Lead- and drug-like compounds: the rule-of-five revolution.

The medicinal chemistry community has become increasingly aware of the value of tracking calculated physical properties such as molecular weight, topological polar surface area, rotatable bonds, and hydrogen bond donors and acceptors. We hypothesized that the shift to high-throughput synthetic practices over the past decade may be another factor that may predispose molecules to fail by steering discovery efforts toward achiral, aromatic compounds. We have proposed two simple and interpretable measures of the complexity of molecules prepared as potential drug candidates. The first is carbon bond saturation as defined by fraction sp3 (Fsp3) where Fsp3 = (number of sp3 hybridized carbons/total carbon count). The second is simply whether a chiral carbon exists in the molecule. We demonstrate that both complexity (as measured by Fsp3) and the presence of chiral centers correlate with success as compounds transition from discovery, through clinical testing, to drugs. In an attempt to explain these observations,...

Escape from flatland: increasing saturation as an approach to improving clinical success.

The application of guidelines linked to the concept of drug-likeness, such as the 'rule of five', has gained wide acceptance as an approach to reduce attrition in drug discovery and development. However, despite this acceptance, analysis of recent trends reveals that the physical properties of molecules that are currently being synthesized in leading drug discovery companies differ significantly from those of recently discovered oral drugs and compounds in clinical development. The consequences of the marked increase in lipophilicity--the most important drug-like physical property--include a greater likelihood of lack of selectivity and attrition in drug development. Tackling the threat of compound-related toxicological attrition needs to move to the mainstream of medicinal chemistry decision-making.

The influence of drug-like concepts on decision-making in medicinal chemistry

Interleukin-8 (IL-8) is a proinflammatory CXC chemokine associated with the promotion of neutrophil chemotaxis and degranulation. This chemokine activates multiple intracellular signaling pathways downstream of two cell-surface, G protein-coupled receptors (CXCR1 and CXCR2). Increased expression of IL-8 and/or its receptors has been characterized in cancer cells, endothelial cells, infiltrating neutrophils, and tumor-associated macrophages, suggesting that IL-8 may function as a significant regulatory factor within the tumor microenvironment. The induction of IL-8 signaling activates multiple upstream signaling pathways that (a) impinge on gene expression via regulation of numerous transcription factor activities, (b) modulate the cellular proteome at the level of translation, and/or (c) effect the organization of the cell cytoskeleton through posttranslational regulation of regulatory proteins. As a consequence of the diversity of effectors and downstream targets, IL-8 signaling promotes angiogenic responses in endothelial cells, increases proliferation and survival of endothelial and cancer cells, and potentiates the migration of cancer cells, endothelial cells, and infiltrating neutrophils at the tumor site. Accordingly, IL-8 expression correlates with the angiogenesis, tumorigenicity, and metastasis of tumors in numerous xenograft and orthotopic in vivo models. Recently, IL-8 signaling has been implicated in regulating the transcriptional activity of the androgen receptor, underpinning the transition to an androgen-independent proliferation of prostate cancer cells. In addition, stress and drug-induced IL-8 signaling has been shown to confer chemotherapeutic resistance in cancer cells. Therefore, inhibiting the effects of IL-8 signaling may be a significant therapeutic intervention in targeting the tumor microenvironment.

https://clincancerres.aacrjournals.org/content/clincanres/14/21/6735.full.pdf

The Interleukin-8 Pathway in Cancer

The Medicinal Chemist’s Toolbox: An Analysis of Reactions Used in the Pursuit of Drug Candidates

The Medicinal Chemist's Toolbox: An Analysis of Reactions Used in the Pursuit of Drug Candidates

The process of drug discovery applies rigorous selection pressures. Marketed oral drugs will generally possess favorable physiochemical properties with respect to absorption, metabolism, distribution, and clearance. This paper describes a study in which the distributions of physiochemical properties of oral drugs in different phases of clinical development are compared to those already marketed. The aim is to identify the trends in physiochemical properties that favor a drug's successful passage through clinical development and on to the market. Two libraries were created, one of current development oral drugs and one of marketed oral drugs. Statistical analysis of the two showed that the mean molecular weight of orally administered drugs in development decreases on passing through each of the different clinical phases and gradually converges toward the mean molecular weight of marketed oral drugs. It is also clear that the most lipophilic compounds are being discontinued from development.

A comparison of physiochemical property profiles of development and marketed oral drugs.

