Integrating Intramolecular Hydrogen Bonding (IMHB) Considerations in Drug Discovery Using ΔlogP As a Tool

Molecular chameleons in drug discovery

Molecular chameleons possess a flexibility that allows them to dynamically shield or expose polar functionalities in response to the properties of the environment. Although the concept of molecular chameleons was introduced already in 1970, interest in them has grown considerably since the 2010s, when drug discovery has focused to an increased extent on new chemical modalities. Such modalities include cyclic peptides, macrocycles and proteolysis-targeting chimeras, all of which reside in a chemical space far from that of traditional small-molecule drugs. Both cell permeability and aqueous solubility are required for the oral absorption of drugs. Engineering these properties, and potent target binding, into the larger new modalities is a more daunting task than for traditional small-molecule drugs. The ability of chameleons to adapt to different environments may be essential for success. In this Review, we provide both general and theoretical insights into the realm of molecular chameleons. We discuss why chameleons have come into fashion and provide a do-it-yourself toolbox for their design; we then provide a glimpse of how advanced in silico methods can support molecular chameleon design.

Oral Absorption of Middle-to-Large Molecules and Its Improvement, with a Focus on New Modality Drugs

To meet unmet medical needs, middle-to-large molecules, including peptides and oligonucleotides, have emerged as new therapeutic modalities. Owing to their middle-to-large molecular sizes, middle-to-large molecules are not suitable for oral absorption, but there are high expectations around orally bioavailable macromolecular drugs, since oral administration is the most convenient dosing route. Therefore, extensive efforts have been made to create bioavailable middle-to-large molecules or develop absorption enhancement technology, from which some successes have recently been reported. For example, Rybelsus® tablets and Mycapssa® capsules, both of which contain absorption enhancers, were approved as oral medications for type 2 diabetes and acromegaly, respectively. The oral administration of Rybelsus and Mycapssa exposes their pharmacologically active peptides with molecular weights greater than 1000, namely, semaglutide and octreotide, respectively, into systemic circulation. Although these two medications represent major achievements in the development of orally absorbable peptide formulations, the oral bioavailability of peptides after taking Rybelsus and Mycapssa is still only around 1%. In this article, we review the approaches and recent advances of orally bioavailable middle-to-large molecules and discuss challenges for improving their oral absorption.

Development and test of highly accurate endpoint free energy methods. 3: partition coefficient prediction using a Poisson-Boltzmann method combined with a solvent accessible surface area model for SAMPL challenges

Accurately predicting solvation free energy is the key to predict protein-ligand binding free energy. In addition, the partition coefficient (log P), which is an important physicochemical property that determines the distribution of a drug in vivo, can be derived directly from transfer free energies, i.e., the difference between solvation free energies (SFEs) in different solvents. Within the Statistical Assessment of the Modeling of Proteins and Ligands (SAMPL) 9 challenge, we applied the Poisson-Boltzmann (PB) surface area (SA) approach to predict the toluene/water transfer free energy and partition coefficient (log Ptoluene/water) from SFEs. For each solute, only a single conformation automatically generated by the free software Open Babel was used. The PB calculation directly adopts our previously optimized boundary definition - a set of general AMBER force field 2 (GAFF2) atom-type based sphere radii for solute atoms. For the non-polar SA model, we newly developed the solvent-related molecular surface tension parameters γ and offset b for toluene and cyclohexane targeting experimental SFEs. This approach yielded the highest predictive accuracy in terms of root mean square error (RMSE) of 1.52 kcal mol-1 in transfer free energy for 16 small drug molecules among all 18 submissions in the SAMPL9 blind prediction challenge. The re-evaluation of the challenge set using multi-conformation strategies based on molecular dynamics (MD) simulations further reduces the prediction RMSE to 1.33 kcal mol-1. At the same time, an additional evaluation of our PBSA method on the SAMPL5 cyclohexane/water distribution coefficient (log Dcyclohexane/water) prediction revealed that our model outperformed COSMO-RS, the best submission model with RMSEPBSA = 1.88 versus RMSECOSMO-RS = 2.11 log units. Two external log Ptoluene/water and log Pcyclohexane/water datasets that contain 110 and 87 data points, respectively, are collected for extra validation and provide an in-depth insight into the error source of the PBSA method.

