-tolerated
16
17 direct-acting antiviral (DAA) combination therapies used clinically to cure HCV. In fact, five of
18
19
20 twelve new bRo5 drugs approved by the FDA in the past two years are HCV NS5A inhibitors
21
22 including ledipasvir, ombitasvir, daclatasvir, elbasvir and velpatasvir. However, the discovery
23
24
and development of NS5A inhibitors faced significant challenges. NS5A has no known
25
26
27 enzymatic activity and while it interacts with many viral and host proteins as well as RNA, its
28
29 precise biological functions have yet to be elucidated. As a result, discovery of the early classes
30
31
32
of NS5A inhibitors resulted from investigation of compounds that inhibited HCV replication in a
33
34 replicon assay, with concomitant development of resistant variants that mapped to NS5A. A
35
36 recent review34 highlighted many of the early NS5A inhibitors and although diverse in structure
37
38
39 (Table 3), a common feature of the inhibitors included the selection of resistance-associated
40
41 variants at Y93 of genotype 1b (GT1b), particularly Y93H. A key challenge for the early
42
43 compounds was modest potency against GT1b and significantly weaker potency against GT1a
44
45
46 compared to GT1b. It’s important to note that worldwide HCV GT1 is the most prevalent form
47
48 and in the US approximately 55% of GT1 infections are GT1a. In addition, the chemical series in
49
50
Table 3 suffered from poor drug-like properties including high cLogP and high molecular
51
52
53 weights. The combination of modest potency and poor properties highlights a key challenge for
54
55 the early series in achieving the very high exposures in vivo that would be required to adequately
56
57
58
suppress viral replication. AbbVie investigated a series of naphthyridine- and pyrrolopyrimidine-
59
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20
1
2
3
based compounds, represented by compound 6 (Table 3), that demonstrated nanomolar potency
4
5
6 against GT1b, but were >20-fold weaker against GT1a.35 Compound 6 demonstrated a robust
7
8 viral load decline in a GT1b HCV-infected chimpanzee and selected resistance-associated
9
10
11
variants within NS5A, thus providing in vivo proof of concept for the antiviral efficacy of the
12
13 series. Mostly bRo5, the compounds in the series generally showed good passive permeability
14
15 (PAMPA Papp >2 x 10-6 cm/s), while suffering for poor metabolic stability. Ultimately, the series
16
17
18 lacked adequate tractable SAR, potency against GT1a and oral PK to enable further
19
20 development.
21
22
23 Table 3. Early HCV NS5A Inhibitors
24
25
26
27 GT1b GT1a
No. Structure MW cLogP AB-MPS
28 EC50 (nM) EC50 (nM)
29
30 1 7 1240 644.7 6.2 17.7
31
32
33
34 2 160 NA 499.6 6.3 13.0
35
36
37
38 3 6 NA 572.7 4.1 13.4
39
40
41
42 4 0.4 >50000 599.7 2.5 13.8
43
44
45
46
47 5 <1000 NA 649.7 3.7 16.6
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49
50
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52
53 6 2 188 564.7 5.5 16.8
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21
1
2
3
Although counterintuitive, moving toward less drug-like chemical matter resulted in the
4
5
6 discovery of successful NS5A inhibitors. X-ray crystallographic studies of NS5A domain I
7
8 protein fragments from both GT1a and 1b have revealed the formation of symmetrical
9
10
11
dimers.36,37 While the biological relevance of these dimeric forms is unknown, it is believed that
12
13 inhibitors may function by binding to these structures, providing stability to the dimeric form and
14
15 thereby impacting several aspects of HCV expression and regulation.38,39 This mode of action is
16
17
18 supported by the discovery of highly potent NS5A inhibitors with symmetric dimer or dimer-like
19
20 structures, which presumably provide improved interactions with a dimeric form of the NS5A
21
22 protein. The discovery of symmetry-based NS5A inhibitors resulted in compounds with
23
24
25 dramatically improved potencies, particularly against GT1b. At the same time, the dimeric
26
27 structural motif resulted in significantly higher molecular weight compounds with poor
28
29
physicochemical properties and additional challenges for series progression and development.
30
31
32 Daclatasvir, a symmetric compound discovered as part of a lead optimization campaign starting
33
34 from dimers derived from chemically unstable compound 3, was the first HCV NS5A inhibitor
35
36
37 to demonstrate proof of concept in human clinical trials.40 A symmetry-based medicinal
38
39 chemistry approach in our laboratories identified several novel series compounds that were
40
41 potent inhibitors of both GT1a and 1b replicons and two series are shown in Table 4.
42
43
44 Dimerization of the scaffold found in compound 6 resulted in Series A compounds such as 7 and
45
46 8 which showed subnanomolar potencies against GT1b. The GT1a potency, however, was highly
47
48 dependent on the linking strategy, with the N-phenyl benzyl linkage in 8 providing single-digit
49
50
51 nanomolar GT1a potency, while the ethylene diamine linked amide 7 was inactive. The
52
53 compounds in Series A generally had low solubility (phosphate pH 7.2 = 0.5-7.4 µM) and
54
55
56
negligible permeability in the PAMPA assay. Attempts to reduce the high lipophilicity and NAR
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58
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22
1
2
3
resulted in compounds with similarly poor properties but markedly weaker potencies and none of
4
5
6 the nine compounds tested in rat PK has measurable plasma drug levels. Another symmetry-
7
8 based medicinal chemistry approach identified N-phenyl-core compounds (Series B in Table 4)
9
10
11
that were potent inhibitors of both GT1a and 1b replicons, with lower lipophilicity and NAR.41
12
13 Like compound 8, compound 9 demonstrated good potency at GT1a and 1b, although it was 72-
14
15 fold more potent against GT1b than GT1a. In contrast to 8, compound 9 showed moderate oral
16
17
18 bioavailability in rat (28%). Compound 10, with its conformationally constrained pyrrolidine
19
20 core, demonstrated dramatically higher replicon potency, particularly for GT1a, compared to the
21
22 acyclic analog 10. Addition of a t-butyl group to the central phenyl ring resulted in the discovery
23
24
25 of 11 (ABT-267, ombitasvir), which demonstrated 14 pM and 5 pM potency against GT1a and
26
27 GT1b, respectively.41 The S,S-trans stereochemistry was found to be the optimal substitution
28
29
pattern for the central pyrrolidine ring, with the R,R stereoisomer being significantly less active
30
31
32 against GT1a.
