High-throughput and reliable assessments of the ionization constant of monoprotic organic acids through an arginine based mixed mode HPLC.

The charge state of a molecule is the single most prominent attribute ruling out its interactions with the surrounding environment. In a previous study, the retention of acids on the new Celeris™ Arginine (ARG) column was found to be predominantly driven by electrostatics and, specifically, their charge state. Therefore, we analysed 41 compounds in liquid chromatography with ultraviolet detection to study possible relationships between the analytical retention on this phase and the pKa of the acidic solutes. Highly significant relationships were observed indicating either a linear (r2 = 0.86) or a quadratic (r2= 0.89) trend. To improve the throughput of the method, this was transferred to LC mass spectrometry, allowing the analysis of a molecule every 3 mins. The developed method was found to be fast, reliable, accurate, easily automatable and simple to set up. Finally, the analytical column's being industrially manufactured and commercially available offers broad applicability.

Chamelogk: A Chromatographic Chameleonicity Quantifier to Design Orally Bioavailable Beyond-Rule-of-5 Drugs.

New chemical modalities in drug discovery include molecules belonging to the bRo5 chemical space. Because of their complex and flexible structure, bRo5 compounds often suffer from a poor solubility/permeability profile. Chameleonicity describes the capacity of a molecule to adapt to the environment through conformational changes; the design of molecular chameleons is a medicinal chemistry strategy simultaneously optimizing solubility and permeability. A default method to quantify chameleonicity in early drug discovery is still missing. Here we introduce Chamelogk, an automated, fast, and cheap chromatographic descriptor of chameleonicity. Moreover, we report measurements for 55 Ro5 and bRo5 compounds and validate our method with literature data. Then, selected case studies (macrocycles, nonmacrocyclic compounds, and PROTACs) are used to illustrate the application of Chamelogk in combination with lipophilicity (BRlogD) and polarity (Δ log kwIAM) descriptors. Overall, we show how Chamelogk deserves being included in property-based drug discovery strategies to design oral bioavailable bRo5 compounds.

Ionization and lipophilicity in nonpolar media mimicking the cell membrane interior.

Ionization and lipophilicity may vary with the environment. Therefore, in this study we provide some insight in the performances of different experimental techniques (potentiometry, UV-vis, shake-flask and chromatography) to determine ionization and lipophilicity in more nonpolar systems than those commonly used in drug discovery. To this purpose a pool of 11 compounds of pharmaceutical interest was firstly submitted to a few experimental techniques to measure pKa in water, water/acetonitrile mixtures and pure acetonitrile. Then we measured logP/logD with shake-flask and potentiometry in octanol/water and toluene/water and also determined a chromatographic lipophilicity index (log k'80 PLRP-S) in a nonpolar system. Results show that ionization decreases for both acids and bases in a coherent, significant but not dramatical extent when water is present in the system, but the picture is completely different in pure acetonitrile. Lipophilicity may vary or not with the environment according to the chemical structure of the investigated compounds as also revealed by electrostatic potential maps. Since the internal core of cell membranes is largely nonpolar, our results support the need of extending the pool of physicochemical descriptors to be determined in the various stages of drug discovery programs and indicate some experimental strategies for their determination.

Refinement of Computational Access to Molecular Physicochemical Properties: From Ro5 to bRo5.

There is a need of computational tools to rank bRo5 drug candidates in the very early phases of drug discovery when chemical matter is unavailable. In this study, we selected three compounds: (a) a Ro5 drug (Pomalidomide), (b) a bRo5 orally available drug (Saquinavir), and (c) a polar PROTAC (CMP 98) to focus on computational access to physicochemical properties. To provide a benchmark, the three compounds were first experimentally characterized for their lipophilicity, polarity, IMHBs, and chameleonicity. To reproduce the experimental information content, we generated conformer ensembles with conformational sampling and molecular dynamics in both water and nonpolar solvents. Then we calculated Rgyr, 3D PSA, and IMHB number. An innovative pool of strategies for data analysis was then provided. Overall, we report a contribution to close the gap between experimental and computational methods for characterizing bRo5 physicochemical properties.

Designing Soluble PROTACs: Strategies and Preliminary Guidelines.