Intramolecular O···H Hydrogen Bonding of Salicylic Acid: Further Insights from O 1s XPS and 1H NMR Spectra Using DFT Calculations

Intramolecular hydrogen bonding (HB) is a complex phenomenon that extends beyond a simple valence event, affecting the core electrons of a molecule. Salicylic acid (SA) and its conformers provide an excellent model compound for studying intramolecular HB as the proton donor (H) and acceptor (O) can be toggled by rotating the C-O and C-C bonds to form up to seven potential conformers through various HB. In this study, we computationally investigated intramolecular interactions in SA conformers with and without such HB, by examining their calculated O 1s core electron-binding energy (CEBE) and ¹H NMR chemical shifts validated using recent measurements. The quantum mechanically stable SA conformers are fully defined by three rotatable bonds in the compound, which are abstracted as SA(η₁η₂η₃) digital structures, where η_i = 0 if the η_i angles match the most stable SA conformer (000) and η_i = 1 otherwise. Our findings suggest that the stability is dominated by the appearance of the intergroup intramolecular HB of H_p···O (where O is in the carboxylic acid functional group and H_p is the phenolic proton in -OH_p), and η₃ serves as a switch of such HB. As a result, the (η₁η₂0) SA conformers containing such H_p···O HB are more stable than other SA conformers (η₁η₂1) without such the H_p···O HB. The present density functional theory calculations reveal that this H_p···O HB results in splitting of the O 1s CEBEs of two hydroxyl groups (-OH) by up to 1 eV and deshielding the H_p proton ¹H NMR (δH_p) up to 11.68 ppm for the (η₁η₂0) conformers. Without such H_p···O HB, the O 1s XPS binding energies of two -OH groups will be closely located in the same band, and the ¹H NMR chemical shift of the H_p atom will be as small as an 4.09 ppm SA conformer [SA-G(101)]. The present study indicates that the O 1s CEBE splitting between two -OH groups serves as an indicator of the presence of the H_p···O HB in SA conformers, which is also supported by the ¹H NMR results.

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 pK_a 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.

Conformational Sampling Deciphers the Chameleonic Properties of a VHL-Based Degrader

Chameleonicity (the capacity of a molecule to adapt its conformations to the environment) may help to identify orally bioavailable drugs in the beyond-Rule-of-5 chemical space. Computational methods to predict the chameleonic behaviour of degraders have not yet been reported and the identification of molecular chameleons still relies on experimental evidence. Therefore, there is a need to tune predictions with experimental data. Here, we employ PROTAC-1 (a passively cell-permeable degrader), for which NMR and physicochemical data prove the chameleonic behaviour, to benchmark the capacity of two conformational sampling algorithms and selection schemes. To characterize the conformational ensembles in both polar and nonpolar environments, we compute three molecular properties proven to be essential for cell permeability: conformer shape (radius of gyration), polarity (3D PSA), and the number of intramolecular hydrogen bonds. Energetic criteria were also considered. Infographics monitored the simultaneous variation of those properties in computed and NMR conformers. Overall, we provide key points for tuning conformational sampling tools to reproduce PROTAC-1 chameleonicity according to NMR evidence. This study is expected to improve the design of PROTAC drugs and the development of computational sustainable strategies to exploit the potential of new modalities in drug discovery.

SiO2-supported HClO4 catalyzed synthesis of (Z)-thiazolylhydrazonoindolin-2-ones and their electrochemical properties

In this paper, an environmentally benign silica-supported perchloric acid (HClO₄-SiO₂) catalyzed green FCDR strategy has been developed for the synthesis of (Z)-THIs (6) with high stereospecificity via an intramolecular hydrogen bond (IHB) directed approach, involving the reaction of methyl ketones (1), N-bromosuccinimide (NBS) (2), isatins (4) and thiosemicarbazide (5) in ethanol at reflux temperature for 45-60 min in one-pot. The reaction proceeds through the construction of C-Br (α-bromination), C-S & C-N (heterocyclization), and CN (condensation) bonds in one pot. The absolute structure of the compound (Z)-3-(2-(4-(4-bromophenyl)thiazol-2-yl)hydrazono)indolin-2-one (6e) has been confirmed by single-crystal XRD analysis. Further, the role of IHB on Z-configuration of the synthesized (Z)-THIs is proved by single-crystal XRD and ¹H NMR studies. Wide substrate scope, good functional group tolerance, scalability, improved safety since the method circumvents the use of highly lachrymatric α-bromoketones as starting materials, high product yields (up to 98%), short reaction times, reusable solid Brønsted acid catalyst (HClO₄-SiO₂), and products that do not require column chromatography purification are all attractive features of this FCDR strategy. Electrochemical properties of THIs (6) are examined by cyclic voltammetry. The HOMO and LUMO energy level of THIs, 6a, 6c, 6d, 6j, 6o-6v, 6y, and 6aa are comparable with the reported ambipolar materials, and the HOMO levels of other THIs, 6b, 6e-6i, 6n, 6w, 6x, 6z and 6 ab-6ae are similar with the most commonly used hole transporting materials (HTMs).

