Beyond Size, Ionization State, and Lipophilicity: Influence of Molecular Topology on Absorption, Distribution, Metabolism, Excretion, and Toxicity for Druglike Compounds

Beyond cytotoxic potency: disposition features required to design ADC payload

1. Antibody-drug conjugates (ADCs) have demonstrated impressive clinical usefulness in treating several types of cancer, with the notion of widening of the therapeutic index of the cytotoxic payload through the minimisation of the systemic toxicity. Therefore, choosing the most appropriate payload molecule is a particularly important part of the early design phase of ADC development, especially given the highly competitive environment ADCs find themselves in today.2. The focus of the current review is to describe critical attributes/considerations needed in the discovery and ultimately development of cytotoxic payloads in support of ADC design. In addition to potency, several key dispositional characteristics including solubility, permeability and bystander effect, pharmacokinetics, metabolism, and drug-drug interactions, are described as being an integral part of the integrated activities required in the design of clinically safe and useful ADC therapeutic agents.

Structure-based virtual screening of mangiferin derivatives with antidiabetic action: a molecular docking and dynamics study and MPO-based drug-likeness approach

Extracts from Mangifera indica leaves and its main component, mangiferin, have proven antidiabetic activity. In this study, mangiferin and its natural derivatives Homomangiferin (HMF), Isomangiferin (IMF), Neomangiferin (NMF), Glucomangiferin (GMF), Mangiferin 6'-gallate (MFG), and Norathyriol (NRT) were compared regarding their action on Diabetes mellitus (DM), employing docking and molecular dynamics (MD) simulations to analyze interactions with the aldose reductase enzyme, the precursor to the conversion of glucose into sorbitol. Notably, HMF showed significant affinity to residues in the active site of the enzyme, including Trp 79, His 110, Trp 111, Phe 122, and Phe 300, with an energy of - 7.2 kcal/mol, observed in the molecular docking simulations. MD reinforced the formation of stable complexes for HMF and MFG with the aldose reductase, with interaction potential energies (IPE) in the order of - 300.812 ± 52 kJ/mol and - 304.812 ± 52 kJ/mol, respectively. The drug-likeness assessment, by multiparameter optimization (MPO), highlighted that HMF and IMF have similarities with polyphenols and glycosidic flavonoids recently patented as antidiabetics, revealing that high polarity (TPSA > 180 Å2) is a favorable property for subcutaneous administration, especially because of the gradual passive cell permeability values in biological tissues, with Papp values estimated at < 10 × 10-6 cm/s. These compounds are metabolically stable against metabolic enzymes, resulting in a low toxic incidence by metabolic activation, corroborating with a lethal dose (LD50) greater than 2000 mg/kg. In this way, HMF showed a systematic alignment between predicted pharmacokinetics and pharmacodynamics, characterizing it as the most favorable substance for inhibiting aldose reductase.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-024-03978-9.

Identification and dynamics of novel scaffolds against Enterococcus faecium serine hydroxymethyltransferase enzyme: a potential target for antibiotics development

Serine hydroxymethyltransferase enzyme is a significant player in purine, thymidylate, and L-serine biosynthesis and has been tagged as a potential target for cancer, viruses, and parasites. However, this enzyme as an anti-bacterial druggable target has not been explored much. Herein, in this work, different computational chemistry and biophysics techniques were applied to identify potential computational predicted inhibitory molecules against Enterococcus faecium serine hydroxymethyltransferase enzyme. By structure based virtual screening process of ASINEX antibacterial library against the enzyme two main compounds: Top-1_BDC_21204033 and Top-2_BDC_20700155 were reported as best binding molecules. The Top-1_BDC_21204033 and Top-2_BDC_20700155 binding energy value is -9.3 and -8.9 kcal/mol, respectively. The control molecule binding energy score is -6.55 kcal/mol. The mean RMSD of Top-1-BDC_21204033, Top-2-BDC_20700155 and control is 3.7 Å (maximum 5.03 Å), 1.7 Å (maximum 3.05 Å), and 3.84 Å (maximum of 6.7 Å), respectively. During the simulation time, the intermolecular docked conformation and interactions were seen stable despite of few small jumps by the compounds/control, responsible for high RMSD in some frames. The MM/GBSA and MM/PBSA binding free energy of lead Top-2-BDC_20700155 complex is -79.52 and -82.63 kcal/mol, respectively. This complex was seen as the most stable compared to the control. Furthermore, the lead molecules and control showed good druglikeness and pharmacokinetics profile. The lead molecules were non-toxic and non-mutagenic. In short, the compounds are promising in terms of binding to the serine hydroxymethyltransferase enzyme and need to be subjected to experimental studies.Communicated by Ramaswamy H. Sarma.

The Role of Allylic Strain for Conformational Control in Medicinal Chemistry

It is axiomatic in medicinal chemistry that optimization of the potency of a small molecule at a macromolecular target requires complementarity between the ligand and target. In order to minimize the conformational penalty on binding, both enthalpically and entropically, it is therefore preferred to have the ligand preorganized in the bound conformation. In this Perspective, we highlight the role of allylic strain in controlling conformational preferences. Allylic strain was originally described for carbon-based allylic systems, but the same principles apply to other types of structure with sp² or pseudo-sp² arrangements. These systems include benzylic (including heteroaryl methyl) positions, amides, N-aryl groups, aryl ethers, and nucleotides. We have derived torsion profiles from small molecule X-ray structures for these systems. Through multiple examples, we show how these effects have been applied in drug discovery and how they can be used prospectively to influence conformation in the design process.