Solubility optimization is a crucial step to obtaining oral PROTACs. Here we measured the thermodynamic solubilities (log S) of 21 commercial PROTACs. Next, we measured BRlogD and log kwIAM (lipophilicity), EPSA, and Δ log kwIAM (polarity) and showed that lipophilicity plays a major role in governing log S, but a contribution of polarity cannot be neglected. Two-/three-dimensional descriptors calculated on conformers arising from conformational sampling and steered molecular dynamics failed in modeling solubility. Infographic tools were used to identify a privileged region of soluble PROTACs in a chemical space defined by BRlogD, log kwIAM and topological polar surface area, while machine learning provided a log S classification model. Finally, for three pairs of PROTACs we measured the solubility, lipophilicity, and polarity of the building blocks and identified the limits of estimating PROTAC solubility from the synthetic components. Overall, this paper provides promising guidelines for optimizing PROTAC solubility in early drug discovery programs.

Application of the anthraquinone drug rhein as an axial ligand in bifunctional Pt(IV) complexes to obtain antiproliferative agents against human glioblastoma cells.

Octahedral Pt(IV) prodrugs are an effective way to combine cisplatin-like moieties and a second drug to obtain selective and stimuli responsive bifunctional antiproliferative compounds. Recently, two bifunctional Pt(IV) complexes have shown interesting in vitro and in vivo effects in glioblastoma, the most aggressive primary brain tumor. An interesting observation indicates that 4,5-dihydroxy-9,10-dioxo-9,10-dihydroanthracene-2-carboxylic acid (rhein) can inhibit in vivo glioma tumor progression. Furthermore, a prodrug in which cisplatin was combined with two molecules of rhein showed a potency higher than that of cisplatin toward cisplatin-resistant lung carcinoma cells. However, the high lipophilicity of this type of complex affects their solubility and bioavailability. To overcome these limits, in the present work, three Pt(IV) derivatives were obtained by differently linking one molecule of rhein and one acetato ligand at the axial position to a cisplatin core. The complexes proved to be similar to or more potent than the parent cisplatin and rhein, and the reference drug temozolomide on two human glioblastoma cell lines (U87-MG and T98G). They retained their activity under hypoxia and caused a significant reduction in the motility of both cell lines, which can be related to their ability to inhibit MMP2 and MMP9 matrix metalloproteinases. Finally, physicochemical and computational studies indicated that these Pt(IV) derivatives are more prone than rhein to cross the blood-brain barrier.

Acid-base and lipophilic properties of peptide nucleic acid derivatives.

The first combined experimental and theoretical study on the ionization and lipophilic properties of peptide nucleic acid (PNA) derivatives, including eleven PNA monomers and two PNA decamers, is described. The acidity constants (pKa) of individual acidic and basic centers of PNA monomers were measured by automated potentiometric pH titrations in water/methanol solution, and these values were found to be in agreement with those obtained by MoKa software. These results indicate that single nucleobases do not change their pKa values when included in PNA monomers and oligomers. In addition, immobilized artificial membrane chromatography was employed to evaluate the lipophilic properties of PNA monomers and oligomers, which showed the PNA derivatives had poor affinity towards membrane phospholipids, and confirmed their scarce cell penetrating ability. Overall, our study not only is of potential relevance to evaluate the pharmacokinetic properties of PNA, but also constitutes a reliable basis to properly modify PNA to obtain mimics with enhanced cell penetration properties.

Managing Experimental 3D Structures in the Beyond-Rule-of-5 Chemical Space: The Case of Rifampicin.

