Small molecule conformational preferences derived from crystal structure data. A medicinal chemistry focused analysis

Fragment-based ligand design of novel potent inhibitors of tankyrases

Tankyrases constitute potential drug targets for cancer and myelin-degrading diseases. We have applied a structure- and biophysics-driven fragment-based ligand design strategy to discover a novel family of potent inhibitors for human tankyrases. Biophysical screening based on a thermal shift assay identified highly efficient fragments binding in the nicotinamide-binding site, a local hot spot for fragment binding. Evolution of the fragment hit 4-methyl-1,2-dihydroquinolin-2-one (2) along its 7-vector yields dramatic affinity improvements in the first cycle of expansion. A crystal structure of 7-(2-fluorophenyl)-4-methylquinolin-2(1H)-one (11) reveals that the nonplanar compound extends with its fluorine atom into a pocket, which coincides with a region of the active site where structural differences are seen between tankyrases and other poly(ADP-ribose) polymerase (PARP) family members. A further cycle of optimization yielded compounds with affinities and IC50 values in the low nanomolar range and with good solubility, PARP selectivity, and ligand efficiency.

Characterization of biaryl torsional energetics and its treatment in OPLS all-atom force fields

The frequency of biaryl substructures in a database of approved oral drugs has been analyzed. This led to designation of 20 prototypical biaryls plus 10 arylpyridinones for parametrization in the OPLS all-atom force fields. Bond stretching, angle-bending, and torsional parameters were developed to reproduce the MP2 geometries and torsional energy profiles. The transferability of the new parameters was tested through their application to three additional biaryls. The torsional energetics for the 33 biaryl molecules are analyzed and factors leading to preferences for planar and nonplanar geometries are identified. For liquid biphenyl, the computed density and heat of vaporization at the boiling point (255 °C) are also reported.

Increasing the efficiency of ligands for FK506-binding protein 51 by conformational control

The design of efficient ligands remains a key challenge in drug discovery. In the quest for lead-like ligands for the FK506-binding protein 51 (FKBP51), we designed two new classes of bicyclic sulfonamides to probe the contribution of conformational energy in these ligands. The [4.3.1] scaffold had consistently higher affinity compared to the [3.3.1] or monocyclic scaffolds, which could be attributed to better preorganization of two key recognition motifs. Surprisingly, the binding of the rigid [4.3.1] scaffold was enthalpy-driven and entropically disfavored compared to the flexible analogues. Cocrystal structures at atomic resolution revealed that the sulfonamide nitrogen in the bicyclic scaffolds can accept an unusual hydrogen bond from Tyr(113) that mimics the putative FKBP transition state. This resulted in the first lead-like, functionally active ligand for FKBP51. Our work exemplifies how atom-efficient ligands can be achieved by careful conformational control even in very open and thus difficult binding sites such as FKBP51.

De novo fragment design: a medicinal chemistry approach to fragment-based lead generation

The use of fragments with low binding affinity for their targets as starting points has received much attention recently. Screening of fragment libraries has been the most common method to find attractive starting points. Herein, we describe a unique, alternative approach to generating fragment leads. A binding model was developed and a set of guidelines were then selected to use this model to design fragments, enabling our discovery of a novel fragment with high LE.

Torsion angle preferences in druglike chemical space: a comprehensive guide

Crystal structure databases offer ample opportunities to derive small molecule conformation preferences, but the derived knowledge is not systematically applied in drug discovery research. We address this gap by a comprehensive and extendable expert system enabling quick assessment of the probability of a given conformation to occur. It is based on a hierarchical system of torsion patterns that cover a large part of druglike chemical space. Each torsion pattern has associated frequency histograms generated from CSD and PDB data and, derived from the histograms, traffic-light rules for frequently observed, rare, and highly unlikely torsion ranges. Structures imported into the corresponding software are annotated according to these rules. We present the concept behind the tree of torsion patterns, the design of an intuitive user interface for the management and usage of the torsion library, and we illustrate how the system helps analyze and understand conformation properties of substructures widely used in medicinal chemistry.

Novel route to chaetomellic acid A and analogues: serendipitous discovery of a more competent FTase inhibitor

A new practical route to chaetomellic acid A (ACA), based on the copper catalysed radical cyclization (RC) of (Z)-3-(2,2-dichloropropanoyl)-2-pentadecylidene-1,3-thiazinane, is described. Remarkably, the process entailed: (i) a one-pot preparation of the intermediate N-α-perchloroacyl-2-(Z)-alkyliden-1,3-thiazinanes starting from N-(3-hydroxypropyl)palmitamide, (ii) a two step smooth transformation of the RC products into ACA and (iii) only one intermediate chromatographic purification step. The method offers a versatile approach to the preparation of ACA analogues, through the synthesis of an intermediate maleic anhydride with a vinylic group at the end of the aliphatic tail, a function that can be transformed through a thiol-ene coupling. Serendipitously, the disodium salt of 2-(9-(butylthio)nonyl)-3-methylmaleic acid, that we prepared as a representative sulfurated ACA analogue, was a more competent FTase inhibitor than ACA. This behaviour was analysed by a molecular docking study.