33
34
35 It is well known from the development of HIV PIs that plasma protein binding (PPB) can
36
37
38 markedly decrease the clinical efficacy of antiviral compounds.42 Like many bRo5 drugs, the
39
40 NS5A inhibitors in Table 4 were >99 bound to human plasma proteins, and accurate
41
42 determination of their free fractions presented a considerable challenge without access to
43
44
45 radiolabeled materials due to the very low drug concentrations. In order to assess the magnitude
46
47 of the effect of PPB on potency by a practical method, we evaluated the replicon assay potency
48
49
in the presence of 40% human plasma (HP). The GT1a potencies of the highly lipophilic
50
51
52 compounds 7 and 8 shifted by 15- to 30-fold in the presence of 40% HP. Compound 9 showed a
53
54 smaller shift and the EC50 values increased by 7- to 10-fold when the assay was performed in
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60
23
1
2
3
the presence of 40% HP. Compound 11 retained high potency when the assay was performed in
4
5
6 the presence of HP, with 186 pM and 56 pM potencies against GT1a and GT1b, respectively.
7
8
9 Table 4. Structures, Replicon Potencies, Oral Bioavailability and Properties of NS5A Inhibitors.
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24 EC50 (nM) 0% HPa EC50 (nM) 40% HPa Oral F
No. R1 R2 Series MW cLogP TPSA
25 GT1a GT1b GT1a GT1b Rat
26
27 7 NA A >10000 0.37 >32000 11 NA 887.1 8.3 212
28
29 8 NA A 4.9 0.05 70 1.0 0 892.2 12.0 157
30
31
32 9 Me B 7.2 0.10 69 0.69 28 840.0 0.5 179
33
34 F
35
36 10 Me B 0.26 0.006 15.5 0.53 23 884.1 0.6 179
37 N
38
39
40
11 H B 0.014 0.005 0.19 0.056 25 894.1 1.3 179
41
42
43 a
44
EC50 determined using methods previously reported41
45
46
47 Retrospective application of the AB-MPS function to the symmetry-based NS5A series
48
49 was informative. As shown in Figure 7, there was generally good correlation between the
50
51
52
observed FaFg values obtained from rat PK studies and the AB-MPS value, with the lower
53
54 scoring compounds exhibiting higher FaFg. While all of the compounds demonstrated high AB-
55
56 MPS scores, this retrospective analysis demonstrates that prospective application of AB-MPS
57
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24
1
2
3
may shed light on structural modifications that are more likely to yield acceptable PK, although
4
5
6 applying an absolute cutoff for the maximum AB-MPS values would not be prudent. In fact, the
7
8 AB-MPS values for the marketed NS5A inhibitors are as follows: ledipasvir (21.2), ombitasvir
9
10
11
(23.5), daclatasvir (19.1), elbasvir (22.1) and velpatasvir (21.1).
12
13
14
15
16
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18
19
20
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22
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25
26
27
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32
33
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46
47
48
49
50
51 Figure 7. AB-MPS values for symmetry-based NS5A inhibitor versus observed FaFg in rat PK.
52
53 Red = FaFg ≤ 0.06, blue = 0.06 < FaFg ≤ 0.39, green = FaFg > 0.39. Comparison circles are
54
55 shown for alpha level = 0.05. White solid line = median, white dashed line = average.
56
57
58
59
60
25
1
2
3
As mentioned previously, establishing a tractable IVIVC for permeability and oral
4
5
6 absorption in preclinical species can be particularly challenging for bRo5 chemical series and the
7
8 symmetry-based NS5A series presented such a challenge. The compounds in Series A and B
9
10
11
demonstrated low passive permeability values (PAMPA Papp <0.01 x10-6 cm/s). In contrast to the
12
13 excellent preclinical and clinical PK profile, 11 demonstrated negligible in vitro PAMPA
14
15 permeability (Papp = 0.006 x10-6 cm/s) and Caco-2 data were unclear due to low recovery and
16
17
18 non-specific binding. Without tractable high-throughput permeability data, use of preclinical PK
19
20 screening was required to enable triage and advancement of the compound series. The high
21
22 TPSA for compounds in Table 4 (e.g., 179 for compound 10) is also of note in that high TPSA
23
24
25 values > 140 are generally associated with poor permeability and oral bioavailability.20 It has
26
27 recently been hypothesized that NS5A inhibitors may, through formation of intramolecular
28
29
hydrogen bonds (IHB) in nonpolar environments such as lipid bilayers, effectively mask their
30
31
32 high polarity.43,44 NMR methods and more recently chromatographic techniques such as EPSA45-
33
34 47
have been shown to be useful for detection of IHB. We retrospectively measured the EPSA
35
36
37 values and found that the EPSA for 10 was 83 and was indeed lower than the TPSA value and in
38
39 the range of EPSA values associated with acceptable permeability (i.e., EPSA < 100).46 The
40
41 EPSA measured for 11 was also lower than the TPSA with a value of 104 which is near the
42
43
44 upper range observed for acceptable permeability. NMR analysis of compound 11 in DMSO
45
46 indicated temperature coefficients (TC) of −5.5 ppb/K and −9 ppb/K for the aryl and valine
47
48 amides, respectively. These TCs are inconsistent with strong IHB formation. Interestingly, the
49
50
51 EPSA values for Series A compounds were similar to the high TPSA values, consistent with
52
53 their lack of oral bioavailability.