The beyond-Rule-of-5 (bRo5) chemical space is a source of new oral drugs and includes large and flexible compounds. Because of their size and conformational variability, bRo5 molecules assume different privileged conformations in the compartments of human body, i. e., they can exhibit chameleonic properties. The elucidation of the ensemble of 3D structures explored by such molecules under different conditions is therefore critical to check the role played by chameleonicity to modulate cell permeability. Here we characterized the conformational ensembles of rifampicin, a bRo5 drug, in polar and nonpolar solvents and in the solid state. We performed NMR experiments, analyzed their results with a novel algorithm and set-up a pool of ad hoc in silico strategies to investigate crystallographic structures retrieved from the CSD. Moreover, a polarity descriptor often related to permeability (SA-3D-PSA) was calculated for all the conformers and its variation with the environment analyzed. Results showed that the conformational behavior of rifampicin in solution and in the solid state is not superposable. The identification of dynamic intramolecular hydrogen bonds can be assessed by NMR spectroscopy but not by X-ray structures. Moreover, SA-3D-PSA revealed that dynamic IMHBs do not provide rifampicin with chameleonic properties. Overall, this study highlights that the peculiarity of rifampicin, which is cell permeable probably because of the presence of static IMHBs but is devoid of any chameleonic behavior, can be assessed by a proper analysis of experimental 3D structures.

Characterization of the new CelerisTM Arginine column: Retentive behaviour through a combination of chemometric tools and potential in drug analysis.

CelerisTM Arginine (ARG) is a mixed-mode stationary phase recently released on the market. To characterize its analytical behavior, the retention factors of a pool (n=100, of which 36 neutrals, 26 acids and 38 bases) of pharmaceutically relevant compounds have been measured on this phase over eight percentages (from 10 to 90% v/v) of acetonitrile (MeCN) as organic modifier. The ARG phase exhibited enhanced affinity for the molecules that are in their anionic form at the experimental pH, whilst basic compounds, albeit over a wide range of lipophilicity and pKa values, were on average poorly retained. To dissect the separation mechanism of the ARG phase, the overall analytical retention has been deconvoluted into the individual contributions of intermolecular forces by a QSPR/ Partial Least Square (PLS)/Block Relevance (BR) analysis tool recently developed by us. For the neutrals, the most relevant blocks were found to be Size, describing the interaction due to the dimension of the molecule, and O, representing the solute's hydrogen bond donor properties. The change in sign from positive to negative of the Size block, which occurs between 10% and 20% MeCN, allowed to visually appreciate the switch in the separation mode from reversed phase to normal phase. Some good statistic models for rationalizing the analytical behaviour of neutrals were developed from VS+ descriptors. However, their performance in modelling the analytical retention of acids was substandard, probably due to the intrinsic inefficacy of VS+ descriptors in handling electric charges. This instance was addressed by a complimentary MLR strategy, which led to successfully model the retention of acids on the ARG column and to shed light into their retention mechanism, which seemed to be substantially driven by electrostatics.

Permeability prediction in the beyond-Rule-of 5 chemical space: Focus on cyclic hexapeptides.

Cyclic peptides (CPs) are gaining more and more relevance in drug discovery. Since one of their main drawbacks is poor permeability, the discovery of new orally available CP drugs requires computational tools that predict CP permeability in very early drug discovery. In this study we used a literature dataset of 62 cyclic hexapeptides to evaluate the performances of a number of in silico tools based on different computational theory to model and rationalize PAMPA and Caco-2 permeability values. In particular, we submitted the dataset to a) online calculators, b) QSPR strategies, c) a physics-based tool, d) a mixed approach and e) a kinetic method. This latter is an emergent strategy in which a few relevant conformations retrieved from a set of molecular dynamics (MD) simulations by the Markov State Model (MSM) are used to establish the compounds permeability. Both free and commercial software were used. Results were compared with a model based on experimental physicochemical descriptors. All the computational approaches but online calculators performed quite well and show that lipophilicity and not polarity is the main determinant of the investigated event. A second major outcome of the study is that the impact of flexibility on the permeability of the considered dataset cannot be unambiguously assessed. Finally, our comparative analysis, which also included not common applied strategies, allowed a sound evaluation of the pros and cons of the applied computational approaches.

Rifampicin as an example of beyond-rule-of-5 compound: Ionization beyond water and lipophilicity beyond octanol/water.

Ionization and lipophilicity in early drug discovery are commonly characterized in water and octanol/water, respectively and thus do not consider the non-polar features of the biomembrane core. This is particularly limiting for bRo5 compounds which may adapt their properties (e.g. ionization and lipophilicity) to the environment. In this paper we used experimental methods to characterize rifampicin for its ionization properties in various water/cosolvent mixtures and in pure MeCN and its lipophilicity in octanol/water and toluene/water systems. Moreover, we also measured log k'80 PLRP-S, a chromatographic index of lipophilicity in non-polar media. Results show that the existence domain of neutral rifampicin is limited compared to the zwitterion, but the lipophilic cationic species is extremely relevant in non-polar environments.