Conformer generation with OMEGA: learning from the data set and the analysis of failures

We recently published a high quality validation set for testing conformer generators, consisting of structures from both the PDB and the CSD (Hawkins, P. C. D. et al. J. Chem. Inf. Model. 2010, 50, 572.), and tested the performance of our conformer generator, OMEGA, on these sets. In the present publication, we focus on understanding the suitability of those data sets for validation and identifying and learning from OMEGA's failures. We compare, for the first time we are aware of, the coverage of the applicable property spaces between the validation data sets we used and the parent compound sets to determine if our data sets adequately sample these property spaces. We also introduce the concept of torsion fingerprinting and compare this method of dissimilation to the more traditional graph-centric diversification methods we used in our previous publication. To improve our ability to programmatically identify cases where the crystallographic conformation is not well reproduced computationally, we introduce a new metric to compare conformations, RMSTanimoto. This new metric is used alongside those from our previous publication to efficiently identify reproduction failures. We find RMSTanimoto to be particularly effective in identifying failures for the smallest molecules in our data sets. Analysis of the nature of these failures, particularly those for the CSD, sheds further light on the issue of strain in crystallographic structures. Some of the residual failure cases not resolved by simple changes in OMEGA's defaults present significant challenges to conformer generation engines like OMEGA and are a source of new avenues to further improve their performance, while others illustrate the pitfalls of validating against crystallographic ligand conformations, particularly those from the PDB.

Salvinorin B meth-oxy-methyl ether

The title compound [MOM-SalB; systematic name: methyl (2S,4aR,6aR,7R,9S,10aS,10bR)-2-(3-fur­yl)-9-meth­oxy­meth­oxy-6a,10b-dimethyl-4,10-dioxo-2,4a,5,6,7,8,9,10a-octa­hydro-1H-benzo[f]isochromene-7-carboxyl­ate], C₂₃H₃₀O₈, is a deriv­ative of the κ-opioid salvinorin A with enhanced potency, selectivity, and duration of action. Superimposition of their crystal structures reveals, surprisingly, that the terminal C and O atoms of the MOM group overlap with the corresponding atoms in salvinorin A, which are separated by an additional bond. This counter-intuitive isosterism is possible because the MOM ether adopts the ‘classic anomeric’ conformation (gauche–gauche), tracing a helix around the planar acetate of salvinorin A. This overlap is not seen in the recently reported structure of the tetra­hydro­pyranyl ether, which is less potent. The classic anomeric conformation is strongly favoured in alk­oxy­methyl ethers, but not in substituted acetals, which may contribute to their reduced potency. This structure may prove useful in evaluating models of the activated κ-opioid receptor.

Biasing conformational ensembles towards bioactive-like conformers for ligand-based drug design

IMPORTANCE OF THE FIELD

In silico or virtual screening has become a common practice in contemporary computer-aided drug discovery efforts and currently constitutes a reasonably mature paradigm. Application of ligand-based approaches to virtual screening requires the ability to identify the bioactive conformers of drug-like compounds as these conformers are expected to elicit the biological activity. However, given the complexity of the energy potential surfaces of such ligands and in particular those exhibiting some degree of flexibility and the limitation of contemporary energy functions, this is not an easy task.

AREAS COVERED IN THIS REVIEW

The current contribution provides an in-depth review of recent developments in the field of generating conformational ensembles of drug-like compounds with a particular emphasis of focusing such ensembles on bioactive conformers using both energy and structural criteria. The literature reviewed in this manuscript roughly covers the last decade.

WHAT THE READER WILL GAIN

Readers of this review will gain an appreciation for the complexity of identifying bioactive conformers of drug-like compounds and an exposure to the different computational methods which were developed in order to tackle this problem as well as to the remaining challenges in this field.

TAKE HOME MESSAGE

The identification of ensembles of bioactive conformers of drug-like compounds is far from being a solved problem. Recent research has advanced the field to the point where bioactive conformers could be readily identified from within conformational ensembles generated by contemporary computational tools. However, as such conformers are inevitably accompanied by many other non-relevant conformations, a focusing mechanism is required. New methods in this field are showing promise but more work is clearly needed. New research lines are proposed which are believed to enhance the performances and with it the usefulness of 3D ligand-based methods in drug discovery and development.