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.

A story of peptides, lipophilicity and chromatography - back and forth in time

Peptides, as part of the beyond the rule of 5 (bRo5) chemical space, represent a unique class of pharmaceutical compounds. Because of their exceptional position in the chemical space between traditional small molecules (molecular weight (MW) < 500 Da) and large therapeutic proteins (MW > 5000 Da), peptides became promising candidates for targeting challenging binding sites, including even targets traditionally considered as undruggable - e.g. intracellular protein-protein interactions. However, basic knowledge about physicochemical properties that are important for a drug to be membrane permeable is missing but would enhance the drug discovery process of bRo5 molecules. Consequently, there is a demand for quick and simple lipophilicity determination methods for peptides. In comparison to the traditional lipophilicity determination methods via shake flask and in silico prediction, chromatography-based methods could have multiple benefits such as the requirement of low analyte amount, insensitivity to impurities and high throughput. Herein we elucidate the role of peptide lipophilicity and different lipophilicity values. Further, we summarize peptide analysis via common chromatographic techniques, in specific reversed phase liquid chromatography, hydrophilic interaction liquid chromatography and supercritical fluid chromatography and their role in drug discovery and development process.

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.

Molecular characteristics of several drugs evaluated from solvent/water partition measurements: Solvation parameters and intramolecular hydrogen bond indicator

A wide set of well-known drugs, most of them included in the Abraham´s reference database, covering a wide variety of chemical structures and therapeutical functionalities were chosen in order to determine some molecular properties from solvent/water partition measurements. Partition data from aqueous solutions and four different solvents (n-dodecane, toluene, chloroform and n-octanol) were measured and reported. From them, Abraham´s molecular descriptors of selected compounds (A, B and S, accounting for hydrogen bond donor, hydrogen bond acceptor and dipolarity/polaritzability, respectively) were estimated. A and B values derived from the experimental measurements strongly agree with the tabulated ones showing the suitability of the used procedure to achieve reliable values for new molecules. However, obtained S values differ from those previously reported for several compounds. Moreover, values for a new indicator of the propensity to form intramolecular hydrogen bonds (Δlog P_oct-tol) were estimated from the experimental data and also calculated according to both, the Abraham´s model and the molecular structures (SMD). The quality of both series of calculated descriptors was evaluated by contrast with the experimental values and satisfactory results were obtained in both instances. Thus, the Abraham´s way is useful when molecular descriptors are available but very good estimations can be achieved by SMD, which only requires the drug´s molecular structure.

Amide-to-Ester Substitution as a Strategy for Optimizing PROTAC Permeability and Cellular Activity

Criteria for predicting the druglike properties of "beyond Rule of 5" Proteolysis Targeting Chimeras (PROTAC) degraders are underdeveloped. PROTAC components are often combined via amide couplings due to their reliability. Amides, however, can give rise to poor absorption, distribution, metabolism, and excretion (ADME) properties. We hypothesized that a bioisosteric amide-to-ester substitution could lead to improvements in both physicochemical properties and bioactivity. Using model compounds, bearing either amides or esters, we identify parameters for optimal lipophilicity and permeability. We applied these learnings to design a set of novel amide-to-ester-substituted, VHL-based BET degraders with the goal to increase permeability. Our ester PROTACs retained intracellular stability, were overall more potent degraders than their amide counterparts, and showed an earlier onset of the hook effect. These enhancements were driven by greater cell permeability rather than improvements in ternary complex formation. This largely unexplored amide-to-ester substitution provides a simple strategy to enhance PROTAC permeability and bioactivity and may prove beneficial to other beyond Ro5 molecules.

