Detection of secondary binding sites in proteins using fragment screening.

Proteins need to be tightly regulated as they control biological processes in most normal cellular functions. The precise mechanisms of regulation are rarely completely understood but can involve binding of endogenous ligands and/or partner proteins at specific locations on a protein that can modulate function. Often, these additional secondary binding sites appear separate to the primary binding site, which, for example for an enzyme, may bind a substrate. In previous work, we have uncovered several examples in which secondary binding sites were discovered on proteins using fragment screening approaches. In each case, we were able to establish that the newly identified secondary binding site was biologically relevant as it was able to modulate function by the binding of a small molecule. In this study, we investigate how often secondary binding sites are located on proteins by analyzing 24 protein targets for which we have performed a fragment screen using X-ray crystallography. Our analysis shows that, surprisingly, the majority of proteins contain secondary binding sites based on their ability to bind fragments. Furthermore, sequence analysis of these previously unknown sites indicate high conservation, which suggests that they may have a biological function, perhaps via an allosteric mechanism. Comparing the physicochemical properties of the secondary sites with known primary ligand binding sites also shows broad similarities indicating that many of the secondary sites may be druggable in nature with small molecules that could provide new opportunities to modulate potential therapeutic targets.

A "dial-a-receptor" dynamic combinatorial library.

Making receptors to order: A small dynamic combinatorial library (DCL), formed from two dithiols in water, provides a continuous range of six receptors of different sizes. The majority of the 30 tested amines and ammonium ions amplified receptors from this library, thus spanning the complete receptor-size range and showing that this DCL provides a generic platform for the development of receptors for this important class of compounds.

C-H functionalisation tolerant to polar groups could transform fragment-based drug discovery (FBDD).

We have analysed 131 fragment-to-lead (F2L) examples targeting a wide variety of protein families published by academic and industrial laboratories between 2015-2019. Our assessment of X-ray structural data identifies the most common polar functional groups involved in fragment-protein binding are: N-H (hydrogen bond donors on aromatic and aliphatic N-H, amides and anilines; totalling 35%), aromatic nitrogen atoms (hydrogen bond acceptors; totalling 23%), and carbonyl oxygen group atoms (hydrogen bond acceptors on amides, ureas and ketones; totalling 22%). Furthermore, the elaboration of each fragment into its corresponding lead is analysed to identify the nominal synthetic growth vectors. In ∼80% of cases, growth originates from an aromatic or aliphatic carbon on the fragment and more than 50% of the total bonds formed are carbon-carbon bonds. This analysis reveals that growth from carbocentric vectors is key and therefore robust C-H functionalisation methods that tolerate the innate polar functionality on fragments could transform fragment-based drug discovery (FBDD). As a further resource to the community, we have provided the full data of our analysis as well as an online overlay page of the X-ray structures of the fragment hit and leads: https://astx.com/interactive/F2L-2021/.

The impact of the size of dynamic combinatorial libraries on the detectability of molecular recognition induced amplification.

Despite well over a decade of research on dynamic combinatorial chemistry it is still unclear whether large libraries are more or less likely to yield strong binders than small libraries. We have now addressed this question by simulating a set of libraries containing from 65 to 4828 compounds under a range of different building block and template concentrations. We investigated the effect of library size on (i) the probability of detecting any amplification; (ii) the probability of detecting the strongest binding library member present; and (iii) the binding affinity of the most amplified detectable library member. The results indicate bigger libraries are more likely to produce better binders and that the affinity of the best binders identified rises more rapidly than expected statistically on the basis of the number of screened library members. This implies that it should be advantageous to work with DCLs that are much larger than the vast majority reported thus far.

Affinity chromatography in dynamic combinatorial libraries: one-pot amplification and isolation of a strongly binding receptor.

