Tautomerism of Warfarin: Combined Chemoinformatics, Quantum Chemical, and NMR Investigation

Structurally diverse rearranged sesquiterpenoids, including a pair of rare tautomers, from the aerial parts of Daphne penicillata

Eight structurally diverse rearranged sesquiterpenoids, including seven undescribed sesquiterpenoids (1a/1b and 3-8) were obtained from the aerial parts of Daphne penicillata. 1a/1b, 3, 5 and 6 possess rare rearranged guaiane skeletons and 4 represents the first example of rearranged carotene sesquiterpenoids. Their structures and absolute configurations were determined by extensive spectroscopic analyses, NMR and ECD calculations. Interestingly, 1a and 1b were a pair of magical interconverting epimers that may interconvert by retro-aldol condensation. The mechanism of interconversion has been demonstrated indirectly by 9-OH derivatization of 1a/1b and a hypothetical biogenetic pathway was proposed. All compounds were evaluated for anti-inflammatory and cytotoxic activities. Among them, 1a/1b and 2 exhibited potential inhibitory activities on the production of NO against LPS-induced BV2 microglial cells.

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.

Probe into the Molecular Mechanism of Ibuprofen Interaction with Warfarin Bound to Human Serum Albumin in Comparison to Ascorbic and Salicylic Acids: Allosteric Inhibition of Anticoagulant Release

The release of anticoagulant drugs such as warfarin from human serum albumin (HSA) has been important not only mechanistically but also clinically for patients who take multiple drugs simultaneously. In this study, the role of some commonly used drugs, including s-ibuprofen, ascorbic acid, and salicylic acid, was investigated in the release of warfarin bound to HSA in silico. The effects of the aforementioned drugs on the HSA-warfarin complex were investigated with molecular dynamics (MD) simulations using two approaches; in the first perspective, molecular docking was used to model the interaction of each drug with the HSA-warfarin complex, and in the second approach, drugs were positioned randomly and distant from the binary complex (HSA-warfarin) in a physiologically relevant concentration. The results obtained from both approaches indicated that s-ibuprofen and ascorbic acid both displayed allosteric effects on the release of warfarin from HSA. Although ascorbic acid aided in warfarin release, leading to destabilization of HSA, ibuprofen demonstrated a stabilizing effect on releasing the anticoagulant drug through several noncovalent interactions, including hydrophobic, electrostatic, and hydrogen-bonding interactions with the protein. The calculated binding free energy and energy contribution of involved residues using the molecular mechanics-Poisson Boltzmann surface area (MM-PBSA) method, along with root mean square deviation (RMSD) values, protein gyration, and free energy surface (FES) mapping of the protein, provided valuable details on the nature of the interactions of each drug on the release of warfarin from HSA. These results can provide important information on the mechanisms of anticoagulant release that has not been revealed in molecular details previously.

The Curious Case of Aqueous Warfarin: Structural Isomers or Distinct Excited States?

Warfarin is a potent anti-coagulant drug and is on the World Health Organization's List of Essential Medicines. Additionally, it displays fluorescence enhancement upon binding to human serum albumin, making warfarin a prototype fluorescent probe in biology. Despite its biological significance, the current structural assignment of warfarin in aqueous solution is based on indirect evidence in organic solvents. Warfarin is known to exist in different isomeric forms-open-chain, hemiketal, and anionic forms-based on the solvent and pH. Moreover, warfarin displays a dual absorption feature in several solvents, which has been employed to study the ring-chain isomerism between its open-chain and hemiketal isomers. In this study, our pH-dependent experiments on warfarin and structurally constrained warfarin derivatives in aqueous solution demonstrate that the structural assignment of warfarin solely on the basis of its absorption spectrum is erroneous. Using a combination of steady-state and time-resolved spectroscopic experiments, along with quantum chemical calculations, we assign the observed dual absorption to two distinct π → π* transitions in the 4-hydroxycoumarin moiety of warfarin. Furthermore, we unambiguously identify the isomeric form of warfarin that binds to human serum albumin in aqueous buffer.

Tautomer Standardization in Chemical Databases: Deriving Business Rules from Quantum Chemistry

Databases of small, potentially bioactive molecules are ubiquitous across the industry and academia. Designed such that each unique compound should appear only once, the multiplicity of ways in which many compounds can be represented means that these databases require methods for standardizing the representation of chemistry. This is commonly achieved through the use of "Chemistry Business Rules", sets of predefined rules that describe the "house style" of the database in question. At Syngenta, the historical approach to the design of chemistry business rules has been to focus on consistency of representation, with chemical relevance given secondary consideration. In this work, we overturn that convention. Through the use of quantum chemistry calculations, we define a set of chemistry business rules for tautomer standardization that reproduces gas-phase energetic preferences. We go on to show that, compared to our historic approach, this method yields tautomers that are in better agreement with those observed experimentally in condensed phases and that are better suited for use in predictive models.