Rational Control of Molecular Properties Is Mandatory to Exploit the Potential of PROTACs as Oral Drugs

To obtain new oral drugs in the beyond rule of five space, PROTACs among others, molecular properties should be optimized in early drug discovery. Degraders call for design strategies which focus on intramolecular interaction and chameleonicity. In parallel, tailored revalidation of permeability assessment and prediction methods becomes fundamental in this innovative chemical space.

Prediction of Chameleonic Efficiency

Chameleonic properties, i. e., the capacity of a molecule to hide polarity in non-polar environments and expose it in water, help achieving sufficient permeability and solubility for drug molecules with high MW. We present models of experimental measures of polarity for a set of 24 FDA approved drugs (MW 405-1113) and one PROTAC (MW 1034). Conformational ensembles in aqueous and non-polar environments were generated using molecular dynamics. A linear regression model that predicts chromatographic apparent polarity (EPSA) with a mean unsigned error of 10 Ų was derived based on separate terms for donor, acceptor, and total molecular SASA. A good correlation (R² =0.92) with an experimental measure of hydrogen bond donor potential, Δlog P_oct-tol , was found for the mean hydrogen bond donor SASA of the conformational ensemble scaled with Abraham's A hydrogen bond acidity. Two quantitative measures of chameleonic behaviour, the chameleonic efficiency indices, are introduced. We envision that the methods presented herein will be useful to triage designed molecules and prioritize those with the best chance of achieving acceptable permeability and solubility.

A new method for detecting intramolecular H-bonds of aromatic amides based on the de-shielding effect of carbonyl groups on β-protons

Aromatic amide foldamers with highly predictable conformations possess potential for application in the fields of stereoselective recognition, charge transport and catalysis, whose conformations are commonly limited by the intramolecular hydrogen bonding between amide groups and hydrogen-bonding receptors. Herein, on the basis of the de-shielding effect of carbonyl groups on β-protons, we develop a new method for detecting intramolecular hydrogen bonds of aromatic amide compounds. The solvent-related changes in the βH chemical shifts (Δ(δβH)) and NH chemical shifts (Δ(δNH)) of three kinds of amide compounds, which are frequently used as building blocks of aromatic amide foldamers, were recorded in chloroform, nitromethane, acetonitrile and DMSO. The Δ(δβH) method is found to be highly suitable for studying methoxy-benzamides and fluoro-benzamides in chloroform and DMSO. It is worth noting that a reference compound is not required for applying the Δ(δβH) method, which is an advantage over the Δ(δNH) method. In addition, we extend the Δ(δNH) method from methoxy-benzamides to pyridine-carboxamides and fluoro-benzamides in chloroform and DMSO, and propose that nitromethane and acetonitrile will be possible alternatives for the Δ(δNH) method if a test compound is not soluble in chloroform.

Pharmacokinetics-Driven Evaluation of the Antioxidant Activity of Curcuminoids and Their Major Reduced Metabolites-A Medicinal Chemistry Approach

Curcuminoids are the main bioactive components of the well-known Asian spice and traditional medicine turmeric. Curcuminoids have poor chemical stability and bioavailability; in vivo they are rapidly metabolized to a set of bioreduced derivatives and/or glucuronide and sulfate conjugates. The reduced curcuminoid metabolites were also reported to exert various bioactivities in vitro and in vivo. In this work, we aimed to perform a comparative evaluation of curcuminoids and their hydrogenated metabolites from a medicinal chemistry point of view, by determining a set of key pharmacokinetic parameters and evaluating antioxidant potential in relation to such properties.Reduced metabolites were prepared from curcumin and demethoxycurcumin through continuous-flow hydrogenation. As selected pharmacokinetic parameters, kinetic solubility, chemical stability, metabolic stability in human liver microsomes, and parallel artificial membrane permeability assay (PAMPA)-based gastrointestinal and blood-brain barrier permeability were determined. Experimentally determined logP for hydrocurcumins in octanol-water and toluene-water systems provided valuable data on the tendency for intramolecular hydrogen bonding by these compounds. Drug likeness of the compounds were further evaluated by a in silico calculations. Antioxidant properties in diphenyl-2-picrylhydrazyl (DPPH) radical scavenging and oxygen radical absorbance capacity (ORAC) assays were comparatively evaluated through the determination of ligand lipophilic efficiency (LLE). Our results showed dramatically increased water solubility and chemical stability for the reduced metabolites as compared to their corresponding parent compound. Hexahydrocurcumin was found the best candidate for drug development based on a complex pharmacokinetical comparison and high LLE values for its antioxidant properties. Development of tetrahydrocurcumin and tetrahydro-demethoxycurcumin would be limited by their very poor metabolic stability, therefore such an effort would rely on formulations bypassing first-pass metabolism.

