New Opportunities For Drug Design Research Articles

An enantioselective and modular platform for C4ʹ-modified nucleoside analogue synthesis enabled by intramolecular trans-acetalizations

C4ʹ-modified nucleoside analogues continue to attract global attention for their use in antiviral drug development and oligonucleotide-based therapeutics. However, current approaches to C4ʹ-modified nucleoside analogues still involve lengthy (9–16 steps), non-modular routes that are unamenable to library synthesis. Towards addressing the challenges associated with their syntheses, we report a modular 5-step process to a diverse collection of C4ʹ-modified nucleoside analogues through a sequence of intramolecular trans-acetalizations of readily assembled polyhydroxylated frameworks. Overall, the 2–3 fold reduction in step-count compares favorably to even recently reported biocatalytic approaches and should ultimately enable new opportunities in drug design around this popular chemotype.

Revealing the graded activation mechanism of neurotensin receptor 1

Graded activation contributes to the precise regulation of GPCR activity, presenting new opportunities for drug design. In this work, a total of 10 μs enhanced-sampling simulations are performed to provide molecular insights into the binding dynamics differences of the neurotensin receptor 1 (NTSR1) to the full agonist SRI-9829, partial agonist RTI-3a and inverse agonist SR48692. The possible graded activation mechanism of NTSR1 is revealed by an integrated analysis utilizing the reweighted potential of mean force (PMF), deep learning (DL) and transfer entropy (TE). Specifically, the orthosteric pocket is observed to undergo expansion and contraction, with the G-protein-binding site experiencing interconversions among the inactive, intermediate and active-like states. Detailed structural comparisons capture subtle conformational differences arising from ligand binding in allosteric signaling, which can well explain the graded activation. Critical microswitches that contribute to graded activation are efficiently identified with the DL model. TE calculations enable the visualization of allosteric communication networks within the receptor, elucidating the driver-responder relationships associated with signal transduction. Fortunately, the dissociation of the full agonist from the orthosteric pocket is observed. The current findings systematically reveal the mechanism of NTSR1 graded activation, and also provide implications for structure-based drug design.

Repositioning of FDA-Approved antifungal agents to interrogate Acyl-CoA synthetase long chain family member 4 (ACSL4) in ferroptosis

Ferroptosis, first coined in 2012, is an iron-dependent regulated cell death (RCD) characterized by the accumulation of lipid peroxides to toxic levels. This mechanism is currently being evaluated as a target for a variety of diseases offering new opportunities for drug design and development. Recent reports uncovered acyl-CoA synthetase long-chain 4 (ACSL4) as a critical contributor to ferroptosis execution. Therefore, ACSL4 inhibitors are emerging as attractive anti-ferroptotic agents. Herein, we developed a robust screening cascade with orthogonal biophysical and biochemical techniques to identify original human ACSL4 inhibitors. By screening an FDA-approved drug library, we were able to identify and validate new inhibitors with micromolar-range activities against ACSL4. With an IC50 of 280 nM against hACSL4, antifungal agent sertaconazole is to our knowledge, the most potent ACSL4 inhibitor identified so far. In addition, sertaconazole significantly reduced lipid peroxidation and ferroptosis in human differentiated dopaminergic neurons (Lund human mesencephalic LUHMES cells), demonstrating that it is a valuable chemical tool for further investigating the role of ACSL4 in ferroptosis. This study highlights the phenethyl-imidazole scaffold as a novel and promising starting point for the development of anti-ferroptotic agents targeting ACSL4.

Innovative Approach for a Classic Target: Fragment Screening on Trypanothione Reductase Reveals New Opportunities for Drug Design.

Trypanothione reductase (TR) is a key factor in the redox homeostasis of trypanosomatid parasites, critical for survival in the hostile oxidative environment generated by the host to fight infection. TR is considered an attractive target for the development of new trypanocidal agents as it is essential for parasite survival but has no close homolog in humans. However, the high efficiency and turnover of TR challenging targets since only potent inhibitors, with nanomolar IC50, can significantly affect parasite redox state and viability. To aid the design of effective compounds targeting TR, we performed a fragment-based crystal screening at the Diamond Light Source XChem facility using a library optimized for follow-up synthesis steps. The experiment, allowing for testing over 300 compounds, resulted in the identification of 12 new ligands binding five different sites. Interestingly, the screening revealed the existence of an allosteric pocket close to the NADPH binding site, named the “doorstop pocket” since ligands binding at this site interfere with TR activity by hampering the “opening movement” needed to allow cofactor binding. The second remarkable site, known as the Z-site, identified by the screening, is located within the large trypanothione cavity but corresponds to a region not yet exploited for inhibition. The fragments binding to this site are close to each other and have some remarkable features making them ideal for follow-up optimization as a piperazine moiety in three out of five fragments.