54
55
56
57
Discovery of HCV NS3/4A Protease Inhibitors
58
59
60
26
1
2
3
The currently approved therapies for treating chronic HCV infection have significantly
4
5
6 improved the effectiveness and tolerability compared to pegylated (PEG) interferon-α combined
7
8 with ribavirin, achieving high sustained virologic response (SVR) rates in GT1 patients.48-51 Like
9
10
11
HCV NS5A inhibitors, HCV NS3/4A protease inhibitors (PIs) have become key components of
12
13 highly efficacious combinations of DAAs. The currently approved HCV PIs also have significant
14
15 improvements including once daily dosing and improved tolerability compared to first-
16
17
18 generation compounds boceprevir or telaprevir, which required t.i.d. dosing and were
19
20 accompanied by side effects. Our research efforts (in collaboration with Enanta) have focused on
21
22 maximizing the SVR for patients with all HCV genotypes, while simplifying the treatment
23
24
25 regimen. For the HCV PI class, our focus was directed toward the discovery of candidates that
26
27 exhibited a high genetic barrier to viral resistance, broad genotype antiviral potency as well as
28
29
the convenience of once daily dosing without the use of PK boosters, such as ritonavir. As our
30
31
32 starting point, we surveyed a series of quinoxaline macrocyclic compounds and identified
33
34 compound 12 as a promising lead with superior potency against clinically relevant resistant
35
36
37 variants in GT1 (Table 5) which were selected in the clinic with first generation inhibitors.52
38
39 Compound 12 exhibited excellent activity against wild-type (WT) GT1 as well as resistance-
40
41 associated variants GT1a R155K, GT1b R155K and GT1b D168V, within a single-digit fold of
42
43
44 the WT EC50 value. However, the GT1a D168V variant still conferred significant fold resistance
45
46 to 12. In addition, the PK of 12 was characterized by high IV clearance, poor plasma
47
48 concentration following oral dosing, and poor bioavailability in both rat and dog (Table 6). We
49
50
51 conducted SAR to improve both the resistance profile and PK for the series. For example,
52
53 fluorination of the quinoxaline resulted in compound 13 which was equipotent to 12 against WT
54
55
56
GT1 and resistance-associated variants with similar fold resistance. Incorporation of a
57
58
59
60
27
1
2
3
trifluoromethyl group provided incremental improvement to the antiviral activity. Compounds 14
4
5
6 and 15 were equipotent to 12 against WT GT1, while exhibiting improved activity against
7
8 resistance variants of approximately 3- to 10-fold (Table 5). The impact of fluorination and
9
10
11
trifluoromethylation of the quinoxaline group was particularly significant to the PK properties of
12
13 the analogs (Table 6). Compound 13, with the introduction of the C7-F to the quinoxaline,
14
15 exhibited significantly lower clearance (0.07 L/hr/kg) and higher plasma level (AUC/dose
16
17
18 (18 µg·hr/mL, per mg/kg) following oral dosing in dog in comparison to 12. Compound 14,
19
20 bearing the C3-CF3 also showed lower clearance, higher oral plasma concentration and
21
22
23
bioavailability in rat, while demonstrating higher plasma concentrations after oral dosing in dog.
24
25 Incorporating both substitutions to the quinoxaline, compound 15 showed 2-fold lower
26
27 clearance, 18-fold higher plasma concentration following oral dosing in rat, and 7-fold improved
28
29
30 bioavailability in comparison to 12. Similarly, it demonstrated low clearance and high plasma
31
32 concentration following oral dosing in dog, consistent with the trend observed in compounds 13
33
34 and 14.
35
36
37
38 Table 5. In Vitro Activity of HCV NS3/4A PIs in the Replicon Assaya
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55 Stable replicon EC50 (nM) Transient replicon EC50 (nM)/(fold resistance)
56 No.
57 1a 1b 3a 1a variant 1b variant 3a
58
59
60
28
1
2
3 0% 40% 40%
4 b 0% HP 0% HP R155K D168V R155K D168V WT
5 HP HP HP
c
6 12 1.4 30 0.4 9 NT 3 (6) 94 (177) 2 (2) 5 (2) NT
7 13 1.1 11 0.8 7 NT 2 (7) 41 (146) 1.6 (2) 3 (4) NT
8 14 0.5 12 0.4 10 NT 0.4 (4) 33 (290) 0.7 (2) 2 (6) NT
9
15 0.8 7 0.5 7 64 0.3 (3) 14 (149) 0.5 (1) 1.5 (5) 83
10
11 16 0.7 9 0.5 11 NT 0.3 (3) 14 (127) 0.4 (1) 1.3 (4) 124
12 17 0.7 6 0.5 8 7 0.7 (18) 8 (168) 0.4 (4) 0.9 (9) 4
13 18 0.2 7 0.1 3 0.8 2 (65) 3 (97) 0.03 (0.5) 0.1 (2) < 0.3
14
19 0.5 7 2 12 8 0.6 (0.8) 0.4 (2) 8 (33) 3 (11) 4
15 a
16 EC50 determined using methods previously reported.52 bHP = human plasma. cNot tested.
17
18
19 Examining the replacement of the cyclopropyl group of the acylsulfonamide revealed that
20
21
the addition of a methyl group to the cyclopropyl ring had a positive effect on PK while the
22
23
24 antiviral activity profiles remained equivalent to the corresponding un-substituted analogs.
25
26 Compound 16 was equipotent to 15 in the WT and resistant replicons (Table 5). The PK of 16
27
28
29
was superior to 15 with a long half-life, improved clearance and plasma concentration after oral
30
31 dosing in rat or dog (Table 6).
32
33
34 Despite achieving good anti-viral potency in the GT1 replicons and PK properties, the
35
36
37 quinoxaline series did not offer improvement to potency against broad HCV genotypes
38
39 benchmarked by potency in the G3a replicon. Compound 15 showed > 80 fold weaker activity
40
41 against GT3a compared to GT1 stable replicons while compound 16 demonstrated 1.5 fold
42
43
44 weaker potency compared to 15 against GT3a transient replicons.