We report the one-pot amplification and isolation of a nanomolar receptor in a multibuilding block aqueous dynamic combinatorial library using a polymer-bound template. By appropriate choice of a poly(N,N-dimethylacrylamide)-based support, nonselective ion-exchange type behaviour between the oppositely charged cationic guest and polyanionic hosts was overcome, such that the selective molecular recognition arising in aqueous solution reactions is manifest also in the analogous templated solid phase DCL syntheses. The ability of a polymer bound template to identify and isolate a synthetic receptor via dynamic combinatorial chemistry was not compromised by the large size of the library, consisting of well over 140 theoretical members, demonstrating the practical advantages of a polymer-supported DCL methodology.

Practical High-Quality Electrostatic Potential Surfaces for Drug Discovery Using a Graph-Convolutional Deep Neural Network.

Inspecting protein and ligand electrostatic potential (ESP) surfaces in order to optimize electrostatic complementarity is a key activity in drug design. These ESP surfaces need to reflect the true electrostatic nature of the molecules, which typically means time-consuming high-level quantum mechanics (QM) calculations are required. For interactive design much faster alternative methods are required. Here, we present a graph convolutional deep neural network (DNN) model, trained on ESP surfaces derived from high quality QM calculations, that generates ESP surfaces for ligands in a fraction of a second. Additionally, we describe a method for constructing fast QM-trained ESP surfaces for proteins. We show that the DNN model generates ESP surfaces that are in good agreement with QM and that the ESP values correlate well with experimental properties relevant to medicinal chemistry. We believe that these high-quality, interactive ESP surfaces form a powerful tool for driving drug discovery programs forward. The trained model and associated code are available from https://github.com/AstexUK/ESP_DNN.

Crystallographic screening using ultra-low-molecular-weight ligands to guide drug design.

We present a novel crystallographic screening methodology (MiniFrags) that employs high-concentration aqueous soaks with a chemically diverse and ultra-low-molecular-weight library (heavy atom count 5-7) to identify ligand-binding hot and warm spots on proteins. We propose that MiniFrag screening represents a highly effective method for guiding optimisation of fragment-derived lead compounds or chemical tools and that the high screening hit rates reflect enhanced sampling of chemical space.

Two-vial, LC-MS identification of ephedrine receptors from a solution-phase dynamic combinatorial library of over 9000 components.

Reports on dynamic combinatorial chemistry have almost exclusively involved small libraries of 10-100 compounds. We now show how more than 9000 compounds can be screened in a single LC-MS analysis to reveal a series of new receptors that bind ephedrine in water. These results demonstrate the feasibility of screening DCLs that are substantially larger than the solution-phase libraries reported thus far.

Polymer-supported cationic templates for molecular recognition of anionic hosts in water.

Translocating solution-phase molecular recognition of oppositely charged hosts and guests to the solid phase represents a major challenge; we report a successful immobilisation strategy which allows selective host-guest interactions in water unencumbered by unwanted ion exchange-type interactions.

Predicting "Hot" and "Warm" Spots for Fragment Binding.

Computational fragment mapping methods aim to predict hotspots on protein surfaces where small fragments will bind. Such methods are popular for druggability assessment as well as structure-based design. However, to date researchers developing or using such tools have had no clear way of assessing the performance of these methods. Here, we introduce the first diverse, high quality validation set for computational fragment mapping. The set contains 52 diverse examples of fragment binding "hot" and "warm" spots from the Protein Data Bank (PDB). Additionally, we describe PLImap, a novel protocol for fragment mapping based on the Protein-Ligand Informatics force field (PLIff). We evaluate PLImap against the new fragment mapping test set, and compare its performance to that of simple shape-based algorithms and fragment docking using GOLD. PLImap is made publicly available from https://bitbucket.org/AstexUK/pli .

Protein-Ligand Informatics Force Field (PLIff): Toward a Fully Knowledge Driven "Force Field" for Biomolecular Interactions.