Pt(iv) complexes based on cyclohexanediamines and the histone deacetylase inhibitor 2-(2-propynyl)octanoic acid: synthesis, characterization, cell penetration properties and antitumor activity.

The Pt(iv) complexes based on (SP-4-2)-dichlorido(cyclohexane-1,4-diamine)platinum(ii) (kiteplatin) and the histone deacetylase inhibitor 2-(2-propynyl)octanoic acid (POA) were investigated. Since POA contains a chiral carbon, all the possible Pt(iv) isomers were prepared and characterized, and their antiproliferative activity on six cancer cell lines was compared with that of the corresponding Pt(iv) complexes containing the cyclohexane-1R,2R-diamine equatorial ligand. To justify the very good antiproliferative activity (nanomolar IC50), the polarity, lipophilicity, permeability, and cell accumulation of the complexes were studied. Overall, the two series of Pt(iv) complexes showed similar cell penetration properties, being significantly better than that of the Pt(ii) reference compounds. Finally, a representative compound of the whole set of complexes (i.e., that based on cyclohexane-1R,2R-diamine and racemic POA) was tested in vivo on mice bearing Lewis lung carcinoma, showing good tumor growth inhibition with negligible body weight loss.

The Block Relevance (BR) Analysis Makes the Choice of Methods for Measuring Lipophilicity and Permeability Safer and Speeds Up Drug Candidate Prioritization.

The Block Relevance (BR) analysis with its recent implementation in MATLAB is a computational tool that allows deconvoluting the balance of intermolecular interactions governing a given drug discoveryrelated phenomenon described by a QSPR/PLS model. Here we discuss a few applications to show how BR analysis can make faster and more efficient the assessment of the drug-likeness of drug candidates. First, we describe how identifying the best chromatographic system provides reliable log Poct surrogates and log P in apolar environments. Then we focus on permeability and show how BR analysis allows to check the universality of passive permeability among cell types and the identification of the PAMPA method that provides the same picture in terms of balance of intermolecular interactions as cell-based systems.

Degraders early developability assessment: face-to-face with molecular properties.

Pharmaceutical scientists have huge expectations from heterobifunctional small molecule degraders to treat diseases with an unmet medical need. However, degraders are large and flexible and pose significant challenges in terms of cellular uptake and bioavailability. An efficient property-based design is therefore required to discover new oral degrader medicines. Here, we show the non­transferability to degraders of in silico tools routinely implemented in small molecule drug discovery programs; and provide ionization, lipophilicity, polarity and chameleonicity data for a series of seven degraders. We also reveal that permeability can be modeled by Δlog kWIAM - an experimental polarity descriptor. Overall, the paper is a proof-of-concept that shows to discover new oral degrader drugs ad hoc property-based design strategies are required.

Updating the portfolio of physicochemical descriptors related to permeability in the beyond the rule of 5 chemical space.

Beyond rule of 5 (bRo5) molecules are attracting significant interest in modern drug discovery mostly because many novel targets require large and more flexible structures. The main aim of this paper is the identification of ad hoc bRo5 physicochemical descriptors of ionization, lipophilicity, polarity and chameleonicity and their measurement. We used different methods to collect ionization (pKa measures and log k'80 PLRP-S trends), lipophilicity (in octanol/water, in apolar systems and in biomimetic environments), polarity (Δlog Poct-tol, EPSA and Δlog KWIAM) and chameleonicity (ChameLogD) descriptors for 26 bRo5 drugs. A second aim was to check the relationship between physicochemical descriptors and permeability for a subset of compounds for which solid permeability values are reported in the literature. Results showed that the physicochemical profile in the bRo5 chemical space is often experimentally accessible, albeit more tools are required to overcome limitations of individual methods. For the investigated compounds, permeability is governed by Δlog Poct-tol and preliminary data support that chameleonicity could also have an impact.