45
46
47 Table 6. Pharmacokinetic properties of HCV NS3/4A PIsa
48
49
50
Rat Dog
51
52 No. IV PO IV PO
53 c
54 t1/2 CLp t1/2 AUC/D F t1/2 CLp t1/2 AUC/D F FaFg
55 b
12 2.4 4.7 NA 0.008 3.9 1.4 0.47 nf 0.3 13 0.2
56
57 13 NA NA NA NA NA 2 0.07 2 18 123 NA
58
59
60
29
1
2
3 14 1.2 0.21 1.8 4.75 99.5 1 0.34 1.5 6.76 200 1.5
4
5 15 2.1 2.3 1.9 0.14 28 3.5 0.04 2.2 18 74 0.8
6 16 4.1 1.6 4.7 0.19 27 2.9 0.02 2.9 46.8 88 0.9
7 17 3.2 2.5 3.5 0.16 40 2.3 0.02 2 85 140 1.4
8 18 5 1.1 4.6 0.4 43 3.2 0.01 4 138 81 0.8
9
10 19 1.7 3.1 1.5 0.09 27 2.2 0.07 2.1 11.6 76 0.8
a
11 Units: t1/2 (h); Cl (L/h/kg); Cmax (µg/mL); AUC0-24h (µg*h/mL); F (%); Doses (mg/kg). bNot available.
12
c
13 Calculated based on IV dosed at 1 mg/kg and PO dosed at 3 mg/kg
14
15
16 An extensive SAR evaluation identified the phenanthridine-based inhibitors such as 17 as
17
18
19 a promising series to achieve broad genotypic antiviral activity as well as desirable PK
20
21 properties. Through intensive evaluation of the SAR, the substitution of the phenanthridine group
22
23
as well as the capping group of the P3-amine were identified as two areas that significantly
24
25
26 affected the virology and PK. Compound 17, with an 8-fluorophenanthridine group and
27
28 compound 18, with a 3-trifuoromethoxy-8-fluorophenanthridine group, provided equal or better
29
30
31
potency to 15 against GT1 replicons in the presence of 40% human plasma (HP) (Table 5). Both
32
33 compounds also demonstrated comparable EC50 values and fold-resistance against GT1 variants
34
35 to 15. In contrast to the weak GT3a potency of 15, compound 17 exhibited single-digit
36
37
38 nanomolar potency against GT3a replicon, although it was approximately 10-fold weaker against
39
40 GT3 compared to GT1 (Table 5). Compound 18 yielded potency against GT3a that was within
41
42 10-fold of the GT1 EC50 values. By extending the ligand-enzyme interaction into the P4-site,
43
44
45 compound 19, bearing a capped t-butyl alanine P4 group, showed a higher fold-difference
46
47 between GT3a and GT1 replicons in comparison to 18. However, compound 18 provided a
48
49
different resistance profile against GT1 variants in that it exhibited no loss in potency against
50
51
52 GT1aR155K variant and only 2-fold loss in potency against GT1aD168V replicon, a marked
53
54 difference to the capped-P3 analogs. The compounds in the series generally exhibited large shifts
55
56
57
(6- to 35-fold) in the replicon EC50 values obtained in the presence of 40% HP. For example,
58
59
60
30
1
2
3
compound 18 exhibited more than a 30-fold shift in potency against GT1 with the addition of
4
5
6 40% HP, likely a result of the high plasma protein binding. Fluorination of the phenanthridine
7
8 moiety impacted the PK properties as observed in the quinoxaline series (Table 6). Compound
9
10
11
17 with a fluorinated phenanthridine produced similar half-life and plasma concentration
12
13 following oral dosing in rat when compared to compound 16. Similar clearance and nearly 2-fold
14
15 higher plasma concentrations were achieved by 17 dosed in dog in comparison to 16. Compound
16
17
18 18, having an additional C3-trifluoromethoxy group on the phenanthridine exhibited long plasma
19
20 half-life and more than 2-fold higher plasma level following oral dosing in both rat and dog than
21
22 16. On the other hand, compound 19, containing the extended P4 functional groups,
23
24
25 demonstrated limited plasma half-life and concentrations in both animal species following oral
26
27 dosing.
28
29
30
31
Selected physicochemical properties for the compounds appear in Table 7. Retrospective
32
33 determination of AB-MPS revealed a narrow range (from 12 to 14.5) of values indicating that the
34
35 compounds would be predicted to have moderate or high oral availability, consistent with the
36
37
38 observations in Table 6. The AB-MPS values for the marketed NS3/4A are as follows:
39
40 grazoprevir (10.5) and paritaprevir (12.2). By virtue of their macrocyclic structures, the
41
42 compounds have drug-like NRB (<10) despite their high molecular weights (range from 719.8 to
43
44
45 869.9). In general, the quinoxaline compounds (12 to 16) had higher solubility than the
46
47 phenanthridines (17 to 19), a trend that was consistent with the higher cLogD values for 17 to 19.
48
49
The quinoxalines also showed higher in vitro permeability compared to the phenanthridines. The
50
51
52 high FaFg values were observed for all of the compounds suggests that once again relying on PK
53
54 screening served as a superior way to triage compounds than relying on in vitro permeabilities.
55
56
57
Like the HCV NS5A inhibitors, compounds 12 to 19 demonstrated narrowly-ranged and high
58
59
60
31
1
2
3
(175 to 225) TPSA values. As previously mentioned, measurement of EPSA has been used in
4
5
6 predicting permeability and retrospective determination of EPSA values for compounds 12 to 19
7
8 (Table 7) predicted a high probability for these compounds to have acceptable bioavailability. It
9
10
11
was not clear, however, if the poor PAMPA permeability of 17 to 19 and the lack of correlation
12
13 with EPSA resulted from their poor solubility.
14
15
16 Table 7. Physicochemical Properties of HCV NS3/4A PIs
17
18
19
20 No. AB-MPS cLogD TPSA EPSA Solubility
a
Permeability
21
22 12 112 >500 3.5
b
12.05 0.95 202.8
23 c
24 13 11.91 1.09 202.8 108 >500 2.8
c
25 14 11.92 2.08 202.8 104 150 5.4
b
26 15 11.79 2.21 202.8 99 155 5.1
27 16 89 20.6 12.1
b
11.35 2.65 202.8
28 b
29 17 11.22 3.22 189.9 116 1.9 0.19
b
30 18 14.51 4.51 190.9 114 0.65 0.06
b
31 19 13.65 3.65 184.2 104 2.2 0.28
32 a
Critical aggregation concentration (CAC) buffer (pH 7.2), (µM). PAMPA Papp 10 cm/sec. Caco-2 Papp 10-6
b -6 c
33
34 cm/sec.