The Chemical Space of Marine Antibacterials: Diphenyl Ethers, Benzophenones, Xanthones, and Anthraquinones

The emergence of multiresistant bacteria and the shortage of antibacterials in the drug pipeline creates the need to search for novel agents. Evolution drives the optimization of the structure of marine natural products to act as antibacterial agents. Polyketides are a vast and structurally diverse family of compounds that have been isolated from different marine microorganisms. Within the different polyketides, benzophenones, diphenyl ethers, anthraquinones, and xanthones have shown promising antibacterial activity. In this work, a dataset of 246 marine polyketides has been identified. In order to characterize the chemical space occupied by these marine polyketides, molecular descriptors and fingerprints were calculated. Molecular descriptors were analyzed according to the scaffold, and principal component analysis was performed to identify the relationships among the different descriptors. Generally, the identified marine polyketides are unsaturated, water-insoluble compounds. Among the different polyketides, diphenyl ethers tend to be more lipophilic and non-polar than the remaining classes. Molecular fingerprints were used to group the polyketides according to their molecular similarity into clusters. A total of 76 clusters were obtained, with a loose threshold for the Butina clustering algorithm, highlighting the large structural diversity of the marine polyketides. The large structural diversity was also evidenced by the visualization trees map assembled using the tree map (TMAP) unsupervised machine-learning method. The available antibacterial activity data were examined in terms of bacterial strains, and the activity data were used to rank the compounds according to their antibacterial potential. This potential ranking was used to identify the most promising compounds (four compounds) which can inspire the development of new structural analogs with better potency and absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties.

Discovery of structural diverse reversible BTK inhibitors utilized to develop a novel in vivo CD69 and CD86 PK/PD mouse model

For the past two decades, BTK a tyrosine kinase and member of the Tec family has been a drug target of significant interest due to its potential to selectively treat various B cell-mediated diseases such as CLL, MCL, RA, and MS. Owning to the challenges encountered in identifying drug candidates exhibiting the potency block B cell activation via BTK inhibition, the pharmaceutical industry has relied on the use of covalent/irreversible inhibitors to address this unmet medical need. Herein, we describe a medicinal chemistry campaign to identify structurally diverse reversible BTK inhibitors originating from HITS identified using a fragment base screen. The leads were optimized to improve the potency and in vivo ADME properties resulting in a structurally distinct chemical series used to develop and validate a novel in vivo CD69 and CD86 PD assay in rodents.

Revisiting the Use of Quantum Chemical Calculations in LogPoctanol-water Prediction

The partition coefficients of drug and drug-like molecules between an aqueous and organic phase are an important property for developing new therapeutics. The predictive power of computational methods is used extensively to predict partition coefficients of molecules. The application of quantum chemical calculations is used to develop methods to develop structure-activity relationship models for such prediction, either based on molecular fragment methods, or via direct calculation of solvation free energy in solvent continuum. The applicability, merits, and shortcomings of these developments are revisited here.

Manipulations of phenylnorbornyl palladium species for multicomponent construction of a bridged polycyclic privileged scaffold

Hexahydromethanocarbazole is a privileged scaffold in the discovery of new drugs and photoactive organic materials due to its good balance between structural complexity and minimized entropy penalty upon receptor binding. To address the difficulty of synthesizing this highly desirable bridged polycyclic scaffold, we designed a convenient multicomponent reaction cascade as intercepted Heck addition/C-H activation/C-palladacycle formation/electrophilic attack of ANP/N-palladacycle formation/Buchwald amination. A distinguishing feature of this sophisticated strategy is the successive generation of two key phenylnorbornyl palladium species to control the reaction flow towards desired products. DFT calculations further reveal the crucial roles of Cs₂CO₃ and 5,6-diester substitutions on the norbornene reactant in preventing multiple side-reactions. This innovative method exhibits a broad scope with good yields, and therefore will enable the construction of natural-product-like compound libraries based on hexahydromethanocarbazole.

Design, Synthesis, and Biological Evaluations of Pyridyl 4,5,6,7-Tetrahydro-4,7-Methanobenzo[d]isoxazoles as Potent and Selective Inhibitors of 11β-Hydroxylase

Inhibition of CYP11B1 is a promising therapy for severe diseases caused by excessive cortisol. Enantiomer discrimination provides clues to achieve selectivity that CYP11B1 and homologous CYP11B2 were selectively bound by S- and R-fadrozole, respectively, in distinct binding modes. Pyridyl 4,5,6,7-tetrahydro-4,7-methanobenzo[d]isoxazoles showing a similar binding mode to S-fadrozole in CYP11B1 were designed as potent and selective CYP11B1 inhibitors. Compound 7aa exhibited a highly potent CYP11B1 inhibition similar to that of the drug osilodrostat (IC₅₀'s of 9 and 6 nM, respectively) but was 1500-fold more selective over CYP11B2 compared to osilodrostat (selectivity factors of 125 versus 0.08, respectively). Strong reductions of plasma cortisol concentrations by compound 7aa were demonstrated in rats without interference in aldosterone production after oral application. It showed no inhibition against a panel of steroidogenic and hepatic CYP enzymes. Exhibiting a good pharmacokinetic profile, compound 7aa was considered as a drug candidate for further development.

