Small Molecule Drug Design Research Articles

Synthetic Self-Localizing Ligands That Control the Spatial Location of Proteins in Living Cells

Small-molecule ligands that control the spatial location of proteins in living cells would be valuable tools for regulating biological systems. However, the creation of such molecules remains almost unexplored because of the lack of a design methodology. Here we introduce a conceptually new type of synthetic ligands, self-localizing ligands (SLLs), which spontaneously localize to specific subcellular regions in mammalian cells. We show that SLLs bind their target proteins and relocate (tether) them rapidly from the cytoplasm to their targeting sites, thus serving as synthetic protein translocators. SLL-induced protein translocation enables us to manipulate diverse synthetic/endogenous signaling pathways. The method is also applicable to reversible protein translocation and allows control of multiple proteins at different times and locations in the same cell. These results demonstrate the usefulness of SLLs in the spatial (and temporal) control of intracellular protein distribution and biological processes, opening a new direction in the design of small-molecule tools or drugs for cell regulation.

A compound‐based computational approach for the accurate determination of hot spots

A plethora of both experimental and computational methods have been proposed in the past 20 years for the identification of hot spots at a protein-protein interface. The experimental determination of a protein-protein complex followed by alanine scanning mutagenesis, though able to determine hot spots with much precision, is expensive and has no guarantee of success while the accuracy of the current computational methods for hot-spot identification remains low. Here, we present a novel structure-based computational approach that accurately determines hot spots through docking into a set of proteins homologous to only one of the two interacting partners of a compound capable of disrupting the protein-protein interaction (PPI). This approach has been applied to identify the hot spots of human activin receptor type II (ActRII) critical for its binding toward Cripto-I. The subsequent experimental confirmation of the computationally identified hot spots portends a potentially accurate method for hot-spot determination in silico given a compound capable of disrupting the PPI in question. The hot spots of human ActRII first reported here may well become the focal points for the design of small molecule drugs that target the PPI. The determination of their interface may have significant biological implications in that it suggests that Cripto-I plays an important role in both activin and nodal signal pathways.

Structure of class B GPCR corticotropin-releasing factor receptor 1

Structural analysis of class B G-protein-coupled receptors (GPCRs), cell-surface proteins that respond to peptide hormones, has been restricted to the amino-terminal extracellular domain, thus providing little understanding of the membrane-spanning signal transduction domain. The corticotropin-releasing factor receptor type 1 is a class B receptor which mediates the response to stress and has been considered a drug target for depression and anxiety. Here we report the crystal structure of the transmembrane domain of the human corticotropin-releasing factor receptor type 1 in complex with the small-molecule antagonist CP-376395. The structure provides detailed insight into the architecture of class B receptors. Atomic details of the interactions of the receptor with the non-peptide ligand that binds deep within the receptor are described. This structure provides a model for all class B GPCRs and may aid in the design of new small-molecule drugs for diseases of brain and metabolism.

Characterization of a Small Molecule Inhibitor of Plasminogen Activator Inhibitor Type 1 That Accelerates the Transition into the Latent Conformation

A novel class of small molecule inhibitors for plasminogen activator inhibitor type 1 (PAI-1), represented by AZ3976, was identified in a high throughput screening campaign. AZ3976 displayed an IC(50) value of 26 μm in an enzymatic chromogenic assay. In a plasma clot lysis assay, the compound was active with an IC(50) of 16 μm. Surprisingly, AZ3976 did not bind to active PAI-1 but bound to latent PAI-1 with a K(D) of 0.29 μm at 35 °C and a binding stoichiometry of 0.94, as measured by isothermal calorimetry. Reversible binding was confirmed by surface plasmon resonance direct binding experiments. The x-ray structure of AZ3976 in complex with latent PAI-1 was determined at 2.4 Å resolution. The inhibitor was bound in the flexible joint region with the entrance to the cavity located between α-helix D and β-strand 2A. A set of surface plasmon resonance experiments revealed that AZ3976 inhibited PAI-1 by enhancing the latency transition of active PAI-1. Because AZ3976 only had measurable affinity for latent PAI-1, we propose that its mechanism of inhibition is based on binding to a small fraction in equilibrium with active PAI-1, a latent-like prelatent form, from which latent PAI-1 is then generated more rapidly. This mode of action, with induced accelerated latency transition of active PAI-1 may, together with supporting x-ray data, provide improved opportunities for small molecule drug design in the hunt for therapeutically useful PAI-1 inhibitors.