35
36
37
Through systematic SAR we were able to modify the quinoxaline and phenanthridine
38
39
40 macrocyclic series to achieve the target antiviral properties and PK properties which supported a
41
42 once a day dosing regimen. Notably, the fine tuning of the substitutions of the quinoxaline and
43
44
45
phenanthridine moieties and judicious placement of fluorine and trifluoromethyl groups resulted
46
47 in major improvements to the resistance profile as well as the PK of the analogs. Despite the
48
49 potency achieved by the phenanthridine-based analogs against most of the relevant resistance
50
51
52 replicons, the GT1R168V variant remained a difficult resistance mutation to overcome within
53
54 the series. Even though compound 19 showed excellent overall virologic and PK properties, our
55
56 next generation NS3/4A protease inhibitor, 3aR,7S,10S,12R,21E,24aR)-7-tert-butyl-N-
57
58
59
60
32
1
2
3
{(1R,2R)-2-(difluoromethyl)-1-[(1-methylcyclopropane-1-sulfonyl)carbamoyl]cyclopropyl}-
4
5
6 20,20-difluoro-5,8-dioxo-2,3,3a,5,6,7,8,11,12,20,23,24a-dodecahydro-1H,10H-9,12-
7
8 methanocyclopenta[18,19][1,10,17,3,6]trioxadiazacyclononadecino[11,12-b]quinoxaline-10-
9
10
11
carboxamide (ABT-493, glecaprevir; identified by AbbVie and Enanta), exhibited a superior
12
13 resistance profile, pan-genotypic potency, and PK and it is currently being investigated in
14
15 combination with methyl {(2S,3R)-1-[(2S)-2-{5-[(2R,5R)-1-{3,5-difluoro-4-[4-(4-
16
17
18 fluorophenyl)piperidin-1-yl]phenyl}-5-(6-fluoro-2-{(2S)-1-[N-(methoxycarbonyl)-O-methyl-L-
19
20 threonyl]pyrrolidin-2-yl}-1H-benzimidazol-5-yl)pyrrolidin-2-yl]-6-fluoro-1H-benzimidazol-2-
21
22 yl}pyrrolidin-1-yl]-3-methoxy-1-oxobutan-2-yl}carbamate (ABT-530, pibrentasvir) in clinical
23
24
25 trials.53
26
27
28 Discovery of Bcl-2 Family Inhibitors
29
30
31
32
Nearly two decades ago, Abbott began a project aimed at developing inhibitors of the anti-
33
34 apoptotic proteins Bcl-2 and Bcl-xL for use in oncology indications. Bcl-2 and Bcl-xL are
35
36 involved in a signal transduction pathway controlling the intrinsic apoptosis program, and in so
37
38
39 doing undergo protein-protein interactions involving large and hydrophobic protein surfaces. We
40
41 thus anticipated challenges in producing compounds that would have properties necessary for
42
43 oral administration. In fact, compounds resulting from this effort were characterized by two large
44
45
46 groups which interacted with two deep hydrophobic pockets situated several Angstroms apart,
47
48 referred to as P2 and P4 (Figure 8). A notable feature of the series was the discovery that the 3-
49
50
nitro-4-(2-phenylthioethyl)aminophenyl group undergoes hydrophobic collapse and subsequent
51
52
53 π-stacking to efficiently occupy the P4 binding hot spot.54 The proof-of-concept compound
54
55 reported from this effort, 20 (ABT-737, Figure 8), was very potent in cellular assays and animal
56
57
58
models, but was also very poorly bioavailable in animals.54,55 As development of an oral
59
60
33
1
2
3
compound would be necessary for sustained inhibition of the target proteins in the clinic, we next
4
5
6 set out to modify 20 to improve its PK characteristics. This effort resulted in the discovery of 21
7
8 (ABT-263, navitoclax), which is still in clinical development (Figure 8).56,57 Compound 21, like
9
10
11
20, had low-picomolar affinity to both Bcl-2 and Bcl-xL. Compound 21 is larger than 20 (MW =
12
13 974 and 813, respectively), and like 20 it had a number of other parameters lying well outside
14
15 Ro5 space, with an experimental LogD of 6.3, and 16 rotatable bonds. Nevertheless, early PK
16
17
18 studies in animals showed moderate absorption, and a later, enabling formulation produced
19
20 sufficient oral absorption and PK parameters for clinical evaluation.
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41 Figure 8. Structures of Bcl-2 inhibitors 20 and 21.
42
43
44
45 The modifications to the structure of 20 achieved two main goals. First, the transformation of
46
47 the P2-binding group increased the sp3 character of the molecule, and reduced the NAR. Second,
48
49 reduction of the basicity of the amine group and the acidity of the acylsulfonamide likely
50
51
52 increased the fraction of uncharged drug at the gut wall, facilitating better absorption. It has been
53
54 noted that zwitterionic compounds are less likely to fail for toxicology or safety reasons in the
55
56
clinic (compared to basic, neutral or acidic compounds), although they are more likely to fail for
57
58
59
60
34
1
2
3
pharmacokinetic reasons.57 We observed that replacing the dimethylamine with morpholine
4
5
6 resulted in an approximately three unit drop in pKa. In addition, replacement of the nitro group
7
8 reduced the acylsulfonamide acidity, which correlated strongly with higher oral exposure.
9
10
11
However, this modification also correlated with reduced potency. Fortunately, a way around this
12
13 tradeoff was discovered. In seeking to combine electron withdrawing capacity with the
14
15 hydrophobicity the binding pocket required, it was discovered that replacement with a
16
17
18 trifluomethylsulfonyl group resulted in small improvements to both potency and oral exposure.