Probing the biomolecular (DNA/BSA) interaction by new Pd(II) complex via in-depth experimental and computational perspectives: synthesis, characterization, cytotoxicity, and DFT approach

Scientists should not forget that the rate of death as a result of cancer is far more than that of other diseases like influenza or coronavirus (COVID-19), so the research in this field is of cardinal significance. Therefore, a new and hydrophilic palladium(II) complex of the general formula [Pd(bpy)(proli-dtc)]NO₃, in which bpy and proli-dtc are 2,2'-bipyridine and pyrroline dithiocarbamate ligands, respectively, was synthesized and characterized utilizing spectral and analytical procedures. Density functional theory (DFT) calculation was also performed with B3LYP method in the gas phase. The DFT and spectral analysis specified that the Pd(II) atom is found in a square-planar geometry. HOMO/LUMO analysis, quantum chemical parameters and MEP surface of the complex were investigated to acquire an intuition about the nature of the compound. Partition coefficient and water solubility determination showed that both lipophilicity and hydrophilicity of the compound are more than cisplatin. The 50% inhibition concentration (IC₅₀) value was evaluated against K562 cancer cells, the obtained result has revealed a promising cytotoxic effect. DNA and BSA binding of the complex were explored through multi-spectroscopic (UV–Vis, fluorescence, FRET, and CD) and non-spectroscopic (gel electrophoresis, viscosity and docking simulation) techniques. The obtained findings demonstrated that the complex strongly interacts with CT-DNA by hydrophobic interactions and possesses medium interaction with BSA via hydrogen bond and van der Waals forces, thus BSA could efficiently carry out complex transportation. Furthermore, the results of docking simulation agree well with the experimental findings. In conclusion, the new Pd(II) complex has cytotoxic activity and could interact with DNA and BSA effectively.

Modulating Conformational Preferences by Allylic Strain toward Improved Physical Properties and Binding Interactions

The preference of the axial over the equatorial orientation of 2-substitutent for both phenyl-1-piperidines and N-acylpiperidines is studied at the M06-2X level of theory. For phenyl-1-piperidines, the axial 2-substituent is modestly favored over the equatorial one. In contrast, the pseudoallylic strain in N-acylpiperidines dictates the axial orientation of 2-substituent with a ΔG up to -3.2 kcal/mol. The calculations agree well with the statistics from both the Cambridge Structural Database of small-molecule organic crystal structures and the Protein Data Bank. The equilibrium between the twist-boat and chair conformations for N-acylpiperidines with a 2-substituent was further investigated. The twist-boat conformation is found to be around 1.5 kcal/mol less favorable. Finally, the three-dimensionality in shape resulting from minimization of the pseudoallylic strain is characterized, and its implication in protein-ligand interactions is briefly reviewed.

Chemical Space Expansion of Flavonoids: Induction of Mitotic Inhibition by Replacing Ring B with a 10π-Electron System, Benzo[b]thiophene

Natural products, which are enzymatically biosynthesized, have a broad range of biological activities. In particular, many flavonoids are known to contribute to human health with low toxicity. We previously reported that novel benzo[b]thiophenyl (BT) flavones with a 10π-electron BT ring B replacing the usual 6π-electron phenyl ring showed potent antiproliferative activity against human tumor cell lines. Interestingly, the activity profiles against cell cycle progression of the BT-flavones totally changed depending on the combination of substituents at the C-3 and C-5 positions. This finding encouraged an extension of these studies on the impact of BT to related flavonoids, such as chalcones, isoflavones, and aurones. Accordingly, 10 isoflavones, 29 chalcones, and four aurones were synthesized and evaluated for antiproliferative activity against five human tumor cell lines including a multi-drug-resistant cell line. Among these compounds, BT-isoflavone 7, BT-chalcones 48, 52, 57, 66, and 77, and BT-aurone 80 displayed significant antiproliferative effects against all tested tumor cell lines. The structure-antiproliferative activity relationships clearly demonstrated the importance of BT instead of phenyl as ring B for the isoflavone and chalcones, but not the aurones. Flow cytometry and immunocytochemical studies demonstrated that the active BT-flavonoids led to cell cycle arrest at the prometaphase by induction of multipolar spindle formation. The present studies should contribute greatly to the synthesis and functional analysis of biologically active flavonoid derivatives for chemical space expansion.

Highly stereoselective synthesis of spirocyclopropylthiooxindoles and biological evaluation

We present a novel highly stereoselective Rh-catalyzed cyclopropanation of diazothiooxindoles with a broad range of α-functionalized styrenes, enabling facile access of chiral spirocyclopropylthiooxindoles in high to excellent enantiomeric excess.

Discovery of 3-amino-4-{(3S)-3-[(2-ethoxyethoxy)methyl]piperidin-1-yl}thieno[2,3-b]pyridine-2-carboxamide (DS96432529): A potent and orally active bone anabolic agent

The continuing investigation of SAR of 3-aminothieno[2,3-b]pyridine-2-carboxamide derivatives has been described. In this study, C4-piperidine derivatives with polar functional groups were synthesized to develop orally available bone anabolic agents. The optimized compound 9o (DS96432529), which exhibited the best PK profile and high in vitro activity, showed the highest in vivo efficacy in this series. Moreover, significant synergistic effects were observed following co-administration of DS96432529 and alendronate or parathyroid hormone. The mechanism of action is most likely mediated through CDK8 inhibition.

