Rational Ligand Design Research Articles

Computationally-Guided Development of a Chelated NHC-P Iridium(I) Complex for the Directed Hydrogen Isotope Exchange of Aryl Sulfones.

Herein, we report the rational, computationally-guided design of an iridium(I) catalyst system capable of enabling directed hydrogen isotope exchange (HIE) with the challenging sulfone directing group. Substrate binding energy was used as a parameter to guide rational ligand design via an in silico catalyst screen, resulting in a lead series of chelated iridium(I) NHC-phosphine complexes. Subsequent preparative studies show that the optimal catalyst system displays high levels of activity in HIE, and we demonstrate the labeling of a broad scope of substituted aryl sulfones. We also show that the activity of the catalyst is maintained at low pressures of deuterium gas and apply these conditions to tritium radiolabeling, including the expedient synthesis of a tritium-labeled drug molecule.

Rational design of new multitarget histamine H3 receptor ligands as potential candidates for treatment of Alzheimer's disease.

Design and development of multitarget-directed ligands (MTDLs) has become a very important approach in the search of new therapies for Alzheimer's disease (AD). In our present research, a number of xanthone derivatives were first designed using a pharmacophore model for histamine H3 receptor (H3R) antagonists/inverse agonists, and virtual docking was then performed for the enzyme acetylcholinesterase. Next, 23 compounds were synthesised and evaluated invitro for human H3R (hH3R) affinity and inhibitory activity on cholinesterases. Most of the target compounds showed hH3R affinities in nanomolar range and exhibited cholinesterase inhibitory activity with IC50 values in submicromolar range. Furthermore, the inhibitory effects of monoamine oxidases (MAO) A and B were investigated. The results showed low micromolar and selective human MAO B (hMAO B) inhibition. Two azepane derivatives, namely 23 (2-(5-(azepan-1-yl)pentyloxy)-9H-xanthen-9-one) and 25 (2-(5-(azepan-1-yl)pentyloxy)-7-chloro-9H-xanthen-9-one), were especially very promising and showed high affinity for hH3R (Ki=170nM and 100nM respectively) and high inhibitory activity for acetylcholinesterase (IC50=180nM and 136nM respectively). Moreover, these compounds showed moderate inhibitory activity for butyrylcholinesterase (IC50=880nM and 394nM respectively) and hMAO B (IC50=775nM and 897nM respectively). Furthermore, molecular docking studies were performed for hH3R, human cholinesterases and hMAO B to describe the mode of interactions with these biological targets. Next, the two most promising compounds 23 and 25 were selected for invivo studies. The results showed significant memory-enhancing effect of compound 23 in dizocilpine-induced amnesia in rats in two tests: step-through inhibitory avoidance paradigm (SIAP) and transfer latency paradigm time (TLPT). In addition, favourable analgesic effects of compound 23 were observed in neuropathic pain models. Therefore, compound 23 is a particularly promising structure for further design of new MTDLs for AD.

Structural Insights into the Specificity of Ligand Binding and Coactivator Assembly by Estrogen-Related Receptor β

Estrogen-related receptor β (ERRβ) is a nuclear receptor critical for many biological processes. Despite the biological and pharmaceutical importance of ERRβ, deciphering the structure of ERRβ has been hampered by the difficulties in obtaining a pure and stable protein for structural studies. In fact, the ERRβ ligand-binding domain remains the last unsolved ERR structure and also one of only a few unknown nuclear receptor structures. Here, we report the identification of a critical single-residue mutation resulted in robust solubility and stability of an active ERRβ ligand-binding domain, thereby providing a protein tool enabling the first probe into the biochemical and structural studies of this important receptor. The crystal structure reveals key structural features that have enabled the integration of the molecular determinants of signals transduced across the ligand binding and coregulator recruitment by all three ERR subtypes, which also provides a framework for the rational design of selective and potent ligands for the treatment of various ERR-mediated diseases.