Glucagon-like peptide-1 receptor dimerization differentially regulates agonist signaling but does not affect small molecule allostery

The glucagon-like peptide-1 receptor (GLP-1R) is a family B G protein-coupled receptor and an important drug target for the treatment of type II diabetes, with activation of pancreatic GLP-1Rs eliciting glucose-dependent insulin secretion. Currently, approved therapeutics acting at this receptor are peptide based, and there is substantial interest in small molecule modulators for the GLP-1R. Using a variety of resonance energy transfer techniques, we demonstrate that the GLP-1R forms homodimers and that transmembrane helix 4 (TM4) provides the primary dimerization interface. We show that disruption of dimerization using a TM4 peptide, a minigene construct encoding TM4, or by mutation of TM4, eliminates G protein-dependent high-affinity binding to GLP-1(7-36)NH(2) but has selective effects on receptor signaling. There was <10-fold decrease in potency in cAMP accumulation or ERK1/2 phosphorylation assays but marked loss of intracellular calcium mobilization by peptide agonists. In contrast, there was near-complete abrogation of the cAMP response to an allosteric agonist, compound 2, but preservation of ERK phosphorylation. Collectively, this indicates that GLP-1R dimerization is important for control of signal bias. Furthermore, we reveal that two small molecule ligands are unaltered in their ability to allosterically modulate signaling from peptide ligands, demonstrating that these modulators act in cis within a single receptor protomer, and this has important implications for small molecule drug design.

Natural Peptides with Potential Applications in Drug Development, Diagnosis, and/or Biotechnology

Natural Peptides with Potential Applications in Drug Development, Diagnosis, and/or Biotechnology

Towards structure-based protein drug design

Structure-based drug design for chemical molecules has been widely used in drug discovery in the last 30 years. Many successful applications have been reported, especially in the field of virtual screening based on molecular docking. Recently, there has been much progress in fragment-based as well as de novo drug discovery. As many protein-protein interactions can be used as key targets for drug design, one of the solutions is to design protein drugs based directly on the protein complexes or the target structure. Compared with protein-ligand interactions, protein-protein interactions are more complicated and present more challenges for design. Over the last decade, both sampling efficiency and scoring accuracy of protein-protein docking have increased significantly. We have developed several strategies for structure-based protein drug design. A grafting strategy for key interaction residues has been developed and successfully applied in designing erythropoietin receptor-binding proteins. Similarly to small-molecule design, we also tested de novo protein-binder design and a virtual screen of protein binders using protein-protein docking calculations. In comparison with the development of structure-based small-molecule drug design, we believe that structure-based protein drug design has come of age.

Interaction between CK2α and CK2β, the Subunits of Protein Kinase CK2: Thermodynamic Contributions of Key Residues on the CK2α Surface

The protein Ser/Thr kinase CK2 (former name: casein kinase II) exists predominantly as a heterotetrameric holoenzyme composed of two catalytic subunits (CK2α) bound to a dimer of noncatalytic subunits (CK2β). We undertook a study to further understand how these subunits interact to form the tetramer. To this end, we used recombinant, C-terminal truncated forms of human CK2 subunits that are able to form the holoenzyme. We analyzed the interaction thermodynamics between the binding of CK2α and CK2β as well as the impact of changes in temperature, pH, and the ionization enthalpy of the buffer using isothermal titration calorimetry (ITC). With structure-guided alanine scanning mutagenesis we truncated individual side chains in the hydrophobic amino acid cluster located within the CK2α interface to identify experimentally the amino acids that dominate affinity. The ITC results indicate that Leu41 or Phe54 single mutations were most disruptive to binding of CK2β. Additionally, these CK2α mutants retained their kinase activity. Furthermore, the substitution of Leu41 in combination with Phe54 showed that the individual mutations were not additive, suggesting that the cooperative action of both residues played a role. Interestingly, the replacement of Ile69, which has a central position in the interaction surface of CK2α, only had modest effects. The differences between Leu41, Phe54, and Ile69 in interaction relevance correlate with solvent accessibility changes during the transition from unbound to CK2β-bound CK2α. Identifying residues on CK2α that play a key role in CK2α/CK2β interactions is important for the future generation of small molecule drug design.