Evaluating the enthalpic contribution to ligand binding using QM calculations: effect of methodology on geometries and interaction energies

As a result of research on ligand efficiency in the pharmaceutical industry, there is greater focus on optimizing the strength of polar interactions within receptors, so that the contribution of overall size and lipophilicity to binding can be decreased. A number of quantum mechanical (QM) methods involving simple probes are available to assess the H-bonding potential of different heterocycles or functional groups. However, in most receptors, multiple features are present, and these have distinct directionality, meaning very minimalist models may not be so ideal to describe the interactions. We describe how the use of gas phase QM models of kinase protein-ligand complex, which can more closely mimic the polar features of the active site region, can prove useful in assessing alterations to a core template, or different substituents. We investigate some practical issues surrounding the use of QM cluster models in structure based design (SBD). These include the choice of the method; semi-empirical, density functional theory or ab-initio, the choice of the basis set, whether to include implicit or explicit solvation, whether BSSE should be included, etc. We find a combination of the M06-2X method and the 6-31G* basis set is sufficiently rapid, and accurate, for the computation of structural and energetic parameters for this system.

Methyl effects on protein-ligand binding

The effects of addition of a methyl group to a lead compound on biological activity are examined. A literature analysis of >2000 cases reveals that an activity boost of a factor of 10 or more is found with an 8% frequency, and a 100-fold boost is a 1 in 200 event. Four cases in the latter category are analyzed in depth to elucidate any unusual aspects of the protein-ligand binding, distribution of water molecules, and changes in conformational energetics. The analyses include Monte Carlo/free-energy perturbation (MC/FEP) calculations for methyl replacements in inhibitor series for p38α MAP kinase, ACK1, PTP1B, and thrombin. Methyl substitutions ortho to an aryl ring can be particularly effective at improving activity by inducing a propitious conformational change. The greatest improvements in activity arise from coupling the conformational gain with the burial of the methyl group in a hydrophobic region of the protein.

Structural systematics and conformational analyses of a 3 × 3 isomer grid of fluoro-N-(pyridyl)benzamides: physicochemical correlations, polymorphism and isomorphous relationships

An isomer grid of nine fluoro-N-(pyridyl)benzamides (Fxx) (x = para-/meta-/ortho-) has been examined to correlate structural relationships between the experimental crystal structure and ab initio calculations, based on the effect of fluorine (Fx) and pyridine N-atom (x) substitution patterns on molecular conformation. Eight isomers form N—H...N hydrogen bonds, and only one (Fom) aggregates via intermolecular N—H...O=C interactions exclusively. The Fpm and Fom isomers both crystallize as two polymorphs with Fpm_O (N—H...O=C chains, P-syn ) and Fpm_N (N—H...N chains, P-anti ) both in P21/n (Z′ = 1) differing by their meta-N atom locations (P-syn , P-anti ; Npyridine referenced to N—H), whereas the disordered Fom_O is mostly P-syn (Z′ = 6) compared with Fom_F (P-anti ) (Z′ = 1). In the Fxo triad twisted dimers form cyclic R 2 2(8) rings via N—H...N interactions. Computational modelling and conformational preferences of the isomer grid demonstrate that the solid-state conformations generally conform with the most stable calculated conformations except for the Fxm triad, while calculations of the Fox triad predict the intramolecular N—H...F interaction established by spectroscopic and crystallographic data. Comparisons of Fxx with related isomer grids reveal a high degree of similarity in solid-state aggregation and physicochemical properties, while correlation of the melting point behaviour indicates the significance of the substituent position on melting point behaviour rather than the nature of the substituent.

Validating and understanding ring conformations using small molecule crystallographic data

Understanding the conformational preferences of ring structures is fundamental to structure-based drug design. Although the Cambridge Structural Database (CSD) provides information on the preferred conformations of small molecules, analyzing this data can be very time-consuming. In order to overcome this hurdle, tools have been developed for quickly extracting geometrical preferences from the CSD. Here we describe how the program Mogul has been extended to analyze and compare ring conformations, using a library derived from over 900 000 ring fragments in the CSD. We illustrate how these can be used to understand the conformational preferences of molecules in a crystal lattice and bound to proteins.

The good, the bad and the twisted: a survey of ligand geometry in protein crystal structures

The protein databank now contains the structures of over 11,000 ligands bound to proteins. These structures are invaluable in applied areas such as structure-based drug design, but are also the substrate for understanding the energetics of intermolecular interactions with proteins. Despite their obvious importance, the careful analysis of ligands bound to protein structures lags behind the analysis of the protein structures themselves. We present an analysis of the geometry of ligands bound to proteins and highlight the role of small molecule crystal structures in enabling molecular modellers to critically evaluate a ligand model's quality and investigate protein-induced strain.