19
20 While the trifluomethylsulfonyl and nitro groups have similar electron withdrawing effects on
21
22 the acylsulfonamide, we reasoned that the much larger trifluomethylsulfonyl group required a
23
24
25 modification of the protein surface upon binding, which is perhaps responsible for the
26
27 unexpected nature of the effect of this substitution.
28
29
30
31
In addition to a reduced charge at physiologically relevant pH, 21 had better metabolic
32
33 stability than 20. With intravenous dosing, 21 had low volumes of distribution and low
34
35 clearance. Orally, absorption is dissolution rate-limited, with 21 achieving 13-22% oral
36
37
38 bioavailability across animal species, and with a formulation suitable for clinical use, reached
39
40 48% F in dogs.58 Clinical studies have shown good PK in humans, with low clearance and a long
41
42 half-life.59
43
44
45
46 Compound 21, like 20, was greater than 99% protein-bound across species, and had
47
48 aqueous solubility below the limits of quantitation (<0.0002 mg/mL). As a result of this, these
49
50
and other project compounds typically showed low nanomolar activity in both FL5.12 cell lines
51
52
53 overexpressing target protein and non-engineered cell lines, when tested in the absence of serum.
54
55 However, cell-based assays run in the presence of 3% (for FL5.12 cells) or 10% (for non-
56
57
58
59
60
35
1
2
3
engineered cell lines) serum typically provided somewhat higher and much more relevant
4
5
6 values.55,56
7
8
9 Most efforts to improve aqueous solubility throughout the project were met with failure.
10
11
12 Compounds with higher TPSA typically maintained affinity, but cellular activity and PK
13
14 parameters were consistently made much poorer. While the medicinal chemist would ideally
15
16 prefer candidate molecules to possess both aqueous solubility and a low enough TPSA to admit
17
18
19 oral absorption (TPSA ≤140), in practice it is very difficult to satisfy both of these when the
20
21 molecule in question is very large. Ultimately, while aqueous solubility would have been
22
23 advantageous, oral absorption was, of course, critical. Once again, data from PAMPA assays and
24
25
26 other ADME screens was usually precluded by the low aqueous solubility of compounds, and so
27
28 establishment of an IVIVC was not possible. Instead, by following oral bioavailability directly
29
30
31
during the last stage of the project through PK screening on dozens of compounds, and even
32
33 more importantly, by employing a PK/PD marker (AUC/EC50) to assess large numbers of late
34
35 compounds, the project group converged on a cluster of low-solubility, high-lipophilicity
36
37
38 compounds that demonstrated acceptable levels of oral absorption.
39
40
41 Table 8. In Vitro Potency and Physicochemical Properties a
42
43
44 Ki (nM) Cell Killing EC50 (nM) Physicochemical Properties
45
RS4;11 Molt-4
46 No. Bcl-2 Bcl-XL MW NRB TPSA cLogD cLogP AB-MPS
47 10% HS 10% HS
48 20 <1 <1 24 622 813 16 131 4.97 9.26 24.3
49 21 0.044 0.055 112 303 974 17 128 7.55 11.51 26.1
50
22 <0.01 14 6 >5000 896 14 172 7.47 11.29 23.8
51
52 23 <0.01 48 8 >5000 868 13 172 6.52 10.38 21.9
a
53 Potency determined using methods previously reported.54-56,61
54
55
56
57
58
59
60
36
1
2
3
Another project was initiated to find selective Bcl-2 inhibitors, and a different structural
4
5
6 series was found, which led to compounds such as 2260 and 23 (ABT-199, venetoclax, Figure
7
8 9),61,62 which has received FDA approval for chronic lymphocytic leukemia (CLL). This series is
9
10
11
primarily characterized by different aromatic groups, with a different connection, comprising the
12
13 bottom half of the P4 pi-stack (Figure 10). Additionally, the P4 ‘tail’ usually lacks an amine
14
15 group. In addition to Bcl-2 selectivity, this series displayed improved oral absorption in general.
16
17
18 Not only were we able to make orally bioavailable compounds with the aryl nitro group present,
19
20 but many compounds with this gross structure displayed much better absorption, with specific
21
22 compounds achieving 60-70% oral bioavailability.
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45 Figure 9. Structures of Bcl-2 inhibitors 22 and 23.
46
47
48 The most interesting aspect of these structures is that their TPSA values are much higher
49
50
51
than for compounds from the previous series. While 21 had a TPSA of 128, those for 22 and 23
52
53 are 172. Molecules from this series nevertheless are similar to 20 and 21 in that they also have
54
55 very low water solubility, and are highly protein-bound (99% or greater across species). It is
56
57
58 possible, though, that the increases in TPSA improve aqueous solubility and/or decrease protein
59
60
37
1
2
3
binding by small amounts, resulting in small but meaningful improvements in the unbound free
4
5
6 fractions of molecules in this class. In any case, this gross structure seems to be able to support
7
8 higher TPSA while still being absorbed through the gut wall, and into target cells. One is
9
10
11
naturally led to the question of why this is so. The salient structural difference between the two
12
13 series is the different routes to formation of the desired P4 π-stacking (Figure 10). This results in
14
15 lower rotatable bond counts for molecules in the Bcl-2 selective class (Table 8). Additionally,
16
17
18 comparison of the entropic cost of achieving the necessary conformation for molecules in the
19
20 two series seems to favor the latter set of compounds, as the ‘bent-back’ structure of 20 and 21
21
22 has five consecutive rotatable bonds that need to be in a particular orientation. The P4-binding
23
24
25 structures of the compound 22 series formally involve six rotatable bonds, but the preferred
26
27 conformation of the acylsulfonamide and potential steric clashes effectively reduce this to three.
28
29
This may lower the effective volume of molecules in the latter series, and reduce the entropic
30
31
32 barrier to achieving the necessary hydrophobic collapse to enable both potency and oral
33
34 absorption.
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50 Figure 10. a. X-ray structure of (21) bound to Bcl-2. b. X-ray of an indole analog of (23) bound
51
52
53 to Bcl-2. Adapted from reference 61.