BAS/BSCR37 Discovery and characterisation of novel peptide agonists and the first antagonist for the cardiovascular peptides, the apelins

The recently discovered apelin family of peptides mediate their actions by a single G-protein coupled receptor, APJ. We have previously shown that apelins have three major actions in the human...

ANCHOR: a web server and database for analysis of protein-protein interaction binding pockets for drug discovery

ANCHOR is a web-based tool whose aim is to facilitate the analysis of protein–protein interfaces with regard to its suitability for small molecule drug design. To this end, ANCHOR exploits the so-called anchor residues, i.e. amino acid side-chains deeply buried at protein–protein interfaces, to indicate possible druggable pockets to be targeted by small molecules. For a given protein–protein complex submitted by the user, ANCHOR calculates the change in solvent accessible surface area (ΔSASA) upon binding for each side-chain, along with an estimate of its contribution to the binding free energy. A Jmol-based tool allows the user to interactively visualize selected anchor residues in their pockets as well as the stereochemical properties of the surrounding region such as hydrogen bonding. ANCHOR includes a Protein Data Bank (PDB) wide database of pre-computed anchor residues from more than 30 000 PDB entries with at least two protein chains. The user can query according to amino acids, buried area (SASA), energy or keywords related to indication areas, e.g. oncogene or diabetes. This database provides a resource to rapidly assess protein–protein interactions for the suitability of small molecules or fragments with bioisostere anchor analogues as possible compounds for pharmaceutical intervention. ANCHOR web server and database are freely available at http://structure.pitt.edu/anchor.

NMR structure of F-actin-binding domain of Arg/Abl2 from Homo sapiens

The Northeast Structural Genomics Consortium has used bioinformatics methods to construct a Human Cancer Pathway Interaction Network (HCPIN),1 a comprehensive 3D structure-function database of human-cancer-associated proteins and protein complexes in the context of their interaction networks. The FABD domain of Arg (Abl-related gene; Abl2) was selected as NESG HCPIN target HR5537. Arg and Abl (Abelson tyrosine kinase; Abl1), the Abl non-receptor tyrosine kinases, link diverse cell surface receptors to the regulation of cytoskeletal dynamics and regulate cytoskeletal reorganization, cell proliferation, survival, adhesion, migration and stress responses in multiple cells types.2–7 Abl and Arg kinases are multi-domain proteins with highly conserved Src kinase homology 3 (SH3), SH2, kinase (SH1) domains in the N-terminal half. The C-terminal halves of these kinases are more divergent, however, the functions encoded by the C-terminus are critical for the overall functions of these proteins.4 Although Abl and Arg exhibit overlapping expression in many tissues, Arg is most highly expressed in brain, thymus, spleen, and muscle.8 Differences in regulation of cell migration by Abl and Arg have also been reported.7 Consistent with the nuclear and cytoplasmic localization of Abl and the predominant cytoplasmic localization of Arg, three nuclear localization signals (NLS), one nuclear export signal NES motifs and a DNA-binding domain are found in Abl but not in Arg.4 Abl and Arg share a C-terminal calponin homology F-actin-binding domain (FABD) with ~44% sequence identity, which distinguishes Abl family kinases from other non-receptor tyrosine kinases.4,9,10 Preceding this shared FABD, Arg has a microtubule-binding (MT) domain and a second talin-like F-actin-binding domain that is characterized by an I/LWEQ sequence while Abl kinase has a globular (G)-actin binding domain.4,9,10,11 Arg uses its FABD to anchoring actin and other cytoskeletal partner for signal transfer and other biological functions.4 Both human Abl FABD and Arg FABD belong to the F_actin_bind protein domain family (Pfam12 entry PF08919) comprised of 21 sequences. The NMR structure of the human Abl FABD, the only available structure in F_actin_bind family, has been reported recently13 ; it forms a compact left-handed four helix bundle in solution. The Arg FABD was selected as HCPIN target by NESG for structure determination.1 The NMR structure of human Arg FABD reported here can serve as a structural basis for elucidating the molecular mechanism of Arg pathway, for studies of protein complex formation, and potentially in small molecule drug design.