Investigating GIPR (Ant)Agonism: A Structural Analysis of GIP and Its Receptor

The glucose-dependent insulinotropic polypeptide (GIP) is a 42-residue metabolic hormone that is actively being targeted for its regulatory role of glycemia and energy balance. Rational design of ligands, however, has been tedious with no structural data of the GIP receptor available. This study investigates structure and function of the GIP receptor (GIPR), using a homology model based on the GLP-1 receptor. Molecular dynamics combined with in vitro mutational data were used to pinpoint residues that play a role in ligand binding and/or receptor activation. Significant differences in binding mode were identified for the naturally occurring agonists GIP(1-30)NH2 and GIP(1-42) compared to high potency antagonists GIP(3-30)NH2 and GIP(5-30)NH2. Residues R1832.60, R1902.67 and R3005.40 are shown to play a key role in the activation of the GIPR and evidence suggests that a disruption of the K293ECL2 – E362ECL3 salt bridge by GIPR antagonists strongly reduces GIPR activation. These findings improve the basis for rational design of ligands targeting the GIPR.

Dioxygen Activation by Internally Aromatic Metallacycle: Crystallographic Structure and Mechanistic Investigations.

SummaryMononuclear metal-peroxo species are invoked as the key intermediates in metalloenzymatic or synthetic catalysis. However, either transience or sluggishness reactivity of synthetic analogs of metal-peroxo species impedes our understanding of oxygen activation mechanism. Herein, we designed and characterized a dioxygen-derived mononuclear osmium-peroxo complex, in which the peroxo ligand is stabilized by internally aromatic metallacycle. We demonstrate that the osmium-peroxo species shows catalytic activity toward promoterless alcohol dehydrogenations. Furthermore, computational studies provide a new mechanism for the osmium-peroxo-mediated alcohol oxidation, starting with the concerted double-hydrogen transfer and followed by the generation of osmium-oxo species. Interestingly, the internally aromatic metallacycle also plays a vital role in catalysis, which mediates the hydrogen transfer from osmium center to the distal oxygen atom of Os–OOH moiety, thus facilitating the Os–OOH→Os=O conversion. We expect that these insights will advance the development of aromatic metallacycle toward aerobic oxidation catalysis.

Silver-Catalyzed Enantioselective Propargylic C-H Bond Amination through Rational Ligand Design.

Asymmetric C-H amination via nitrene transfer is a powerful tool to prepare enantioenriched amine precursors from abundant C-H bonds. Herein, we report a regio- and enantioselective synthesis of γ-alkynyl γ-aminoalcohols via a silver-catalyzed propargylic C-H amination. The protocol was enabled by a new bis(oxazoline) (BOX) ligand designed via a rapid structure-activity relationship (SAR) analysis. The method utilizes accessible carbamate esters bearing γ-propargylic C-H bonds and furnishes versatile products in good yields and excellent enantioselectivity (90-99% ee). The putative Ag-nitrene is proposed to undergo enantiodetermining hydrogen-atom transfer (HAT) during the C-H amination event. Density functional theory calculations shed insight into the origin of enantioselectivity in the HAT step.

A Strategy for the Construction of Triply Interlocked Organometallic Cages by Rational Design of Poly-NHC Precursors.

Three-dimensional (3D) triply interlocked catenanes are a family of chemical topologies that consist of two identical, mechanically interlocked coordination cage components with intriguingly complex structures. Although only a few successful constructions of 3D interlocked catenanes have been achieved to date via metal-mediated assembly, these complex structures have thus far only been targeted by metal-nitrogen/oxygen coordination techniques. Here, taking advantage of rational ligand design, we report the efficient construction of a series of 3D triply interlocked [2]catenanes of the formula [Ag3L2]2, wherein the metal ions exclusively form bonds to N-heterocyclic carbene (NHC) units, and their subsequent transmetalation to the corresponding [Au3L2]2 gold analogues. The formation and transmetalation reactions proceed under mild conditions and are generally applicable. A series of characterization techniques were applied to confirm the formation and structure of the desired 3D triply interlocked architectures: multinuclear NMR spectroscopy, ESI-MS, and single-crystal X-ray diffraction analysis. The solid-state structure of [Ag3(1a)2]2(PF6)6 unambiguously confirms the existence of a 3D catenane that consists of two identical, mechanically interlocked trinuclear hexacarbene cage components. The interlocking of two 3D cages into a [2]catenane is driven by the efficient π···π stacking of triazine-triazine stacks with cooperative interactions between imidazo[1,5-a]pyridine subunits. Notably, the triply interlocked organometallic cages exhibit good stability toward various organic solvents, concentrations, and temperatures, and no disassembly occurred in the presence of coronene or pyrene. The future construction of mechanically interlocked architectures using metal-carbene bonds rather than metal-nitrogen bonds may provide assemblies with interesting properties for as-yet-unimagined applications in fields such as sensors and molecular electrical conductors.