54
55
56
57
58
59
60
38
1
2
3
These, like many larger, highly hydrophobic molecules seem to succeed as drugs through
4
5
6 a fundamentally different route than for most marketed drugs. While small molecules can
7
8 possess good aqueous solubility, and also be absorbed through the gut and penetrate cells, larger
9
10
11
molecules cannot normally possess enough polar surface area to attain significant water
12
13 solubility and still be non-polar enough to be orally absorbed. As oral absorption is paramount,
14
15 the resultant low solubility of these molecules, combined with high protein binding, means that
16
17
18 these molecules inevitably will have very low unbound free fractions. They are in effect
19
20 circulated through the target organism by serum proteins, and it is only the profoundly high
21
22 target binding affinities of the compounds that allows them to work without patients being given
23
24
25 extraordinarily high doses of drug. In addition, for both 21 and 23, lymphatic transport, which
26
27 can come into play for very lipid-soluble molecules, seems to play a significant role.62,63
28
29
30
31
Conclusions
32
33
34 The retrospective correlation of physicochemical and other drug-like properties with the
35
36 probability of success for advancing a drug through clinical trials and to the market has provided
37
38
39 medicinal chemists with valuable insights and principles for the prospective design of new drugs.
40
41 The seminal paper from Lipinski highlighted the relatively narrow chemical space that historical
42
43 oral drugs and potential drug candidates occupy, which led to the formulation of Lipinski’s
44
45
46 Ro5.1, However, in recent years an increasing number of successful new drugs have been
47
48 launched that significantly violate these empirical rules and it is apparent the principles for the
49
50
successful design of bRo5 drugs are poorly understood. We conducted a retrospective analysis of
51
52
53 both our clinical and our preclinical compound collections with their available preclinical PK
54
55 data with a focus on bRo5 chemical matter. At the outset of this undertaking, we had low
56
57
58
expectations that any clear trends could be gleaned from such a diverse collection of project data
59
60
39
1
2
3
given the unique set of medicinal chemistry challenges that each drug discovery project presents
4
5
6 and the myriad of processes involved in the oral delivery of a drug. On the contrary, our analysis
7
8 found that in order for compounds bRo5 to demonstrate acceptable oral absorption, they must
9
10
11
have the right balance of physicochemical properties endemic to successful oral drugs; namely,
12
13 permeability, lipophilicity, NAR, and NRB. While the bRo5 class of drugs may fail some of the
14
15 criteria laid out by Lipinski, successful bRo5 drugs appear to have favorable properties in the
16
17
18 context of driving good permeability and oral absorption. We have developed a simple multi-
19
20 parametric mnemonic AB-MPS which combines the physicochemical properties most closely
21
22
correlated with an increased probability of higher oral bioavailability (ΔLogD, NAR, NRB) and
23
24
25 can be used to help define the likelihood that a compound will have acceptable oral absorption
26
27 bRo5. From our retrospective analysis of HCV NS5A inhibitors and NS3/4A PIs, we also found
28
29
30 that determination of EPSA may be a useful tool for predicting acceptable permeability for bRo5
31
32 chemical series with high TPSA values. At the same time, our retrospective analysis has revealed
33
34 some key challenges remaining for the successful design of bRo5 drugs, including establishing a
35
36
37 tractable correlation for in vitro permeability and oral absorption in preclinical species and a
38
39 detailed knowledge of the effect and specificity of uptake transporters on intestinal absorption.
40
41
Without such information, reliance on PK screening may still be the most reliable approach for
42
43
44 separating promising compounds and series from the poor ones. In addition, using robust cell-
45
46 based in vitro potency assays that can account for permeability and PPB effects, as illustrated for
47
48
49
the HCV and Bcl-2 case studies, may also enable more effective bRo5 compound triage.
50
51 Achieving oral bioavailability of complex small molecules and effectively drugging biological
52
53 targets remains an unpredictable art, and while AB-MPS and EPSA values may provide guidance
54
55
56 beyond the bRo5, detailed preclinical and clinical studies are still required to confirm adequate
57
58
59
60
40
1
2
3
exposure upon oral administration. It is hoped that continued investigation of bRo5 drugs will
4
5
6 reveal additional insights that will enable more rapid and efficient development of drugs for less-
7
8 druggable targets with the potential to lead to medicines for diseases with high unmet medical
9
10
11
need.
12
13
14 Methods
15
16
17
Physicochemical properties were calculated using ChemAxon (ChemAxon Component
18
19 collection for Pipeline Pilot version 1.9_j55) for cLogD and BioVia’s Pipeline Pilot v.9.1
20
21 calculators for NRB, NAR, HBA, HBD, MW, TPSA, N+O, Fsp3, NPR and PBF, with minor
22
23
24 customization as needed. Additionally we used BioByte’s cLogP calculator for calculating the
25
26 octanol-water partition coefficient. Additional calculations and visualizations were conducted
27
28 using Perkin Elmer’s Tibco Spotfire. Analysis of marketed drugs was conducted using
29
30
31 Thompson Reuter’s (now Clarivate Analytics) Integrity drug database as well as Excelra’s
32
33 GOSTAR database. Route of administration was verified with literature sources.
34
35
36
Associated Content
37
38 Supporting Information
39
40 Tables of physicochemical property data for the bRo5 set, Tier 7 set and marketed drug database.
41
42
43 The material is available free of charge on the ACS Publications website.
44
45 Corresponding Author
46
47 *Phone: +1 847-937-7205. E-mail: david.degoey@abbvie.com.
48
49
50
51 Acknowledgements
52
53
54 We thank Rishi Gupta for calculation of physicochemical properties. We thank Patrick Da Silva
55
56 Cordeiro, Erin Jordan and Philip Searle for EPSA determinations. We thank Daniel Bow and
57
58
59
60
41
1
2
3
Kelly Desino for discussion and assistance with DMPK data interpretation. We thank Jason
4
5
6 Shanley, Brian Green, David Grampovnik and Keith McDaniel for their contributions to the
7
8 HCV PI work. We thank John Randolph for his contributions to the HCV NS5A work. We thank
9
10
11
Philip Kym, Anil Vasudevan and Stevan Djuric for support and guidance in the preparation of
12
13 this manuscript.