Structure, solubility, and permeability relationships in a diverse middle molecule library

To develop methodology to predict the potential druggability of middle molecules, we examined the structure, solubility, and permeability relationships of a diverse library (HKDL ver.1) consisting of 510 molecules (359 natural product derivatives, 76 non-natural products, 46 natural products, and 29 non-natural product derivatives). The library included peptides, depsipeptides, macrolides, and lignans, and 476 of the 510 compounds had a molecular weight in the range of 500-2000 Da. The solubility and passive diffusion velocity of the middle molecules were assessed using the parallel artificial membrane permeability assay (PAMPA). Quantitative values of solubility of 471 molecules and passive diffusion velocity of 287 molecules were obtained, and their correlations with the structural features of the molecules were examined. Based on the results, we propose a method to predict the passive diffusion characteristics of middle molecules from their three-dimensional structural features.

Structure property relationships of N-acylsulfonamides and related bioisosteres

The N-acylsulfonamide functional group is a feature of the pharmacophore of several biologically active molecules, including marketed drugs. Although this acidic moiety presents multiple points of attachments that could be exploited to introduce structural diversification, depending on the circumstances, the replacement of the functional group itself with a suitable surrogate, or bioisostere, may be desirable. A number of N-acylsulfonamide bioisosteres have been developed over the years that provide opportunities to modulate both structure and physicochemical properties of this important structural motif. To enable an assessment of the relative impact on physicochemical properties that these replacements may have compared to the N-acylsulfonamide group, we conducted a structure-property relationship study based on matched molecular pairs, in which the N-acylsulfonamide moiety of common template reference structures is replaced with a series of bioisosteres. The data presented, which include an assessment of relative changes in acidity, permeability, lipophilicity and intrinsic solubility, provides a basis for informed decisions when deploying N-acylsulfonamides, or surrogates thereof, in analog design.

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.

Hyaluronic Acid Conjugated Metformin-Phospholipid Sonocomplex: A Biphasic Complexation Approach to Correct Hypoxic Tumour Microenvironment

Purpose

Development of hyaluronic acid conjugated metformin-phospholipid sonocomplexes (HA-MPS), a biphasic complexation product compiled for enhancing both the lipophilicity and targeting potential of Metformin (MET) to CD44 receptors on pancreatic cancer.

Methods

MET was chemically conjugated to hyaluronic acid (HA) via amide coupling reaction. Then, the HA conjugated MET was physically conjugated to Lipoid™S100 via ultrasound irradiation. A combined D-optimal design was implemented to statistically optimize formulation variables. The HA-MPS were characterized through solubility studies, partition coefficient, drug content uniformity, particle size and zeta potential. The optimized HA-MPS was tested via proton nuclear magnetic resonance, infrared spectroscopy to elucidate the nature of physicochemical interactions in the complex which was further scrutinized on molecular level via molecular docking and dynamic simulation.

Results

The solubility and partition studies showed a lipophilicity enhancement up to 67 folds as they adopted inverted micelles configuration based on the packing parameter hypothesis. The optimized HA-MPS showed 11.5 folds lower IC₅₀, extra 25% reduction in oxygen consumption rate, better reduction in hypoxia-inducible factor and reactive oxygen species in MiaPaCa-2 cells.

Conclusion

These results proved better internalization of MET which was reflected by abolishing hypoxic tumour microenvironment, a mainstay toward a normoxic and less resistant pancreatic cancer.

Steering New Drug Discovery Campaigns: Permeability, Solubility, and Physicochemical Properties in the bRo5 Chemical Space

An increasing number of drug discovery programs concern compounds in the beyond rule of 5 (bRo5) chemical space, such as cyclic peptides, macrocycles, and degraders. Recent results show that common paradigms of property-based drug design need revision to be applied to larger and more flexible compounds. A virtual event entitled "Solubility, permeability and physico-chemical properties in the bRo5 chemical space" was organized to provide preliminary guidance on how to make the discovery of oral drugs in the bRo5 space more effective. The four speakers emphasized the importance of the bRo5 space as a source of new oral drugs and provided examples of experimental and computational methods specifically tailored for design and optimization in this chemical space.