A cobalt(II) coordination polymer based on a carboxyl- triazolyl-bifunctional ligand: Synthesis, characterization and catalytic reduction of 4-nitrophenol

In recent years, coordination polymers (CPs) have shown great potential as heterogeneous catalytic platform in various organic synthesis processes. However, the bottlenecks of low stability and inferior activity still limited their practical applications. In this work, by rational design and regulation of functional ligand and synthesis conditions, a new Co-based CP (Co-CP) was successfully obtained using H2O as the sole solvent and was structurally characterized via a series of techniques, including X-ray single crystal diffraction, powder X-ray diffraction (PXRD), thermogravimetric analysis (TGA), fourier transform infrared spectroscopy (FT-IR). The coordination of Co(II) sites together with the mixed carboxyl and triazolyl groups ligands formed 1D bands and further assembled into a 3D crystal structure through hydrogen bonding. As the heterogeneous catalyst, the excellent activity in catalyzing hydrogenation of 4-nitrophenol (4-NP) have achieved over the newly obtained Co-CP under relatively mild conditions. Furthermore, benefiting to the high moisture stability, the catalyst could be re-used for at least five times without obvious degradation in catalytic performance.

Unveiling Molecular Recognition of Sialoglycans by Human Siglec-10.

SummarySiglec-10 is an inhibitory I-type lectin selectively recognizing sialoglycans exposed on cell surfaces, involved in several patho-physiological processes. The key role Siglec-10 plays in the regulation of immune cell functions has made it a potential target for the development of immunotherapeutics against a broad range of diseases. However, the crystal structure of the protein has not been resolved for the time being and the atomic description of Siglec-10 interactions with complex glycans has not been previously unraveled. We present here the first insights of the molecular mechanisms regulating the interaction between Siglec-10 and naturally occurring sialoglycans. We used combined spectroscopic, computational and biophysical approaches to dissect glycans' epitope mapping and conformation upon binding in order to afford a description of the 3D complexes. Our outcomes provide a structural perspective for the rational design and development of high-affinity ligands to control the receptor functionality.

Differential contribution of metabotropic glutamate receptor 5 common allosteric binding site residues to biased allosteric agonism

Allosteric modulators of metabotropic glutamate receptor subtype 5 (mGlu5) represent an attractive therapeutic strategy for multiple CNS disorders. Chemically distinct mGlu5 positive allosteric modulators (PAMs) that interact with a common binding site can demonstrate biased allosteric agonism relative to the orthosteric agonist, DHPG, when comparing activity in signaling assays such as IP1 accumulation, ERK1/2 phosphorylation (pERK1/2) and iCa2+ mobilization. However, the structural basis for such biased agonism is not well understood. Therefore, we evaluated biased allosteric agonism mediated by four mGlu5 PAM-agonists from diverse chemical scaffolds (i.e., DPFE, VU0409551, VU29, and VU0424465) for three measures of mGlu5 activation (i.e., iCa2+ mobilization, IP1 accumulation and ERK1/2 phosphorylation) at eight single-point mutations within the common allosteric binding pocket of mGlu5. In particular, mGlu5 allosteric site mutations had differential effects on the intrinsic efficacy of mGlu5 PAMs for multiple signaling pathways. Specifically, a loss of agonism for iCa2+ mobilization was evident for DPFE and VU0409551 for most mutants, whereas IP1 accumulation and ERK phosphorylation were retained, albeit with reduced maximal responses. Additionally, bias profiles between iCa2+ mobilization and IP1/ERK pathways remained similar to wild type for most mutants. However, W784A and A809G mutants lost bias between IP1 accumulation and ERK phosphorylation for VU0424465, whereas a loss of bias between iCa2+ mobilization and ERK1/2 phosphorylation was evident for F787A, S808A and A809G mutants. These data provide further insight into the structural requirements for allosteric agonism across multiple mGlu5-mediated signaling pathways. An understanding of mGlu5 biased agonism at a structural level may provide the foundation for rational structure-based design of biased allosteric ligands for the treatment of neurological disorders.

High resolution crystal structure of a KRAS promoter G-quadruplex reveals a dimer with extensive poly-A π-stacking interactions for small-molecule recognition.