The apparent intrinsic clearance of 13 drugs has been determined using rat liver microsomes at three different concentrations of microsomal protein. The kinetics was studied using the in vitro half-life method. The nonspecific binding of these drugs to the microsomes was also studied under the same conditions, except for cofactor removal, using equilibrium dialysis. The intrinsic clearances are shown to be dependent on the microsomal concentration, but are approximately constant when corrected for the extent of nonspecific binding to the microsomes. The large difference between observed intrinsic clearance and unbound intrinsic clearance that exists for some compounds, particularly lipophilic bases, is highlighted. A simple model has been developed for understanding the binding of compounds to microsomes and is demonstrated to accurately predict the extent of microsomal binding at one concentration of microsomes from measurement at another. The binding of a further 25 drugs to rat liver microsomes at a microsomal concentration of 1 mg/ml was also studied, along with measurements of lipophilicity using octanol-water partition coefficients. It is shown that the extent of microsomal binding is correlated with lipophilicity, but that basic compounds show a different behavior to acidic and neutral compounds. Microsomal binding is shown to be best predicted using a model where log P is used for basic compounds, and log D(7.4) is used for acidic and neutral compounds. This model has been developed further so that the extent of binding to microsomes of any given concentration can be estimated purely from a knowledge of lipophilicity and ionization.

The influence of nonspecific microsomal binding on apparent intrinsic clearance, and its prediction from physicochemical properties.

The aim of this study was to evaluate a unified method for predicting human in vivo intrinsic clearance (CL(int, in vivo)) and hepatic clearance (CL(h)) from in vitro data in hepatocytes and microsomes by applying the unbound fraction in blood (fu(b)) and in vitro incubations (fu(inc)). Human CL(int, in vivo) was projected using in vitro data together with biological scaling factors and compared with the unbound intrinsic clearance (CL(int, ub, in vivo)) estimated from clinical data using liver models with and without the various fu terms. For incubations conducted with fetal calf serum (n=14), the observed CL(int, in vivo) was modeled well assuming fu(inc) and fu(b) were equivalent. CL(int, ub, in vivo) was predicted best using both fu(b) and fu(inc) for other hepatocyte data (n=56; r(2)=0.78, p=3.3 x 10(-19), average fold error=5.2). A similar model for CL(int, ub, in vivo) was established for microsomal data (n=37; r(2)=0.77, p=1.2 x 10(-12), average fold error=6.1). Using the model for CL(int, ub, in vivo) (including a further empirical scaling factor), the CL(h) in humans was also calculated according to the well stirred liver model for the most extensive dataset. CL(int, in vivo) and CL(h) were both predicted well using in vitro human data from several laboratories for acidic, basic, and neutral drugs. The direct use of this model using only in vitro human data to predict the metabolic component of CL(h) is attractive, as it does not require extra information from preclinical studies in animals.

https://dmd.aspetjournals.org/content/dmd/early/2005/06/02/dmd.105.004259.full.pdf

A unified model for predicting human hepatic, metabolic clearance from in vitro intrinsic clearance data in hepatocytes and microsomes

Partitioning of Ionizing Molecules between Aqueous Buffers and Phospholipid Vesicles

The binding of 17 drugs to rat hepatocytes has been determined using equilibrium dialysis in combination with metabolic inhibitors and a kinetic model for the binding and dialysis processes. Metabolic inhibitors were used to retard the main routes of metabolism such that the half-life for turnover of the drugs was comparable to or greater than the time scale of the equilibrium dialysis process. Further experiments were carried out to determine the kinetics of diffusion of the compounds across the dialysis membrane and the observed extent of binding to hepatocytes. Knowledge of the rate of metabolism of the drugs in the presence of the inhibitors, the kinetics of the dialysis process, and the observed extent of binding was then used with a kinetic model of the system to give true free fractions of the drugs in live hepatocytes. Further studies show that, for this set of compounds, there is no significant difference in the extent of binding to live or dead hepatocytes. The extent of hepatocyte binding is correlated with lipophilicity, and the best model for binding uses log P for basic compounds and log D(7.4) for acidic and neutral compounds. Hepatocyte binding is also demonstrated to be highly correlated with microsome binding.

Rupert P. Austin

Papers

A comparison of physiochemical property profiles of development and marketed oral drugs.

The influence of nonspecific microsomal binding on apparent intrinsic clearance, and its prediction from physicochemical properties.

A unified model for predicting human hepatic, metabolic clearance from in vitro intrinsic clearance data in hepatocytes and microsomes

Partitioning of Ionizing Molecules between Aqueous Buffers and Phospholipid Vesicles

The binding of drugs to hepatocytes and its relationship to physicochemical properties.