ChemBead Enabled High-Throughput Cross-Electrophile Coupling Reveals a New Complementary Ligand

High-throughput experimentation (HTE) methods are central to modern medicinal chemistry. While many HTE approaches to C-N and Csp2 -Csp2 bonds are available, options for Csp2 -Csp3 bonds are limited. We report here how the adaptation of nickel-catalyzed cross-electrophile coupling of aryl bromides with alkyl halides to HTE is enabled by AbbVie ChemBeads technology. By using this approach, we were able to quickly map out the reactivity space at a global level with a challenging array of 3×222 micromolar reactions. The observed hit rate (56 %) is competitive with other often-used HTE reactions and the results are scalable. A key to this level of success was the finding that bipyridine 6-carboxamidine (BpyCam), a ligand that had not previously been shown to be optimal in any reaction, is as general as the best-known ligands with complementary reactivity. Such "cryptic" catalysts may be common and modern HTE methods should facilitate the process of finding these catalysts.

Metal Complexes for Therapeutic Applications

Metal complexes have been widely used for applications in the chemical and physical sciences due to their unique electronic and stereochemical properties. For decades the use of metal complexes for medicinal applications has been postulated and demonstrated. The distinct characteristics of metal complexes, including their molecular geometries (that are not readily accessed by organic molecules), as well as their ligand exchange, redox, catalytic, and photophysical reactions, give these compounds the potential to interact and react with biomolecules in unique ways and by distinct mechanisms of action. Herein, the potential of metal complexes to act as components bioactive therapeutic compounds is discussed.

Effects of substituent pattern on the intracellular target of antiproliferative benzo[b]thiophenyl chromone derivatives

A new biological scaffold was produced by replacing the 6π-electron phenyl ring-B of a natural flavone skeleton with a 10π-electron benzothiophene (BT). Since aromatic rings are important for ligand protein interactions, this expansion of the π-electron system of ring-B might change the bioactivity profile. One of the resulting novel natural product-inspired compounds, 2-(benzo[b]thiophen-3-yl)-5-hydroxy-7-isopropoxy-6-methoxyflavone (6), effectively arrested the cell cycle at the G2/M phase and displayed significant antiproliferative effects with IC₅₀ values of 0.05-0.08 μM against multiple human tumor cell lines, including a multidrug resistant line. A structure-activity relationship study revealed that a 10π-electron system with high aromaticity, juxtaposed 4-oxo and 5-hydroxy groups, and 7-alkoxy groups were important for potent antimitotic activity. Interestingly, two BT-flavonols (3-hydroxyflavone), 16 and 20, with 3-hydroxy and 5-alkoxy groups, induced distinct biological profiles affecting the cell cycle at the G1/S phase by inhibition of DNA replication through an interaction with topoisomerase I.

Recent Experimental Developments in Studying Passive Membrane Transport of Drug Molecules

The ability to measure the passive membrane permeation of drug-like molecules is of fundamental biological and pharmaceutical importance. Of significance, passive diffusion across the cellular membranes plays an effective role in the delivery of many pharmaceutical agents to intracellular targets. Hence, approaches for quantitative measurement of membrane permeability have been the topics of research for decades, resulting in sophisticated biomimetic systems coupled with advanced techniques. In this review, recent developments in experimental approaches along with theoretical models for quantitative and real-time analysis of membrane transport of drug-like molecules through mimetic and living cell membranes are discussed. The focus is on time-resolved fluorescence-based, surface plasmon resonance, and second-harmonic light scattering approaches. The current understanding of how properties of the membrane and permeant affect the permeation process is discussed.

Discovery of 1-[2-(1-methyl-1H-pyrazol-5-yl)-[1,2,4]triazolo[1,5-a]pyridin-6-yl]-3-(pyridin-4-ylmethyl)urea as a potent NAMPT (nicotinamide phosphoribosyltransferase) activator with attenuated CYP inhibition

Nicotinamide phosphoribosyltransferase (NAMPT) catalyzes the rate-limiting step of the NAD⁺ salvage pathway. Since NAD⁺ plays a pivotal role in many biological processes including metabolism and aging, activation of NAMPT is an attractive therapeutic target for treatment of diverse array of diseases. Herein, we report the continued optimization of novel urea-containing derivatives which were identified as potent NAMPT activators. Early optimization of HTS hits afforded compound 12, with a triazolopyridine core, as a lead compound. CYP direct inhibition (DI) was identified as an issue of concern, and was resolved through modulation of lipophilicity to culminate in 1-[2-(1-methyl-1H-pyrazol-5-yl)-[1,2,4]triazolo[1,5-a]pyridin-6-yl]-3-(pyridin-4-ylmethyl)urea (21), which showed potent NAMPT activity accompanied with attenuated CYP DI towards multiple CYP isoforms.