Aberrant KRAS signaling is a driver of many cancers and yet remains an elusive target for drug therapy. The nuclease hypersensitive element of the KRAS promoter has been reported to form secondary DNA structures called G-quadruplexes (G4s) which may play important roles in regulating KRAS expression, and has spurred interest in structural elucidation studies of the KRAS G-quadruplexes. Here, we report the first high-resolution crystal structure (1.6 Å) of a KRAS G-quadruplex as a 5′-head-to-head dimer with extensive poly-A π-stacking interactions observed across the dimer. Molecular dynamics simulations confirmed that the poly-A π-stacking interactions are also maintained in the G4 monomers. Docking and molecular dynamics simulations with two G4 ligands that display high stabilization of the KRAS G4 indicated the poly-A loop was a binding site for these ligands in addition to the 5′-G-tetrad. Given sequence and structural variability in the loop regions provide the opportunity for small-molecule targeting of specific G4s, we envisage this high-resolution crystal structure for the KRAS G-quadruplex will aid in the rational design of ligands to selectively target KRAS.

Rigid π-Extended Boron Difluoride Complex with Mega-Stokes Shift for Bioimaging.

The rational design of a rigid π-extended ligand, suitable for the formation of four-coordinate boron complexes, has led to the synthesis of the fused hexacyclic structure of carbazolo[2,1-c]phenanthridine. The photophysical characterization of the novel fluorophore revealed a significant Stokes shift whose intramolecular charge transfer origin has been corroborated by computational calculations. The usefulness of the reported N,N-difluoroboryl complex as fluorescent probe with large Stokes shift has been demonstrated for cancer cells imaging.

Design of first in class bitopic ligands targeting the sodium binding pocket in opioid receptors

Opioid agonists have been used in the field of pain management for centuries, but are considered a major public health concern, especially in the US. One of the biggest challenges consists in understanding the ability to target specifically the different subtypes of opioid receptors and to trigger a specific functional response correlating with an in vivo analgesic response devoid of side‐effects.These opioid receptors are part of the GPCRs family, which is known to have common features across different subfamilies. One important feature of these receptors is the presence of allosteric binding pockets, which is progressively gaining momentum as a novel target for current therapeutic strategies. We hypothesized that targeting an allosteric site could potentially allow for receptor functional selectivity, helping to reduce the overall side effects profile. One site, in particular, known as the Na+ binding pocket, is known to play a key role in GPCR function and is thought to be the center of the functional mechanism, with several bias switches characterized in the pocket residues (Katritch et al., Trends Biochem Sci. 2014).Here we report structure‐based rational drug design of bitopic ligands targeting the Na+ pocket of mu (MOR) and kappa opioid receptors (KOR). Our designed bitopics show high affinity, subtype selectivity, G‐protein bias and analgesic actions in mice. Mutations in Na+ binding pocket diminished functional potency validating allosteric site targeting. Together, results suggest the possibility of achieving subtype selectivity and identification of an additional subpocket in both MOR and KOR to reduce βarrestin‐2 recruitment by targeting an allosteric pocket in the opioid receptors. The highly conserved constitution of the Na+ binding pocket opens the opportunity for rational discovery of new GPCR modulators with desired functional, and potentially therapeutic profile for opioids as well as other class A GPCRs.Support or Funding InformationWe gratefully acknowledge the financial support from Faculty Research Incentive Fund, NIDA, NIAAA and US department of defense. We also would like to thank the Philippe Foundation for their financial support.

Structural Insights and Thermodynamics of Membrane‐Facilitated Binding and Unbinding Mechanisms of Long‐Acting β2‐Adrenergic Agonists