The Protein Data Bank (PDB) contains a wealth of data on nonbonded biomolecular interactions. If this information could be distilled down to nonbonded interaction potentials, these would have some key advantages over standard force fields. However, there are some important outstanding issues to address in order to do this successfully. This paper introduces the protein-ligand informatics "force field", PLIff, which begins to address these key challenges ( https://bitbucket.org/AstexUK/pli ). As a result of their knowledge-based nature, the next-generation nonbonded potentials that make up PLIff automatically capture a wide range of interaction types, including special interactions that are often poorly described by standard force fields. We illustrate how PLIff may be used in structure-based design applications, including interaction fields, fragment mapping, and protein-ligand docking. PLIff performs at least as well as state-of-the art scoring functions in terms of pose predictions and ranking compounds in a virtual screening context.

A synthetic receptor for nicotine from a dynamic combinatorial library.

Designing synthetic receptors that bind biologically relevant guests in an aqueous solution remains a considerable challenge. We now report a new synthetic receptor for nicotine, selected from a dynamic combinatorial library, that binds this guest in water at neutral pH through a combination of hydrophobic and π-π interactions.

Estimating equilibrium constants for aggregation from the product distribution of a dynamic combinatorial library.

Multicomponent chemical systems that exhibit a network of covalent and intermolecular interactions may produce interesting and often unexpected chemical or physical behavior. The formation of aggregates is a well-recognized example and presents a particular analytical challenge. We now report the development of a numerical fitting method capable of estimating equilibrium constants for the formation of aggregates from the product distribution of a dynamic combinatorial library containing self-recognizing library members.

Systems chemistry.

The study of complex mixtures of interacting synthetic molecules has historically not received much attention from chemists, even though research into complexity is well established in the neighbouring fields. However, with the huge recent interest in systems biology and the availability of modern analytical techniques this situation is likely to change. In this tutorial review we discuss some of the incentives for developing systems chemistry and we highlight the pioneering work in which molecular networks are making a splash. A distinction is made between networks under thermodynamic and kinetic control. The former include dynamic combinatorial libraries while the latter involve pseudo-dynamic combinatorial libraries, oscillating reactions and networks of autocatalytic and replicating compounds. These studies provide fundamental insights into the organisational principles of molecular networks and how these give rise to emergent properties such as amplification and feedback loops, and may eventually shed light on the origin of life. The knowledge obtained from the study of molecular networks should ultimately enable us to engineer new systems with properties and functions unlike any conventional materials.

Controlling the biological effects of spermine using a synthetic receptor.

Polyamines play an important role in biology, yet their exact function in many processes is poorly understood. Artificial host molecules capable of sequestering polyamines could be useful tools for studying their cellular function. However, designing synthetic receptors with affinities sufficient to compete with biological polyamine receptors remains a huge challenge. Binding affinities of synthetic hosts are typically separated by a gap of several orders of magnitude from those of biomolecules. We now report that a dynamic combinatorial selection approach can deliver a synthetic receptor that bridges this gap. The selected receptor binds spermine with a dissociation constant of 22 nM, sufficient to remove it from its natural host DNA and reverse some of the biological effects of spermine on the nucleic acid. In low concentrations, spermine induces the formation of left-handed DNA, but upon addition of our receptor, the DNA reverts back to its right-handed form. NMR studies and computer simulations suggest that the spermine complex has the form of a pseudo-rotaxane. The spermine receptor is a promising lead for the development of therapeutics or molecular probes for elucidating spermine's role in cell biology.

Anion-templated assembly of [2]rotaxanes.

Anion templation is used to develop a general method for rotaxane synthesis. The anion-templated synthesis of three new [2]rotaxanes containing positively charged pyridinium axles and neutral isophthalamide macrocyclic components is described. The incorporation of electron withdrawing substituents, such as the nitro group, into the 5-position of an isophthalamide bis-vinyl acyclic precursor results in a significant improvement in [2]rotaxane assembly yields. Rotaxane anion binding strengths are also enhanced whilst the rotaxane's unique interlocked binding domain ensures selectivity for chloride--the templating anion--is maintained.