Development of a Hierarchical Support Vector Regression-Based In Silico Model for Caco-2 Permeability

Drug absorption is one of the critical factors that should be taken into account in the process of drug discovery and development. The human colon carcinoma cell layer (Caco-2) model has been frequently used as a surrogate to preliminarily investigate the intestinal absorption. In this study, a quantitative structure–activity relationship (QSAR) model was generated using the innovative machine learning-based hierarchical support vector regression (HSVR) scheme to depict the exceedingly confounding passive diffusion and transporter-mediated active transport. The HSVR model displayed good agreement with the experimental values of the training samples, test samples, and outlier samples. The predictivity of HSVR was further validated by a mock test and verified by various stringent statistical criteria. Consequently, this HSVR model can be employed to forecast the Caco-2 permeability to assist drug discovery and development.

Opportunities for Tapping into Three-Dimensional Chemical Space through a Quaternary Carbon

A quaternary carbon bears four other carbon substituents or combination of four non-hydrogen substituents at four vertices of a tetrahedron. The spirocyclic quaternary carbon positioned at the center of a bioactive molecule offers conformational rigidity, which in turn reduces the penalty for conformational entropy. The quaternary carbon is a predominant feature of natural product structures and has been associated with more effective and selective binding to target proteins compared to planar compounds with a high sp² count. The presence of a quaternary carbon stereocenter allows the exploration of novel chemical space to obtain new molecules with enhanced three-dimensionality. These characteristics, coupled to an increasing awareness to develop sp³-rich molecules, boosted utility of quaternary carbon stereocenters in bioactive compounds. It is hoped that this Perspective will inspire the chemist to utilize quaternary carbon stereocenters to enhance potency, selectivity, and other drug-like properties.

Facts, Patterns, and Principles in Drug Discovery: Appraising the Rule of 5 with Measured Physicochemical Data

The rule of 5 was designed to estimate the likelihood of poor absorption or permeation, noting the impact of poor solubility. This Perspective explores the impact of various physicochemical descriptors and contemporary lipophilicity measurements on permeability and solubility, showing that the distribution coefficient log D_7.4 (rather than log P) is the most impactful parameter. Molecular weight, almost invariably the defining characteristic of "beyond the rule of 5" compounds, has little impact on solubility when log D_7.4 measurements and aromaticity are considered. Predicting permeation is more complex, given passive and carrier transport mechanisms; however, notable patterns of behavior are apparent, giving insight even "beyond the rule of 5". Recommended best practices should involve using the facts (measurements) and the patterns they reveal to establish informative principles rather than fastidious rules.

FlavoDb: a web-based chemical repository of flavonoid compounds

There are many online resources that focus on chemical diversity of natural compounds, but only handful of resources exist that focus solely on flavonoid compounds and integrate structural and functional properties; however, extensive collated flavonoid literature is still unavailable to scientific community. Here we present an open access database 'FlavoDb' that is focused on providing physicochemical properties as well as topological descriptors that can be effectively implemented in deducing large scale quantitative structure property models of flavonoid compounds. In the current version of database, we present data on 1, 19,400 flavonoid compounds, thereby covering most of the known structural space of flavonoid class of compounds. Moreover, effective structure searching tool presented here is expected to provide an interactive and easy-to-use tool for obtaining flavonoid-based literature and allied information. Data from FlavoDb can be freely accessed via its intuitive graphical user interface made available at following web address: http://bioinfo.net.in/flavodb/home.html.

Aldehyde oxidase and its role as a drug metabolizing enzyme

Aldehyde oxidase (AO) is a cytosolic enzyme that belongs to the family of structurally related molybdoflavoproteins like xanthine oxidase (XO). The enzyme is characterized by broad substrate specificity and marked species differences. It catalyzes the oxidation of aromatic and aliphatic aldehydes and various heteroaromatic rings as well as reduction of several functional groups. The references to AO and its role in metabolism date back to the 1950s, but the importance of this enzyme in the metabolism of drugs has emerged in the past fifteen years. Several reviews on the role of AO in drug metabolism have been published in the past decade indicative of the growing interest in the enzyme and its influence in drug metabolism. Here, we present a comprehensive monograph of AO as a drug metabolizing enzyme with emphasis on marketed drugs as well as other xenobiotics, as substrates and inhibitors. Although the number of drugs that are primarily metabolized by AO are few, the impact of AO on drug development has been extensive. We also discuss the effect of AO on the systemic exposure and clearance these clinical candidates. The review provides a comprehensive analysis of drug discovery compounds involving AO with the focus on developmental candidates that were reported in the past five years with regards to pharmacokinetics and toxicity. While there is only one known report of AO-mediated clinically relevant drug-drug interaction (DDI), a detailed description of inhibitors and inducers of AO known to date has been presented here and the potential risks associated with DDI. The increasing recognition of the importance of AO has led to significant progress in predicting the site of AO-mediated metabolism using computational methods. Additionally, marked species difference in expression of AO makes it is difficult to predict human clearance with high confidence. The progress made towards developing in vivo, in vitro and in silico approaches for predicting AO metabolism and estimating human clearance of compounds that are metabolized by AO have also been discussed.