ObjectiveThe β2‐adrenergic receptor (β2‐AR) is a member of the G protein‐coupled receptor family. β2‐AR agonists such as salbutamol, salmeterol, and formoterol constitute the frontline treatment for both asthma and chronic obstructive pulmonary disorder. These drugs differ significantly in their onset and duration of actions. The structural basis and mechanisms underlying these differences in pharmacology are unknown. Experimental studies suggest that a “microkinetic model” in which the plasma membrane acts as a depot enriching local drug concentration around the receptor adequately explains the long‐lasting effects of lipophilic salmeterol and formoterol. This membrane contribution was also shown to affect drugs’ efficacy by influencing their observed binding kinetics, especially the association rate constant kon. In addition, published mutagenesis studies have shown that transmembrane helices (TMH) 2 and 7 are essential for salmeterol’s affinity to β2‐AR. Our central hypothesis is that distinct structural features of these drugs resulting in specific lipid interactions cause differences in membrane‐involved receptor binding and unbinding events. Specifically, we hypothesize that differences in bilayer depths of ligands would affect their receptor access through the transmembrane helices, and thus the association and dissociation pathways of the long‐acting drugs are likely different from that of short‐acting salbutamol. Here, we present an extensive computational study elucidating thermodynamics and potential lipid‐mediated association and dissociation pathways of salmeterol and formoterol and compare them with that of salbutamol.MethodsThe membrane partitioning characteristics of the ligands in a model membrane (containing POPC lipid and cholesterol) were investigated by steered molecular dynamics and Umbrella Sampling simulations, using NAMD software. The dissociation and association pathways of each ligand were investigated by advanced simulation techniques using the crystal structure of β2‐AR bound to salmeterol (PDB ID 6MXT). The absolute binding free energies were estimated using GROMACS/PLUMED software.ResultsThe association and dissociation paths of salmeterol and formoterol reveal potential membrane‐involved receptor access routes through TMHs 1 and 7. Salbutamol accesses the binding site through a unique aqueous path lined with polar residues. The calculated binding free energies and kinetic parameters are in good agreement with the published experimental values. The residue‐ligand interactions critical for receptor access and binding within the site provide structural basis for membrane‐involved binding mechanisms and agree with the published crystallographic and mutagenesis studies.ConclusionsOur results illustrate the functional role of membrane lipids in influencing access and binding of ligands to β2‐AR. The distinct structural features of the ligands and their specific interactions with membrane lipids appear to influence their binding kinetics. The obtained structural insights can be used for rational design of ligands to exploit membrane interactions for optimal pharmacology.Support or Funding InformationNational Institutes of Health‐NIGMS R15 GM131293‐01Membrane‐involved ligand‐binding to beta2‐ARFigure 1

PDGFR-β Promoter Forms a Vacancy G-Quadruplex that Can Be Filled in by dGMP: Solution Structure and Molecular Recognition of Guanine Metabolites and Drugs.

Aberrant expression of PDGFR-β is associated with a number of diseases. The G-quadruplexes (G4s) formed in PDGFR-β gene promoter are transcriptional modulators and amenable to small molecule targeting. The major G4 formed in the PDGFR-β gene promoter was previously shown to have a broken G-strand. Herein, we report that the PDGFR-β gene promoter sequence forms a vacancy G-quadruplex (vG4) which can be filled in and stabilized by physiologically relevant guanine metabolites, such as dGMP, GMP, and cGMP, as well as guanine-derivative drugs. We determined the NMR structure of the dGMP-fill-in PDGFR-β vG4 in K+ solution. This is the first structure of a guanine-metabolite-fill-in vG4 based on a human gene promoter sequence. Our structure and systematic analysis elucidate the contributions of Hoogsten hydrogen bonds, sugar, and phosphate moieties to the specific G-vacancy fill-in. Intriguingly, an equilibrium of 3'- and 5'-end vG4s is present in the PDGFR-β promoter sequence, and dGMP favors the 5'-end fill-in. Guanine metabolites and drugs were tested and showed a conserved selectivity for the 5'-vacancy, except for cGMP. cGMP binds both the 3'- and 5'-end vG4s and forms two fill-in G4s with similar population. Significantly, guanine metabolites are involved in many physiological and pathological processes in human cells; thus, our results provide a structural basis to understand their potential regulatory functions by interaction with promoter vG4s. Moreover, the NMR structure can guide rational design of ligands that target the PDGFR-β vG4.

Avian Pattern Recognition Receptor Sensing and Signaling.

Pattern recognition receptors (PRRs) are a class of immune sensors that play a critical role in detecting and responding to several conserved patterns of microorganisms. As such, they play a major role in the maintenance of immune homeostasis and anti-microbial defense. Fundamental knowledge pertaining to the discovery of PRR functions and their ligands continue to advance the understanding of immune system and disease resistance, which led to the rational design and/or application of various PRR ligands as vaccine adjuvants. In addition, the conserved nature of many PRRs throughout the animal kingdom has enabled the utilization of the comparative genomics approach in PRR identification and the study of evolution, structural features, and functions in many animal species including avian. In the present review, we focused on PRR sensing and signaling functions in the avian species, domestic chicken, mallard, and domestic goose. In addition to summarizing recent advances in the understanding of avian PRR functions, the present review utilized a comparative biology approach to identify additional PRRs, whose functions have been well studied in mammalians but await functional characterization in avian.