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 (pK_a measures and log k'80 PLRP-S trends), lipophilicity (in octanol/water, in apolar systems and in biomimetic environments), polarity (Δlog P_oct-tol, EPSA and Δlog K_W^IAM) 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 P_oct-tol and preliminary data support that chameleonicity could also have an impact.

Could we expect new praziquantel derivatives? A meta pharmacometrics/pharmacoinformatics analysis of all antischistosomal praziquantel derivatives found in the literature

Praziquantel (PZQ) is the first line drug for the treatment of human Schistosoma spp. worm infections. However, it suffers from low activity towards immature stages of the worm, and its prolonged use induces resistance/tolerance. During the last 40 years, 263 PZQ analogues have been synthesized and tested against Schistosoma spp. worms, but less than 10% of them showed significant activity. Here, we propose a rationalization of the chemical space of the PZQ derivatives by a ligand-based approach. First, we constructed an in-house database with all PZQ derivatives available in the literature. This analysis shows a high heterogeneity in the data. Fortunately, all studies include PZQ as a reference, permitting the classification of compounds into three classes according to their activities. Models involving ligand-based pharmacophore and logistic regression were performed. Five physicochemical parameters were identified as the best to explain the biological activity. In the end, we proposed new PZQ derivatives with modifications at positions 1 and 7, we analysed them with our models, and we observed that they can be more active than the previously synthesized derivatives. The main goal of this work was to conduct the most valuable meta-pharmacometrics/pharmacoinformatics analysis with all Praziquantel medicinal chemistry data available in the literature.

Derivatives of 3-Aminopyrazine-2-carboxamides: Synthesis, Antimicrobial Evaluation, and in Vitro Cytotoxicity

We report the design, synthesis, and in vitro antimicrobial activity of a series of N-substituted 3-aminopyrazine-2-carboxamides with free amino groups in position 3 on the pyrazine ring. Based on various substituents on the carboxamidic moiety, the series is subdivided into benzyl, alkyl, and phenyl derivatives. The three-dimensional structures of the title compounds were predicted using energy minimization and low mode molecular dynamics under AMBER10:EHT forcefield. Compounds were evaluated for antimycobacterial, antibacterial, and antifungal activities in vitro. The most active compound against Mycobacterium tuberculosis H37Rv (Mtb) was 3-amino-N-(2,4-dimethoxyphenyl)pyrazine-2-carboxamide (17, MIC = 12.5 µg/mL, 46 µM). Antimycobacterial activity against Mtb and M. kansasii along with antibacterial activity increased among the alkyl derivatives with increasing the length of carbon side chain. Antibacterial activity was observed for phenyl and alkyl derivatives, but not for benzyl derivatives. Antifungal activity was observed in all structural subtypes, mainly against Trichophyton interdigitale and Candida albicans. The four most active compounds (compounds 10, 16, 17, 20) were evaluated for their in vitro cytotoxicity in HepG2 cancer cell line; only compound 20 was found to exert some level of cytotoxicity. Compounds belonging to the current series were compared to previously published, structurally related compounds in terms of antimicrobial activity to draw structure activity relationships conclusions.

Use of a Conformational-Switching Mechanism to Modulate Exposed Polarity: Discovery of CCR2 Antagonist BMS-741672

We encountered a dilemma in the course of studying a series of antagonists of the G-protein coupled receptor CC chemokine receptor-2 (CCR2): compounds with polar C3 side chains exhibited good ion channel selectivity but poor oral bioavailability, whereas compounds with lipophilic C3 side chains exhibited good oral bioavailability in preclinical species but poor ion channel selectivity. Attempts to solve this through the direct modulation of physicochemical properties failed. However, the installation of a protonation-dependent conformational switching mechanism resolved the problem because it enabled a highly selective and relatively polar molecule to access a small population of a conformer with lower polar surface area and higher membrane permeability. Optimization of the overall properties in this series yielded the CCR2 antagonist BMS-741672 (7), which embodied properties suitable for study in human clinical trials.