Embracing the Diversity of Halogen Bonding Motifs in Fragment-Based Drug Discovery-Construction of a Diversity-Optimized Halogen-Enriched Fragment Library

Halogen bonds have recently gained attention in life sciences and drug discovery. However, it can be difficult to harness their full potential, when newly introducing them into an established hit or lead structure by molecular design. A possible solution to overcome this problem is the use of halogen-enriched fragment libraries (HEFLibs), which consist of chemical probes that provide the opportunity to identify halogen bonds as one of the main features of the binding mode. Initially, we have suggested the HEFLibs concept when constructing a focused library for finding p53 mutant stabilizers. Herein, we broaden and extent this concept aiming for a general HEFLib comprising a huge diversity of binding motifs and, thus, increasing the applicability to various targets. Using the construction principle of feature trees, we represent each halogenated fragment by treating all simple to complex substituents as modifiers of the central (hetero)arylhalide. This approach allows us to focus on the proximal binding interface around the halogen bond and, thus, its integration into a network of interactions based on the fragment's binding motif. As a first illustrative example, we generated a library of 198 fragments that unifies a two-fold strategy: Besides achieving a diversity-optimized basis of the library, we have extended this "core" by structurally similar "satellite compounds" that exhibit quite different halogen bonding interfaces. Tuning effects, i.e., increasing the magnitude of the σ-hole, can have an essential influence on the strength of the halogen bond. We were able to implement this key feature into the diversity selection, based on the rapid and efficient prediction of the highest positive electrostatic potential on the electron isodensity surface, representing the σ-hole, by VmaxPred.

The Development of a Weighted Index to Optimise Compound Libraries for High Throughput Screening

1880 known drugs were collected and analysed for their mainstream molecular descriptors: MW, log P, HA, HD, RB and PSA. The statistical distributions were fitted to Gaussian functions for each of the descriptors. This gave a mathematical tool to calculate a weighted score, or an Index, for each descriptor. Known Drug Indexes (KDIs) were derived either by summation or multiplication of the Indexes, giving one number for each molecule calculated. The KDI summation and multiplication methods give a theoretical maxima of 6 and 1 respectively. According to both methods, methysergide (5.89/0.90), amsacrine (5.89/0.89) and fluorometholone (5.88/0.88) have the scores of the most well-balanced pharmaceuticals. The KDIs are advantageous tools in identifying the most well-balanced screening compounds based on the properties of known drugs; the screening collection can be optimised to only include quality compounds, which in turn produce tractable hit and lead compounds from the screening campaign.

In silico identification of promiscuous scaffolds as potential inhibitors of 1-deoxy-d-xylulose 5-phosphate reductoisomerase for treatment of Falciparum malaria

CONTEXT

Malaria remains one of the prevalent infectious diseases worldwide. Plasmodium falciparum 1-deoxy-d-xylulose-5-phosphate reductoisomerase (PfDXR) plays a role in isoprenoid biosynthesis in the malaria parasite, making this parasite enzyme an attractive target for antimalarial drug design. Fosmidomycin is a promising DXR inhibitor, which showed safety as well as efficacy against Plasmodium falciparum malaria in clinical trials. However, due to its poor oral bioavailability and non-drug-like properties, the focus of medicinal chemists is to develop inhibitors with improved pharmacological properties.

OBJECTIVE

This study described the computational design of new and potent inhibitors for deoxyxylulose 5-phosphate reductoisomerase and the prediction of their pharmacokinetic and pharmacodynamic properties.

MATERIAL AND METHODS

A complex-based pharmacophore model was generated from the complex X-ray crystallographic structure of PfDXR using MOE (Molecular Operating Environment). Furthermore, MOE-Dock was used as docking software to predict the binding modes of hits and target enzyme.

RESULTS

Finally, 14 compounds were selected as new and potent inhibitors of PfDXR on the basis of pharmacophore mapping, docking score, binding energy and binding interactions with the active site residues of the target protein. The predicted pharmacokinetic properties showed improved permeability by efficiently crossing blood-brain barrier. While, in silico promiscuity binding data revealed that these hits also have the ability to bind with other P. falciparum drug targets.

DISCUSSION AND CONCLUSION

In conclusion, innovative scaffolds with novel modes of action, improved efficacy and acceptable physiochemical/pharmacokinetic properties were computationally identified.

Parallel Synthesis of 1H-Pyrazolo[3,4-d]pyrimidines via Condensation of N-Pyrazolylamides and Nitriles

A novel parallel medicinal chemistry (PMC)-enabled synthesis of 1H-pyrazolo[3,4-d]pyrimidines employing condensation of easily accessible N-pyrazolylamides and nitriles has been developed. The presented studies describe singleton and library enablements that allowed rapid generation of molecular diversity to examine C4 and C6 vectors. This chemistry enabled access to challenging alkyl substituents, expanding the overall chemical space beyond that available via typical C(sp²)-C(sp²) coupling and S_NAr transformations. Furthermore, monomer group interconversions allowing the use of larger and more diverse amides and carboxylic acids as precursors to nitriles are discussed.

Characterization and Trypanocidal Activity of a Novel Pyranaphthoquinone

Chagas disease is an endemic parasitic infection that occurs in 21 Latin American countries. New therapies for this disease are urgently needed, as the only two drugs available (nifurtimox and benznidazol) have high toxicity and variable efficacy in the disease’s chronic phase. Recently, a new chemical entity (NCE) named Pyranaphthoquinone (IVS320) was synthesized from lawsone. We report herein, a detailed study of the physicochemical properties and in vitro trypanocidal activity of IVS320. A series of assays were performed for characterization, where thermal, diffractometric, and morphological analysis were performed. In addition, the solubility, permeability, and hygroscopicity of IVS320 were determined. The results show that its poor solubility and low permeability may be due to its high degree of crystallinity (99.19%), which might require the use of proper techniques to increase the IVS320’s aqueous solubility and permeability. The trypanocidal activity study demonstrated that IVS320 is more potent than the reference drug benznidazole, with IC50/24 h of 1.49 ± 0.1 μM, which indicates that IVS320 has potential as a new drug candidate for the treatment of Chagas disease.