Pattern-free generation and quantum mechanical scoring of ring-chain tautomers

In contrast to the computational generation of conventional tautomers, the analogous operation that would produce ring-chain tautomers is rarely available in cheminformatics codes. This is partly due to the perceived unimportance of ring-chain tautomerism and partly because specialized algorithms are required to realize the non-local proton transfers that occur during ring-chain rearrangement. Nevertheless, for some types of organic compounds, including sugars, warfarin analogs, fluorescein dyes and some drug-like compounds, ring-chain tautomerism cannot be ignored. In this work, a novel ring-chain tautomer generation algorithm is presented. It differs from previously proposed solutions in that it does not rely on hard-coded patterns of proton migrations and bond rearrangements, and should therefore be more general and maintainable. We deploy this algorithm as part of a workflow which provides an automated solution for tautomer generation and scoring. The workflow identifies protonatable and deprotonatable sites in the molecule using a previously described approach based on rapid micro-pK_a prediction. These data are used to distribute the active protons among the protonatable sites exhaustively, at which point alternate resonance structures are considered to obtain pairs of atoms with opposite formal charge. These pairs are connected with a single bond and a 3D undistorted geometry is generated. The scoring of the generated tautomers is performed with a subsequent density functional theory calculation employing an implicit solvent model. We demonstrate the performance of our workflow on several types of organic molecules known to exist in ring-chain tautomeric equilibria in solution. In particular, we show that some ring-chain tautomers not found using previously published algorithms are successfully located by ours.

Antagonists of Vitamin K-Popular Coumarin Drugs and New Synthetic and Natural Coumarin Derivatives

Many natural coumarins and their chemically synthesized analogs and derivatives exert diverse properties, such as anticancer, antioxidant, anti-inflammatory, or anticoagulant, with the latter being of the utmost importance. The widely used warfarin, acenocoumarol, and phenprocoumon exert anticoagulant properties by inhibiting the vitamin K epoxide reductase complex. In this interdisciplinary review, we present biochemical principles of the coagulation processes and possible methods for their tuning based on the use of coumarins. We also summarize chemical methods of synthesis of coumarins and discuss structures and properties of those that have been used for a long time, as well as newly synthesized compounds. Brief information on the clinical use of coumarins and other anticoagulant drugs is given, including the severe effects of overdosing and methods for reversing their action.

2-Hydroxyimino-6-aza-pyrimidine nucleosides: synthesis, DFT calculations, and antiviral evaluations

Synthesis, DFT calculations, and antiviral evaluation of a series of novel 2-hydroxyimino-6-aza-pyrimidine ribonucleosides is reported. The hydrogen bonding between the C²N–OH moiety and N³–H and/or N³ moieties shapes the pyrimidine nucleoside as purine.

Predicting the Prevalence of Alternative Warfarin Tautomers in Solution

Warfarin, a widely used oral anticoagulant, is prescribed as a racemic mixture. Each enantiomer of neutral Warfarin can exist in 20 possible tautomeric states leading to complex pharmacokinetics and uncertainty as to the relevant species under different conditions. Here, the ability of alternative computational approaches to predict the preferred tautomeric form(s) of neutral Warfarin in different solvents is examined. It is shown that varying the method used to estimate the heat of formation in vacuum (direct or via homodesmic reactions), whether entropic corrections were included, and the method used to estimate the free enthalpy of solvation (i.e., PCM, COSMO, or SMD implicit models or explicit solvent) lead to large differences in the predicted rank and relative populations of the tautomers. In this case, only a combination of the enthalpy of formation using homodesmic reactions and explicit solvent to estimate the free enthalpy of solvation yielded results compatible with the available experimental data. The work also suggests that a small but significant subset of the possible Warfarin tautomers are likely to be physiologically relevant.

Experimental and pKa prediction aspects of tautomerism of drug-like molecules

Molecules that can tautomerize are a challenge to scientists because one must consider the possible tautomers in most tasks involving chemical structures: for example, searching databases, interpreting experimental property measurements, calculating properties, virtual screening, and analyzing structure-bioactivity relationships. The challenge in interpreting property measurements such as pK_a values feeds into the general lack of extensive information not only of the relative tautomer stability in water but also the properties of the individual tautomers. This lack of information results in the lack of reliability of computational predictions of tautomer stability or properties. In spite of these problems, pK_a calculations are reliable enough that they can be used to filter out high-energy tautomers from databases used for virtual screening. Continuous improvements in both pK_a prediction software and theoretical calculations promise further improvements in solving the challenges of tautomers. The expected availability of high-resolution structures of many more tautomer-protein complexes will help guide the selection of the bioactive tautomer when the structure of the complex is not known.

Inhibition of the prototropic tautomerism in chrysazine by p-sulfonatocalixarene hosts

This study reveals the unusual inhibition of excited-state prototropic tautomerism of Chrysazine by p-sulfonatocalix[4,6]arene hosts.

Experimental and Chemoinformatics Study of Tautomerism in a Database of Commercially Available Screening Samples

We investigated how many cases of the same chemical sold as different products (at possibly different prices) occurred in a prototypical large aggregated database and simultaneously tested the tautomerism definitions in the chemoinformatics toolkit CACTVS. We applied the standard CACTVS tautomeric transforms plus a set of recently developed ring-chain transforms to the Aldrich Market Select (AMS) database of 6 million screening samples and building blocks. In 30 000 cases, two or more AMS products were found to be just different tautomeric forms of the same compound. We purchased and analyzed 166 such tautomer pairs and triplets by 1H and 13C NMR to determine whether the CACTVS transforms accurately predicted what is the same "stuff in the bottle". Essentially all prototropic transforms with examples in the AMS were confirmed. Some of the ring-chain transforms were found to be too "aggressive", i.e. to equate structures with one another that were different compounds.