Non-symmetrically substituted phenoxazinones from laccase-mediated oxidative cross-coupling of aminophenols: an experimental and theoretical insight

Oxidative cross-coupling reactions of substituted o-aminophenols were catalyzed by a commercial laccase to produce non-symmetrically substituted phenoxazinones for the first time. Identification by (1)H-, (13)C- and (31)P-NMR, and by HPLC-PDA and HPLC-MS/MS of exclusively two kinds of substituted phenoxazinones out of four potential heterocyclic frameworks was confirmed by a DFT study. The redox-properties of the substrates, their relative rates of conversion and the rigid docking of selected substrates led to a revisited mechanistic pathway for phenoxazinones biosynthesis. Our suggestions concern both the first formal two-electron oxidation by laccase and the first intermolecular 1,4-conjugated addition which secures the observed regioselectivity.

Computationally-guided optimization of a docking hit to yield catechol diethers as potent anti-HIV agents

A 5-μM docking hit has been optimized to an extraordinarily potent (55 pM) non-nucleoside inhibitor of HIV reverse transcriptase. Use of free energy perturbation (FEP) calculations to predict relative free energies of binding aided the optimizations by identifying optimal substitution patterns for phenyl rings and a linker. The most potent resultant catechol diethers feature terminal uracil and cyanovinylphenyl groups. A halogen bond with Pro95 likely contributes to the extreme potency of compound 42. In addition, several examples are provided illustrating failures of attempted grafting of a substructure from a very active compound onto a seemingly related scaffold to improve its activity.

Cofactor-binding sites in proteins of deviating sequence: comparative analysis and clustering in torsion angle, cavity, and fold space

Small molecules are recognized in protein-binding pockets through surface-exposed physicochemical properties. To optimize binding, they have to adopt a conformation corresponding to a local energy minimum within the formed protein-ligand complex. However, their conformational flexibility makes them competent to bind not only to homologous proteins of the same family but also to proteins of remote similarity with respect to the shape of the binding pockets and folding pattern. Considering drug action, such observations can give rise to unexpected and undesired cross reactivity. In this study, datasets of six different cofactors (ADP, ATP, NAD(P)(H), FAD, and acetyl CoA, sharing an adenosine diphosphate moiety as common substructure), observed in multiple crystal structures of protein-cofactor complexes exhibiting sequence identity below 25%, have been analyzed for the conformational properties of the bound ligands, the distribution of physicochemical properties in the accommodating protein-binding pockets, and the local folding patterns next to the cofactor-binding site. State-of-the-art clustering techniques have been applied to group the different protein-cofactor complexes in the different spaces. Interestingly, clustering in cavity (Cavbase) and fold space (DALI) reveals virtually the same data structuring. Remarkable relationships can be found among the different spaces. They provide information on how conformations are conserved across the host proteins and which distinct local cavity and fold motifs recognize the different portions of the cofactors. In those cases, where different cofactors are found to be accommodated in a similar fashion to the same fold motifs, only a commonly shared substructure of the cofactors is used for the recognition process.

Efficient discovery of potent anti-HIV agents targeting the Tyr181Cys variant of HIV reverse transcriptase

Non-nucleoside reverse transcriptase inhibitors (NNRTIs) that interfere with the replication of human immunodeficiency virus (HIV) are being pursued with guidance from molecular modeling including free-energy perturbation (FEP) calculations for protein-inhibitor binding affinities. The previously reported pyrimidinylphenylamine 1 and its chloro analogue 2 are potent anti-HIV agents; they inhibit replication of wild-type HIV-1 in infected human T-cells with EC(50) values of 2 and 10 nM, respectively. However, they show no activity against viral strains containing the Tyr181Cys (Y181C) mutation in HIV-RT. Modeling indicates that the problem is likely associated with extensive interaction between the dimethylallyloxy substituent and Tyr181. As an alternative, a phenoxy group is computed to be oriented in a manner diminishing the contact with Tyr181. However, this replacement leads to a roughly 1000-fold loss of activity for 3 (2.5 μM). The present report details the efficient, computationally driven evolution of 3 to novel NNRTIs with sub-10 nM potency toward both wild-type HIV-1 and Y181C-containing variants. The critical contributors were FEP substituent scans for the phenoxy and pyrimidine rings and recognition of potential benefits of addition of a cyanovinyl group to the phenoxy ring.

Design, synthesis and docking studies on benzamide derivatives as histone deacetylase inhibitors

A series of benzamide derivatives including two scaffolds were designed and synthesized as potential histone deacetylase inhibitors. Most of synthesized compounds showed moderate enzymatic potency at the same order of magnitude, and compound 12b possessed better potency to the positive control (3.8 μM vs 13.0 μM). It also showed a 50-fold increase in vitro anticancer activity against DU-145 cell-lines. Molecular docking studies were carried out and used to explain the structure-activity relationships observed in vitro. Then we found that the cavity surrounded by ASP104, HIS33, PRO34 and PHE155 may be crucial for the inhibitors' activity. The docking results provide some useful information for future design of more potent inhibitors.