Design, Synthesis, and Structure-Activity Relationship of Tetrahydropyrido[4,3-d]pyrimidine Derivatives as Potent Smoothened Antagonists with in Vivo Activity

Medulloblastoma is one of the most prevalent brain tumors in children. Aberrant hedgehog (Hh) pathway signaling is thought to be involved in the initiation and development of medulloblastoma. Vismodegib, the first FDA-approved cancer therapy based on inhibition of aberrant hedgehog signaling, targets smoothened (Smo), a G-protein coupled receptor (GPCR) central to the Hh pathway. Although vismodegib exhibits promising therapeutic efficacy in tumor treatment, concerns have been raised from its nonlinear pharmacokinetic (PK) profiles at high doses partly due to low aqueous solubility. Many patients experience adverse events such as muscle spasms and weight loss. In addition, drug resistance often arises among tumor cells during treatment with vismodegib. There is clearly an urgent need to explore novel Smo antagonists with improved potency and efficacy. Through a scaffold hopping strategy, we have identified a series of novel tetrahydropyrido[4,3-d]pyrimidine derivatives, which exhibited effective inhibition of Hh signaling. Among them, compound 24 is three times more potent than vismodegib in the NIH3T3-GRE-Luc reporter gene assay. Compound 24 has a lower melting point and much greater solubility compared with vismodegib, resulting in linear PK profiles when dosed orally at 10, 30, and 100 mg/kg in rats. Furthermore, compound 24 showed excellent PK profiles with a 72% oral bioavailability in beagle dogs. Compound 24 demonstrated overall favorable in vitro safety profiles with respect to CYP isoform and hERG inhibition. Finally, compound 24 led to significant regression of subcutaneous tumor generated by primary Ptch1-deficient medulloblastoma cells in SCID mouse. In conclusion, tetrahydropyrido[4,3-d]pyrimidine derivatives represent a novel set of Smo inhibitors that could potentially be utilized to treat medulloblastoma and other Hh pathway related malignancies.

Divergent Synthesis of Cyclopropane-Containing Lead-Like Compounds, Fragments and Building Blocks through a Cobalt Catalyzed Cyclopropanation of Phenyl Vinyl Sulfide

Cyclopropanes provide important design elements in medicinal chemistry and are widely present in drug compounds. Here we describe a strategy and extensive synthetic studies for the preparation of a diverse collection of cyclopropane-containing lead-like compounds, fragments and building blocks exploiting a single precursor. The bifunctional cyclopropane (E/Z)-ethyl 2-(phenylsulfanyl)-cyclopropane-1-carboxylate was designed to allow derivatization through the ester and sulfide functionalities to topologically varied compounds designed to fit in desirable chemical space for drug discovery. A cobalt-catalyzed cyclopropanation of phenyl vinyl sulfide affords these scaffolds on multigram scale. Divergent, orthogonal derivatization is achieved through hydrolysis, reduction, amidation and oxidation reactions as well as sulfoxide-magnesium exchange/functionalization. The cyclopropyl Grignard reagent formed from sulfoxide exchange is stable at 0 °C for > 2 h, which enables trapping with various electrophiles and Pd-catalyzed Negishi cross-coupling reactions. The library prepared, as well as a further virtual elaboration, is analyzed against parameters of lipophilicity (ALog P), MW and molecular shape by using the LLAMA (Lead-Likeness and Molecular Analysis) software, to illustrate the success in generating lead-like compounds and fragments.

Neurovascular Alterations in Alzheimer's Disease: Transporter Expression Profiles and CNS Drug Access

Despite a century of steady and incremental progress toward understanding the underlying biochemical mechanisms, Alzheimer's disease (AD) remains a complicated and enigmatic disease, and greater insight will be necessary before substantive clinical success is realised. Over the last decade in particular, a large body of work has highlighted the cerebral microvasculature as an anatomical region with an increasingly apparent role in the pathogenesis of AD. The causative interplay and temporal cascade that manifest between the brain vasculature and the wider disease progression of AD are not yet fully understood, and further inquiry is required to properly characterise these relationships. The purpose of this review is to highlight the recent advancements in research implicating neurovascular factors in AD, at both the molecular and anatomical levels. We begin with a brief introduction of the biochemical and genetic aspects of AD, before reviewing the essential concepts of the blood-brain barrier (BBB) and the neurovascular unit (NVU). In detail, we then examine the evidence demonstrating involvement of BBB dysfunction in AD pathogenesis, highlighting the importance of neurovascular components in AD. Lastly, we include within this review research that focuses on how altered properties of the BBB in AD impact upon CNS exposure of therapeutic agents and the potential clinical impact that this may have on people with this disease.

Synthesis of two potential anticancer copper(ii) complex drugs: their crystal structure, human serum albumin/DNA binding and anticancer mechanism

Two potential anticancer copper(ii) complex drugs showed better activity than cisplatin against HeLa cells, and efficiently bonded with DNA/HSA.