Selective regulation of aromatase expression for drug discovery

Aromatase is a particularly attractive drug target in the treatment of hormone-responsive breast cancer, and aromatase activity in breast cancer patients is greater in or near the tumor tissue compared with the normal breast tissue. Complex regulation of aromatase expression in human tissues involves alternative promoter sites that provide tissue-specific control. Previous studies in our laboratories suggested a strong association between aromatase ( CYP19) gene expression and the expression of cyclooxygenase ( COX) genes. Additionally, COX selective inhibitors can suppress CYP19 gene expression and decrease aromatase activity. Our current hypothesis is that pharmacological regulation of aromatase can act locally to decrease the biosynthesis of estrogen and may provide additional therapy options for patients with hormone-dependent breast cancer. Two pharmacological approaches are being developed, one approach utilizing small molecule drug design and the second approach involving mRNA silencing technology. The small molecule drug design approach focuses on the synthesis and biological evaluation of a novel series of sulfonanilide analogs derived from COX-2 selective inhibitors. Combinatorial chemistry approaches were used to generate diversely substituted novel sulfonanilides. The compounds suppress aromatase enzyme activity in SK-BR-3 breast cancer cells in a dose and time dependent manner, and structure activity analysis does not find a correlation between aromatase suppression and COX inhibition. Real-time PCR analysis demonstrates that the sulfonanilide analogs decrease aromatase gene transcription in breast cells. Furthermore, the sulfonanilide compounds selectively decrease aromatase gene expression in several breast cancer cells, without exhibiting cytotoxic or apoptotic effects at low micromole concentrations. A ligand-based pharmacophore model for selective aromatase modulation (SAM) by the novel sulfonanilides identified an aromatic ring, two hydrogen bond acceptors, and a hydrophobic function as four key chemical features. In the second approach, short interfering RNAs (siRNA) were designed targeting human aromatase mRNA. Treatment of breast cancer cells with siRNAs targeting aromatase (siAROMs) completely masked the aromatase enzyme activity and resulted in suppression of CYP19 mRNA. Thus, these results suggest that the novel sulfonanilides and the siRNAs targeting aromatase expression may be valuable tools for selective regulation of aromatase in breast cancer.

What is Next for Small-Molecule Drug Discovery?

Humankind has been in the business of discovering drugs for thousands of years. At present, small-molecule drug design is based on specific macromolecular receptors as targets for inhibition or modulation. To this end, a number of clever approaches have evolved over time: computer-aided techniques including structure-activity relationships and synthesis, high-throughput screening, quantitative structure-activity relationships, hypotheses derived from ligand- and/or structure-based information and focused library approaches. In recent years, several alternative strategies have appeared in the form of the emerging paradigms of polypharmacology, systems biology and personalized medicine. These innovations point to key challenges and breakthroughs likely to affect the future of small-molecule drug discovery.

Molecular Modeling of the Peptide Agonist-Binding Site in a Neurokinin-2 Receptor

The neurokinin-2 receptor is a member of the rhodopsin family of G-protein coupled receptors, which represents one of the most relevant target families in small-molecule drug design. NK-2 receptors have been implicated in playing a pathophysiological role in asthma. Activation of the NK-2 receptor by its endogenous peptide agonist, tachykinins, is associated with diverse biological responses like bronchoconstriction, vasodepression, and regulation of endocrine functions. Agonist binding to the receptor is a crucial event in initiating signaling, and therefore characterization of the structural features of the agonists can reveal the molecular basis of receptor activation and help in rational design of novel therapeutics. In this study a molecular model for the interaction of the primary ligand NKA with its G-protein coupled receptor neurokinin-2 receptor has been developed. A three-dimensional model for the NK-2 receptor has been generated by homology modeling using rhodopsin as a template. A knowledge based docking of the NMR derived bioactive conformation of NKA to the receptor has been performed utilizing the ligand binding data obtained from the photoaffinity labeling and site-directed mutagenesis studies. The molecular model for the NKA/NK-2 receptor complex thus obtained sheds light on the topographical features of the binding pocket of the receptor and provides atomic insight into the biochemical data currently available for the receptor. The results of the receptor modeling studies have been used to discuss the molecular determinants for NK-2 receptor selectivity.