Intramolecular hydrogen bonding: An opportunity for improved design in medicinal chemistry

Recent literature shows that intramolecular hydrogen bond (IMHB) formation can positively impact upon the triad of permeability, solubility, and potency of drugs and candidates. IMHB modulation can be applied to compounds in any chemical space as a means for discovering drug candidates with both acceptable potency and absorption, distribution, metabolism, and excretion-Tox profiles. Integrating IMHB formation in design of drugs is, therefore, an exciting and timely challenge for modern medicinal chemistry. In this review, we first provide some background about IMHBs from the medicinal chemist's point of view and highlight some IMHB-associated misconceptions. Second, we propose a classification of IMHBs for drug discovery purposes, review the most common in silico tactics to include IMHBs in lead optimization and list some experimental physicochemical descriptors, which quantify the propensity of compounds to form IMHBs. By focusing on the compounds size and the number of IMHBs that can potentially be formed, we also outline the major difficulties encountered when designing compounds based on the inclusion of IMHBs. Finally, we discuss recent case studies illustrating the application of IMHB to optimize cell permeability and physicochemical properties of small molecules, cyclic peptides and macrocycles.

Modulating intramolecular chalcogen bonds in aromatic (thio)(seleno)phene-based derivatives

Intramolecular chalcogen interactions have been studied for four different derivatives of compounds within two different families, S or Se, to evaluate the effect of these IMChBs in the stability of the interacting and non-interacting systems.

Discovery of a Potent and Orally Bioavailable Cyclophilin Inhibitor Derived from the Sanglifehrin Macrocycle

Cyclophilins are a family of peptidyl-prolyl isomerases that are implicated in a wide range of diseases including hepatitis C. Our aim was to discover through total synthesis an orally bioavailable, non-immunosuppressive cyclophilin (Cyp) inhibitor with potent anti-hepatitis C virus (HCV) activity that could serve as part of an all oral antiviral combination therapy. An initial lead 2 derived from the sanglifehrin A macrocycle was optimized using structure based design to produce a potent and orally bioavailable inhibitor 3. The macrocycle ring size was reduced by one atom, and an internal hydrogen bond drove improved permeability and drug-like properties. 3 demonstrates potent Cyp inhibition ( K_d = 5 nM), potent anti-HCV 2a activity (EC₅₀ = 98 nM), and high oral bioavailability in rat (100%) and dog (55%). The synthetic accessibility and properties of 3 support its potential as an anti-HCV agent and for interrogating the role of Cyp inhibition in a variety of diseases.

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 P_oct is largely used for optimization purposes, in this paper we firstly use the Block Relevance (BR) analysis to theoretically show how log P_oct is not a convenient choice to assess IMHB properties of candidates. Then we discuss the limits of log P_oct and introduce Δlog P_oct-tol, i.e. the difference between log P_oct and log P_tol (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 P_oct-tol values.

Impact of Dynamically Exposed Polarity on Permeability and Solubility of Chameleonic Drugs Beyond the Rule of 5

Conformational flexibility has been proposed to significantly affect drug properties outside rule-of-5 (Ro5) chemical space. Here, we investigated the influence of dynamically exposed polarity on cell permeability and aqueous solubility for a structurally diverse set of drugs and clinical candidates far beyond the Ro5, all of which populated multiple distinct conformations as revealed by X-ray crystallography. Efflux-inhibited (passive) Caco-2 cell permeability correlated strongly with the compounds' minimum solvent-accessible 3D polar surface areas (PSA), whereas aqueous solubility depended less on the specific 3D conformation. Inspection of the crystal structures highlighted flexibly linked aromatic side chains and dynamically forming intramolecular hydrogen bonds as particularly effective in providing "chameleonic" properties that allow compounds to display both high cell permeability and aqueous solubility. These structural features, in combination with permeability predictions based on the correlation to solvent-accessible 3D PSA, should inspire drug design in the challenging chemical space far beyond the Ro5.

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 K_w^IAM data. Then we applied block relevance (BR) analysis to extract from PLS models the relative contribution of intermolecular forces governing log K_w^IAM and Δlog K_w^IAM (a combined descriptor calculated from log K_w^IAM). Finally, the relationship between log K_w^IAM, Δlog K_w^IAM 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.