Target Self‐Enhanced Selectivity in Metal‐Specific DNAzymes

AbstractHighly selective recognition of metal ions by rational ligand design is challenging, and simple metal binding by biological ligands is often obscured by nonspecific interactions. In this work, binding‐triggered catalysis is used and metal selectivity is greatly increased by increasing the number of metal ions involved, as exemplified in a series of in vitro selected RNA‐cleaving DNAzymes. The cleavage junction is modified with a glycyl–histidine‐functionalized tertiary amine moiety to provide multiple potential metal coordination sites. DNAzymes that bind 1, 2, and 3 Zn2+ ions, increased their selectivity for Zn2+ over Co2+ ions from approximately 20‐, 1000‐, to 5000‐fold, respectively. This study offers important insights into metal recognition by combining rational ligand design and combinatorial selection, and it provides a set of new DNAzymes with excellent selectivity for Zn2+ ions.

Target Self-Enhanced Selectivity in Metal-Specific DNAzymes.

Highly selective recognition of metal ions by rational ligand design is challenging, and simple metal binding by biological ligands is often obscured by nonspecific interactions. In this work, binding-triggered catalysis is used and metal selectivity is greatly increased by increasing the number of metal ions involved, as exemplified in a series of in vitro selected RNA-cleaving DNAzymes. The cleavage junction is modified with a glycyl-histidine-functionalized tertiary amine moiety to provide multiple potential metal coordination sites. DNAzymes that bind 1, 2, and 3 Zn2+ ions, increased their selectivity for Zn2+ over Co2+ ions from approximately 20-, 1000-, to 5000-fold, respectively. This study offers important insights into metal recognition by combining rational ligand design and combinatorial selection, and it provides a set of new DNAzymes with excellent selectivity for Zn2+ ions.

Rational design of affinity ligands for bioseparation

Affinity adsorbents have been the cornerstone in protein purification. The selective nature of the molecular recognition interactions established between an affinity ligands and its target provide the basis for efficient capture and isolation of proteins. The plethora of affinity adsorbents available in the market reflects the importance of affinity chromatography in the bioseparation industry. Ligand discovery relies on the implementation of rational design techniques, which provides the foundation for the engineering of novel affinity ligands. The main goal for the design of affinity ligands is to discover or improve functionality, such as increased stability or selectivity. However, the methodologies must adapt to the current needs, namely to the number and diversity of biologicals being developed, and the availability of new tools for big data analysis and artificial intelligence. In this review, we offer an overview on the development of affinity ligands for bioseparation, including the evolution of rational design techniques, dating back to the years of early discovery up to the current and future trends in the field.

Identification and characterization of fragment binding sites for allosteric ligand design using the site identification by ligand competitive saturation hotspots approach (SILCS-Hotspots)

BackgroundFragment-based ligand design is used for the development of novel ligands that target macromolecules, most notably proteins. Central to its success is the identification of fragment binding sites that are spatially adjacent such that fragments occupying those sites may be linked to create drug-like ligands. Current experimental and computational approaches that address this problem typically identify only a limited number of sites as well as use a limited number of fragment types. MethodsThe site-identification by ligand competitive saturation (SILCS) approach is extended to the identification of fragment bindings sites, with the method termed SILCS-Hotspots. The approach involves precomputation of the SILCS FragMaps following which the identification of Hotspots, performed by identifying of all possible fragment binding sites on the full 3D structure of the protein followed by spatial clustering. ResultsThe SILCS-Hotspots approach identifies a large number of sites on the target protein, including many sites not accessible in experimental structures due to low binding affinities and binding sites on the protein interior. The identified sites are shown to recapitulate the location of known drug-like molecules in both allosteric and orthosteric binding sites on seven proteins including the androgen receptor, the CDK2 and Erk5 kinases, PTP1B phosphatase and three GPCRs; the β2-adrenergic, GPR40 fatty-acid binding and M2-muscarinic receptors. Analysis indicates the importance of considering all possible fragment binding sites, and not just those accessible to experimental methods, when identifying novel binding sites and performing ligand design versus just considering the most favorable sites. The approach is shown to identify a larger number of known binding sites of drug-like molecules versus the commonly used FTMap and Fpocket methods. General significanceThe present results indicate the potential utility of the SILCS-Hotspots approach for fragment-based rational design of ligands, including allosteric modulators.