Dynamics differences of SAM‐I riboswitch aptamer between SAM bound and without SAM: insight into conformational rearrangement

Increasing attention has focused on targeting RNAs for small molecule drug design. However, because RNAs are highly flexible, it is still not clear how the interactions between small molecules and RNAs are coupled with the conformational change of RNAs. A riboswitch is an autonomous cis‐regulatory element that controls gene expression in response to the signals from small molecule metabolites, such as amino acids, nucleotides, or enzyme cofactors etc. The SAM‐I riboswitch is one member of this regulatory family that can control the expression of biosynthetic proteins involved in sulfur metabolism through conformational change upon the binding of S‐adenosylmethione (SAM). Although the structure of SAM‐I riboswitch aptamer domain has been solved via X‐ray crystallography, it is just a static view of how SAM binds to SAM‐I riboswitch. In this study, molecular dynamics (MD) simulations are performed on SAM‐I riboswitch aptamer with SAM and without SAM. Principle component analysis (PCA) is applied to explore the global dynamics differences of SAM‐I riboswitch aptamer between SAM present and SAM absent. Additionally, other trajectory analyses are also used to probe the correlation between the local flexibility and the global motion. MD simulation results suggest that dynamics of the P4 helix is affected upon the binding of SAM. This change in dynamic behavior may be related to the conformational changes observed in the SAM‐I riboswitch.

Gas-Phase Unfolding and Disassembly Reveals Stability Differences in Ligand-Bound Multiprotein Complexes

Mass spectrometry (MS) is widely used to assess the binding of small molecules to proteins and their complexes. In many cases, subtle differences in the stability afforded by binding of ligands to protein assemblies cannot be detected by MS. Here we show that monitoring the unfolding of protein subunits, using ion mobility-MS, allows differentiation of the effects of ligand binding not normally observed by MS alone. Using wild-type and disease-associated variants of tetrameric transthyretin, MS data indicate that populations of the variant protein are less stable than wild-type. Ion mobility-MS, however, is able to show that the natural ligand of transthyretin, thyroxine, provides a larger stability increase to the tetramer composed of variant subunits than to the wild-type protein-ligand complex. Overall, therefore, our results have implications for small-molecule drug design directed at multiprotein targets.

Meta-basic estimates the size of druggable human genome

We present here the estimation of the upper limit of the number of molecular targets in the human genome that represent an opportunity for further therapeutic treatment. We select around approximately 6300 human proteins that are similar to sequences of known protein targets collected from DrugBank database. Our bioinformatics study estimates the size of 'druggable' human genome to be around 20% of human proteome, i.e. the number of the possible protein targets for small-molecule drug design in medicinal chemistry. We do not take into account any toxicity prediction, the three-dimensional characteristics of the active site in the predicted 'druggable' protein families, or detailed chemical analysis of known inhibitors/drugs. Instead we rely on remote homology detection method Meta-BASIC, which is based on sequence and structural similarity. The prepared dataset of all predicted protein targets from human genome presents the unique opportunity for developing and benchmarking various in silico chemo/bio-informatics methods in the context of the virtual high throughput screening.

Drug discovery beyond the ‘rule-of-five’

Although a very useful guideline for orally bioavailable small-molecule drug design, the 'rule-of-five' (also known as 'Lipinski's rule of drug-likeness') has to some extent been overemphasized. Firstly, only 51% of all FDA-approved small-molecule drugs are both used orally and comply with the 'rule-of-five'. This does not even include the increasing number of biologicals of which several have reached 'blockbuster' status. Secondly, it does not cover natural product and semisynthetic natural product drugs, which constitute over one-third of all marketed small-molecule drugs. A more balanced and programmatic approach to drug discovery should be more productive than to rely on an overemphasis of 'rule-of-five' compliance. Rather it should consider proactively the development of parenteral drugs in parallel to oral drugs and to consider the development of therapeutic antibodies in parallel to small-molecule drugs. These are particularly relevant for efforts against 'first-in-class' and/or particularly challenging targets such as proteases and those involving protein-protein interactions. In addition, more effort should be invested in natural product research. Emerging novel technologies such as synthetic biology (genetic engineering of living organisms to produce small-molecule therapeutics) may address several challenging issues of natural product-based drug discovery including synthetic feasibility and ligand efficiency.