Chromatographic HILIC indexes to characterize the lipophilicity of zwitterions.

Reverse phase high pressure liquid chromatography (RP-HPLC) is widely employed in drug discovery for lipophilicity measurements. Hydrophilic interaction liquid chromatography (HILIC) may represent a good alternative to RP-HPLC in the determination of the lipophilicity of hydrophilic compounds like zwitterions. In this paper three different HILIC stationary phases (ZIC®-HILIC, ZIC®-pHILIC and ZIC®-cHILIC) and two different mobile phases (80%ACN/20%buffer and 90%ACN/10%buffer) were combined to set-up six chromatographic systems. A computational tool named Block Relevance (BR) analysis was firstly used to deconvolute the balance of intermolecular forces governing retention in the six systems. Then the lipophilicity profiles (log k vs pH) of ten model ampholytes were determined. Results support that the lipophilicity of zwitterions at any pH can be successfully determined with a ZIC®-cHILIC stationary phase and an 80%ACN/20%buffer mobile phase. To extend the dataset and confirm results, a second series of zwitterionic drugs was also analyzed.

Solubility prediction in the bRo5 chemical space: where are we right now?

Modelling the solubility of compounds in the "beyond Rule of 5" (bRo5) chemical space is in its infancy and to date only a few studies have been reported in the literature. Based on our own results, and those already published, we conclude that consideration of conformational flexibility and chameleon like behaviour is important, but quantitative models that account for these properties remain to be developed. Inclusion of 3D information appears to be somewhat less important than for cell permeability and extremely challenging due to the difficulties of accurate conformational sampling in the bRo5 space. Currently, methods for modelling of solubility will have to be tailored to the set of investigated compounds.

Permeability prediction for zwitterions via chromatographic indexes and classification into 'certain' and 'uncertain'.

Background: The development of zwitterions to a drug is likely to be more challenging than compounds of other charge types. Results: Two chromatographic indexes (log k'80 PLRP-S and log KWIAM) can be successfully used as permeability classifiers of ampholytes. Moreover, a pragmatic classification into ordinary ampholytes; zwitterions 'certain' (i.e., the zwitterionic species is dominant in the physiological pH range); and zwitterions 'uncertain' (multiple species are present in the physiological pH range) enables to study the permeability of ampholytic compounds in relation to species distribution. Methodology: Potentiometry (pKa), reversed-phase (RP)-chromatography, tri-layer parallel artificial membrane permeability assays, quantitative structure-property relationships (QSPR) and block relevance (BR) analysis, receiver operating characteristic (ROC) curves. Conclusion: Structures considered as poorly permeable like zwitterions can be integrated in drug discovery programs by applying ad hoc experimental and computational tools.

Log P as a tool in intramolecular hydrogen bond considerations.

Intramolecular hydrogen bonding (IMHB) considerations are gaining relevance in drug discovery and a molecular descriptor which can predict very early the capacity of a compound to form IMHB is needed to speed up the optimization process of drug candidates. Although log Poct is largely used for optimization purposes, in this paper we firstly use the Block Relevance (BR) analysis to theoretically show how log Poct is not a convenient choice to assess IMHB properties of candidates. Then we discuss the limits of log Poct and introduce Δlog Poct-tol, i.e. the difference between log Poct and log Ptol (the logarithm of the partition coefficient in the toluene/water system). Finally, we provided some examples also including bRo5 protease inhibitors, to clarify how to interpret Δlog Poct-tol values.

Learning how to use IAM chromatography for predicting permeability.

The interest for IAM (Immobilized Artificial Membranes) chromatography in the prediction of drug permeability is increasing. Here we firstly set-up a dataset of 253 molecules including neutral and ionized drugs and few organic compounds for which we either measured or retrieved from the literature IAM.PC.DD2 log KwIAM data. Then we applied block relevance (BR) analysis to extract from PLS models the relative contribution of intermolecular forces governing log KwIAM and Δlog KwIAM (a combined descriptor calculated from log KwIAM). Finally, the relationship between log KwIAM, Δlog KwIAM and passive permeability determined in both PAMPA and MDCK-LE systems was looked for. Models provided the basis for a rational application of IAM chromatography in permeability prediction.