Systematic Optimization of Liquid-Liquid Extraction for Isolation of Unidentified Components

We present a systematic approach for predicting the best solvents for selective extraction of components with unknown structure from complex mixtures (e.g., natural products)-a tool promising dramatic simplification of extraction process optimization. Its key advantage is that identification of the component(s) is unnecessary-prediction is based on a small set of experimental distribution coefficients (obtained using a combination of shake-flask extraction and chromatographic analysis) rather than structure-based descriptors. The methodology is suitable for the very common situations in practice where the desired compound needs to be separated from unknown impurities (i.e., selectively extracted from the mixture), as well as for large-scale and high-throughput work. The proof-of-concept methodology was developed and evaluated using an extensive set of experimental distribution data of lignin-related compounds obtained in this work.

High throughput methods to measure the propensity of compounds to form intramolecular hydrogen bonding

Implementation of IMHB considerations in drug discovery needs robust and validated descriptors to experimentally verify the propensity of compounds to exhibit IMHBs. The first part of the paper presents an overview of the most common techniques to measure the propensity of compounds to form IMHBs. Then we review and discuss recently proposed high throughput (HT) physicochemical descriptors (i.e. Δlog Poct-tol, EPSA and log k'80 PLRP-S) which provide the same information. Analysis of the available data enabled us to extract guidelines for the application of these descriptors in drug discovery programs.

The influence of hydrogen bonding on partition coefficients

This Perspective explores how consideration of hydrogen bonding can be used to both predict and better understand partition coefficients. It is shown how polarity of both compounds and substructures can be estimated from measured alkane/water partition coefficients. When polarity is defined in this manner, hydrogen bond donors are typically less polar than hydrogen bond acceptors. Analysis of alkane/water partition coefficients in conjunction with molecular electrostatic potential calculations suggests that aromatic chloro substituents may be less lipophilic than is generally believed and that some of the effect of chloro-substitution stems from making the aromatic π-cloud less available to hydrogen bond donors. Relationships between polarity and calculated hydrogen bond basicity are derived for aromatic nitrogen and carbonyl oxygen. Aligned hydrogen bond acceptors appear to present special challenges for prediction of alkane/water partition coefficients and this may reflect 'frustration' of solvation resulting from overlapping hydration spheres. It is also shown how calculated hydrogen bond basicity can be used to model the effect of aromatic aza-substitution on octanol/water partition coefficients.

A simple and facile NMR method for the determination of hydrogen bonding by amide N–H protons in protein models and other compounds

It is shown that measurements of the ¹H chemical shifts of amide N–H protons in chloroform and in DMSO solvents are sufficient to determine the extent of hydrogen bonding of the N–H protons in a variety of compounds containing the amide group.

Updating molecular properties during early drug discovery

Current multiparameter optimization (MPO) strategies make use of few experimental physicochemical descriptors (i.e., solubility at physiological pH and lipophilicity in the octanol/water system). Here, we show how new trends in drug discovery (i.e., large and flexible molecules for 'difficult' targets) call for the integration of ad hoc descriptors in MPO approaches. In particular, to rank, select, and optimize drug candidates, it could be relevant to have experimental data relating to the acid-base properties and the folding of the molecule to mask polar groups (so-called 'chameleonic' properties). We propose two strategies to quantify ionization and chameleonic properties and discuss their practical integration in property criteria profiles.

Cell permeability beyond the rule of 5

Drug discovery for difficult targets that have large and flat binding sites is often better suited to compounds beyond the "rule of 5" (bRo5). However, such compounds carry higher pharmacokinetic risks, such as low solubility and permeability, and increased efflux and metabolism. Interestingly, recent drug approvals and studies suggest that cell permeable and orally bioavailable drugs can be discovered far into bRo5 space. Tactics such as reduction or shielding of polarity by N-methylation, bulky side chains and intramolecular hydrogen bonds may be used to increase cell permeability in this space, but often results in decreased solubility. Conformationally flexible compounds can, however, combine high permeability and solubility, properties that are keys for cell permeability and intestinal absorption. Recent developments in computational conformational analysis will aid design of such compounds and hence prediction of cell permeability. Transporter mediated efflux occurs for most investigated drugs in bRo5 space, however it is commonly overcome by high local intestinal concentrations on oral administration. In contrast, there is little data to support significant impact of transporter-mediated intestinal absorption in bRo5 space. Current knowledge of compound properties that govern transporter effects of bRo5 drugs is limited and requires further fundamental and comprehensive studies.