Newly Approved and Promising Antidiabetic Agents

Type 2 diabetes is an endocrine/metabolic disease characterized by hyperglycemia. It is now well established that insulin resistance and pancreatic β-cell dysfunction/failure are the two major components of the physiopathology of the disease. Current available therapies do not successfully enable patients with type 2 diabetes to reach glycemic goals. Even with intensive treatment type 2 diabetic patients may face spikes in blood glucose after meals, weight gain, and a loss of effectiveness of their treatments over time. The novel agents recently developed by the Pharmaceutical Industry may either provide an alternative therapeutic strategy or offer useful adjuncts to existing therapies.Glucagon-like peptide 1 (GLP-1), produced in the small intestine and amylin, produced by β cells in the pancreas, also have glucose lowering effects. Amylin is an hormone secreted after a meal, having a complementary action to insulin. GLP-1, also released in a post-prandial manner, promotes insulin production and secretion, reduces glucagon secretion, delays gastric emptying and induces a feeling of fullness. The most promising effect of GLP-1 is its ability to increase β-cell mass by stimulating neogenesis and reducing apoptosis in rodents. However the fact that GLP-1 is rapidly degraded by dipeptidylpeptidase IV (DPPIV) in vivo reduces its usefulness. Thus, in order to improve therapeutic efficacy, two approaches have been investigated: the development of GLP-1 analogs resistant to degradation or the development of DPP-IV inhibitors. Synthetic analogs of amylin (pramlintide), GLP-1 (exenatide) and inhibitors of the degradation of GLP-1 (sitagliptin, DPP-IV inhibitor) are now available for clinical use.Promising biological targets being investigated include those leading to insulin sensitization (11β-HSD-1 inhibitors and antagonists of glucocorticoids receptor), reducing hepatic glucose output (antagonist of glucagon receptor, inhibitors of glycogen phosphorylase and fructose-1,6-biphosphatase) and finally increasing urinary elimination of excess glucose (SGLT inhibitors). A particular role is played by glucokinase activators (GKA) which can both increase insulin secretion and improve hepatic glucose metabolism.In this review, we present a summary of the data available on newly approved treatments (amylin and GLP-1 analogs as well as DPP-IV inhibitors) and give an overview of the targets currently being studied for the treatment of type 2 diabetes with an emphasis on the small molecule drug design.

Aromatase and COX in breast cancer: Enzyme inhibitors and beyond

Aromatase expression and enzyme activity in breast cancer patients is greater in or near the tumor tissue compared with the normal breast tissue. Complex regulation of aromatase expression in human tissues involves alternative promoter sites that provide tissue-specific control. Previous studies in our laboratories suggested a strong association between aromatase ( CYP19) gene expression and the expression of cyclooxygenase ( COX) genes. Additionally, nonsteroidal anti-inflammatory drugs (NSAIDs) and COX selective inhibitors can suppress CYP19 gene expression and decrease aromatase activity. Our current hypothesis is that pharmacological regulation of aromatase and/or cyclooxygenases can act locally to decrease the biosynthesis of estrogen and may provide additional therapy options for patients with hormone-dependent breast cancer. Two pharmacological approaches are being developed, one involving mRNA silencing by selective short interfering RNAs (siRNA) molecules and the second utilizing small molecule drug design. In the first approach, short interfering RNAs were designed against either human aromatase mRNA or human COX-2 mRNA. Treatment of breast cancer cells with siAROMs completely masked the aromatase enzyme activity. Treatment with COX-2 siRNAs decreased the expression of COX-2 mRNA; furthermore, the siCOX-2-mediated decrease also resulted in suppression of CYP19 mRNA. The small molecule drug design approach focuses on the synthesis and biological evaluation of a novel series of sulfonanilide analogs derived from the COX-2 selective inhibitors. The compounds suppress aromatase enzyme activity in SK-BR-3 breast cancer cells in a dose and time-dependent manner, and structure activity analysis does not find a correlation between aromatase suppression and COX inhibition. Real-time PCR analysis demonstrates that the sulfonanilide analogs decrease aromatase gene transcription in breast cells. Thus, these results suggest that the siRNAs and novel sulfonanilides targeting aromatase expression may be valuable tools for selective regulation of aromatase in breast cancer.