14
15
16 Abbreviations Used
17
18
19 ADME, absorption, distribution, metabolism, and excretion; AUC, area under the plasma
20
21 concentration−time curve; Bcl-2, B-cell lymphoma 2; Bcl-xL, B-cell lymphoma-extra large;
22
23 bRo5, beyond the Rule of 5; DAA, direct-acting antiviral agent; DMPK, drug metabolism and
24
25
26 pharmacokinetics; Fsp3, fraction of sp3 carbons; GT, genotype (e.g., GT1a); HBA, number of
27
28 hydrogen bond acceptors; HBD, number of hydrogen bond donors; HCV, hepatitis C virus;
29
30
31
IVIVC, in vitro/in vivo correlation; MW, molecular weight; NAR, number of aromatic rings;
32
33 NPR, normalized principal moments of inertia ratio; NRB, number of rotatable bonds; PBF,
34
35 plane of best fit; PK, pharmacokinetic; R-gyr, radius of gyration; Ro5, rule of 5; SAR,
36
37
38 structure−activity relationship; SVR, sustained viral response; TPSA, topological polar surface
39
40 area.
41
42
43 Biographies
44
45 David A. DeGoey is a Research Fellow at AbbVie. He received a B.S. degree in chemistry from
46
47 the University of Wisconsin Madison in 1988 and earned a Ph.D. in chemistry from Harvard
48
49
50 University in 1995, studying in the laboratory of Professor Yoshito Kishi. He joined Abbott
51
52 Laboratories in 1995 (now AbbVie since the company split in 2013) where he has spent a large
53
54 portion of his career in infectious diseases research working on the discovery of antifungal,
55
56
57 antibacterial and antiviral agents, including many targets with bRo5 chemical matter such as HIV
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59
60
42
1
2
3
and hepatitis C. He co-led the medicinal chemistry team that discovered the HCV NS5A
4
5
6 inhibitor, ombitasvir, which was approved for the treatment of HCV in combination with
7
8 paritaprevir, ritonavir and dasabuvir.
9
10
11
Hui-Ju Chen is a Senior Research Scientist at AbbVie. She received a B.S. degree in chemistry
12
13 from National Taiwan University and earned a Ph.D. in chemistry from The University of Texas
14
15 at Austin under the guidance of Professor Stephen F. Martin. She joined Abbott Laboratories in
16
17
18 1995 (now AbbVie) and has been involved in discovery projects in the infectious diseases
19
20 research area as well as immunology and anti-inflammatory areas.
21
22 Philip B. Cox is a Senior Principal Scientist at AbbVie. Phil received a BSc (Hons) degree in
23
24
25 Chemistry from the University of Salford in 1987 and then a PhD at the University of Exeter in
26
27 1991 (Professor Stan Roberts). After two postdoctoral fellowships at WSU and CWRU
28
29
(Professor Phil Garner), Phil began his industrial career in 1997 with Evotec, where he was a
30
31
32 project leader overseeing discovery chemistry projects. Phil then moved to Pharmacia and
33
34 subsequently Pfizer, Ann Arbor, where he was a member of the lead discovery group. In 2007,
35
36
37 Phil moved to Abbott Labs (now AbbVie), where he currently leads chemistry efforts in FBDD
38
39 projects. Phil is also an Adjunct Faculty in the Chemistry Department at Washington State
40
41 University.
42
43
44 Michael D. Wendt is a Principal Research Scientist at AbbVie. He received a B.S. degree in
45
46 chemistry from the University of Wisconsin-Madison in 1984, then obtained his Ph.D. in
47
48 chemistry from Yale University in 1992, working with Jerome A. Berson. After a post-doctoral
49
50
51 tour with William Roush at Indiana, he joined Abbott Laboratories in 1994. He has been in
52
53 Oncology since 1996, and has spent most of that time working on Bcl-2 family inhibitors. He
54
55
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43
1
2
3
was part of the group that discovered navitoclax and venetoclax, the latter of which has been
4
5
6 approved for the treatment of CLL.
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49 Tahir, S. K.; Tse, C.; Wendt, M. D.; Xiao, Y.; Xue, J. C.; Zhang, H.; Humerickhouse, R. A.;
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24 Table of Contents Graphic:
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42 List of all figures/tables/charts
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44 Table 1. New FDA approvals (2014-present) of oral bRo5 drugs
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47 Figure 1. Effect of multiple physicochemical properties on oral bioavailability F
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49 Figure 2. Effect of cLogD on PAMPA permeability
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Table 2. Physicochemical Property Averages by Rat Oral Bioavailability Quartile
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54 Figure 3. Box plot of binned oral F versus AB-MPS value
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56 Figure 4. Box plot of binned oral FaFg versus AB-MPS value
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Figure 5. Box plot of binned PAMPA versus AB-MPS value for bRo5 compounds
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6 Figure 6. Box plot of binned Route of Administration versus AB-MPS value for bRo5
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8 compounds
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Table 3. Early HCV NS5A Inhibitors
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13 Table 4. Structures, Replicon Potencies, Oral Bioavailability and Properties of NS5A Inhibitors
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15 Figure 7. AB-MPS values for symmetry-based NS5A inhibitor versus observed FaFg in rat PK
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18 Table 5. In Vitro Activity of HCV NS3/4A PIs in the Replicon Assay
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20 Table 6. Pharmacokinetic properties of HCV NS3/4A PIs
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22 Table 7. Physicochemical Properties of HCV NS3/4A PIs
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25 Figure 8. Structures of Bcl-2 inhibitors 20 and 21
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27 Table 8. In Vitro Potency and Physicochemical Properties
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Figure 9. Structures of Bcl-2 inhibitors 22 and 23
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32 Figure 10. a. X-ray structure of ABT-263 (21) bound to Bcl-2. b. X-ray of an indole analog of
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34 ABT-199 (23) bound to Bcl-2.
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Beyond The Rule of 5: Lessons Learned From AbbVie's Drugs and Compound Collection

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Journal of Medicinal Chemistry is published by the American Chemical Society. 1155

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