Fragment library design, synthesis and expansion: nurturing a synthesis and training platform

The availability of suitable diverse fragment- and lead-oriented screening compounds is key for the identification of suitable chemical starting points for drug discovery programs. The physicochemical properties of molecules are crucial in determining the success of small molecules in clinical development, yet reports suggest that pharmaceutical and academic sectors often produce molecules with poor drug-like properties. We present a platform to design novel, high quality and diverse fragment- and lead-oriented libraries with appropriate physicochemical properties in a cost-efficient manner. This approach has the potential to assist the way libraries are constructed by significantly addressing the historical uneven exploration of chemical space for drug discovery. Additionally, this platform can teach undergraduates and graduates about compound library design.

Scaffold-hopping from xanthines to tricyclic guanines: A case study of dipeptidyl peptidase 4 (DPP4) inhibitors

Molecular modeling of unbound tricyclic guanine scaffolds indicated that they can serve as effective bioisosteric replacements of xanthines. This notion was further confirmed by a combination of X-ray crystallography and SAR studies, indicating that tricyclic guanine DPP4 inhibitors mimic the binding mode of xanthine inhibitors, exemplified by linagliptin. Realization of the bioisosteric relationship between these scaffolds potentially will lead to a wider application of cyclic guanines as xanthine replacements in drug discovery programs for a variety of biological targets. Newly designed DPP4 inhibitors achieved sub-nanomolar potency range and demonstrated oral activity in vivo in mouse glucose tolerance test.

On the origins of three-dimensionality in drug-like molecules

AIM

Many medicinal chemistry-relevant structures and core scaffolds tend toward geometric planarity, which hampers the optimization of physicochemical properties desirable in drug-like molecules. As challenging drug target classes emerge, the exploitation of molecular three-dimensionality in lead optimization is becoming increasingly important. While recent interest has emphasized the importance of enhanced three-dimensionality in molecular fragment designs, the extent to which this is required in core scaffolds remains unclear.

MATERIALS & METHODS

Three computational methods, Scaffold Tree deconstruction, Synthetic Disconnection Rules retrosynthetic deconstruction and virtual library enumeration, are applied, together with the descriptors plane of best fit and principal moments of inertia, to investigate the origins of three-dimensionality in drug-like molecules.

CONCLUSION

This study informs on the stage at which molecular three-dimensionality should be considered in drug design.

In vitro oral drug permeation models: the importance of taking physiological and physico-chemical factors into consideration

INTRODUCTION

The assessment of intestinal membrane permeability properties of new chemical entities is a crucial step in the drug discovery and development process and a variety of in vitro models, methods and techniques are available to estimate the extent of oral drug absorption in humans. However, variations in certain physiological and physico-chemical factors are often not reflected in the results and the complex dynamic interplay between these factors is sometimes oversimplified with in vitro models. Areas covered: In vitro models to evaluate drug pharmacokinetics are briefly outlined, while both physiological and physico-chemical factors that may have an influence on these techniques are critically reviewed. The shortcomings identified for some of the in vitro techniques are discussed in conjunction with novel ways to improve and thereby overcome some challenges. Expert opinion: Although conventional in vitro methods and theories are used as basic guidelines to predict drug absorption, critical evaluations have identified some shortcomings. Advancements in technology have made it possible to investigate and understand the role of physiological and physico-chemical factors in drug delivery more clearly, which can be used to improve and refine the techniques to more closely mimic the in vivo environment.

Molecular inflation, attrition and the rule of five

Physicochemical properties underlie all aspects of drug action and are critical for solubility, permeability and successful formulation. Specific physicochemical properties shown to be relevant to oral drugs are size, lipophilicity, ionisation, hydrogen bonding, polarity, aromaticity and shape. The rule of 5 (Ro5) and subsequent studies have raised awareness of the importance of compound quality amongst bioactive molecules. Lipophilicity, probably the most important physical property of oral drugs, has on average changed little over time in oral drugs, until increases in drugs published after 1990. In contrast other molecular properties such as average size have increased significantly. Factors influencing property inflation include the targets pursued, where antivirals frequently violate the Ro5, risk/benefit considerations, and variable drug discovery practices. The compounds published in patents from the pharmaceutical industry are on average larger, more lipophilic and less complex than marketed oral drugs. The variation between individual companies' patented compounds is due to different practices and not to the targets pursued. Overall, there is demonstrable physical property attrition in moving from patents to candidate drugs to marketed drugs. The pharmaceutical industry's recent poor productivity has been due, in part, to progression of molecules that are unable to unambiguously test clinical efficacy, and attrition can therefore be improved by ensuring candidate drug quality is 'fit for purpose.' The combined ligand efficiency (LE) and lipophilic ligand efficiency (LLE) values of many marketed drugs are optimised relative to other molecules acting at the same target. Application of LLE in optimisation can help identify improved leads, even with challenging targets that seem to require lipophilic ligands. Because of their targets, some projects may need to pursue 'beyond Ro5' physicochemical space; such projects will require non-standard lead generation and optimisation and should not dominate in a well-balanced portfolio. Compound quality is controllable by lead selection and optimisation and should not be a cause of clinical failure.

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.

Stacking with No Planarity?

This viewpoint describes the results obtained from matched molecular pair analyses and quantum mechanics calculations that show unsaturated rings found in drug-like molecules may be replaced with their saturated counterparts without losing potency even if they are engaged in stacking interactions with the side chains of aromatic residues.