Intermolecular amination of allenes via 2-fold photocatalytic nitrene transfer reactions

The amination with monovalent, nitrogen-based intermediates constitutes an important reaction for the construction of valuable amines. The high basicity of reagents, reaction intermediates, or products, however, poses significant challenges to metal-catalyzed amination through coordination and blocking of catalytically active sites and hampering of their efficiency. In this context, high-yielding intermolecular amination reactions of allenes remain an unsolved challenge in organic synthesis, and general methods are not available. Herein, we describe a photochemical approach toward the intermolecular amination of allenes via free nitrene radical anions as the key reactive intermediate. This reaction proceeds without the participation of catalyst-bound nitrogen species and can thus overcome current limitations. We report on the application in the amination of allenes to give azetidine and cyclopropyl amines with a broad and general substrate scope. Experimental and theoretical studies were performed to provide an understanding of the reaction mechanism and rationalize the high efficiency of this photocatalytic approach. • Photocatalysis enables the intermolecular amination of allenes • Azetidines via 2-fold amination • Cyclopropyl amines via trapping of intermediate cyclopropyl imines • Experimental and theoretical studies explain the reaction mechanism Amines are the most important functional group in drug discovery and can be ubiquitously found in the vast majority of drugs. The synthesis of amines thus represents a key research topic in chemistry. Latest developments thus focus, e.g., on the reduction of economic and ecologic footprints of amination reactions or on the development of novel synthesis methods to expand chemical space and new opportunities in drug design. While basic properties of amines are highly desired in the design of new drugs, the same properties pose significant challenges to classic metal-catalyzed amination reactions. Herein, we demonstrate that photocatalysis leverages amination reactions via free nitrene intermediates to allow for intermolecular amination reaction of allenes, which, even today, represents one of the big challenges in the field. The photocatalytic reaction of iodinanes enables mild and efficient intermolecular amination reactions of allenes. This strategy overcomes current limitations of metal-catalyzed amination reactions and provides a high-yielding access to azetidines or cyclopropyl amines depending on the reaction conditions. Experimental and theoretical studies were performed to provide an understanding of the underlying reaction mechanism.

Boltzmann Docking Identifies Allosteric Small Molecule Modulators of Protein Activity

Computational approaches can facilitate the design of clinically relevant small molecule inhibitors. Classical drug design focuses primarily on targeting a protein's active site based on its x-ray crystal structure. One drawback to this approach is crystal structures do not report on protein dynamics and do not capitalize on the presence of hidden cryptic pockets. Cryptic pockets are transient allosteric sites invisible to conventional structural biology techniques and present new opportunities for drug design. Here we introduce Boltzmann docking as a method to identify small molecules that bind to cryptic pockets and allosterically modulate enzymatic activity. We leverage knowledge of protein dynamics from molecular dynamics simulations and Markov State Models (MSMs) to identify cryptic pockets. MSMs are a network representation of a protein's free energy landscape that provides representative states and their populations. Boltzmann docking screens a library of small molecules against multiple MSM states containing a target cryptic pocket and generates a new Boltzmann score that is a population weighted average of the individual states’ docking scores. We successfully applied this approach to identify multiple allosteric modulators of TEM β-lactamase activity, and are currently looking to identify novel inhibitors of the Ebola viral protein VP35. Boltzmann docking should provide a general framework to identify allosteric modulators of protein activity, especially for targets widely considered “undruggable” owing to the lack of an obvious binding site in their crystal structures.

Proton-Coupled Conformational Allostery Modulates the Inhibitor Selectivity for β-Secretase.

Many important pharmaceutical targets, such as aspartyl proteases and kinases, exhibit pH-dependent dynamics, functions and inhibition. Accurate prediction of their binding free energies is challenging because current computational techniques neglect the effects of pH. Here we combine free energy perturbation calculations with continuous constant pH molecular dynamics to explore the selectivity of a small-molecule inhibitor for β-secretase (BACE1), an important drug target for Alzheimer's disease. The calculations predicted identical affinity for BACE1 and the closely related cathepsin D at high pH; however, at pH 4.6 the inhibitor is selective for BACE1 by 1.3 kcal/mol, in excellent agreement with experiment. Surprisingly, the pH-dependent selectivity can be attributed to the protonation of His45, which allosterically modulates a loop-inhibitor interaction. Allosteric regulation induced by proton binding is likely common in biology; considering such allosteric sites could lead to exciting new opportunities in drug design.

Study of Functional and Allosteric Sites in Protein Superfamilies

The interaction of proteins (enzymes) with a variety of low-molecular-weight compounds, as well as protein-protein interactions, is the most important factor in the regulation of their functional properties. To date, research effort has routinely focused on studying ligand binding to the functional sites of proteins (active sites of enzymes), whereas the molecular mechanisms of allosteric regulation, as well as binding to other pockets and cavities in protein structures, remained poorly understood. Recent studies have shown that allostery may be an intrinsic property of virtually all proteins. Novel approaches are needed to systematically analyze the architecture and role of various binding sites and establish the relationship between structure, function, and regulation. Computational biology, bioinformatics, and molecular modeling can be used to search for new regulatory centers, characterize their structural peculiarities, as well as compare different pockets in homologous proteins, study the molecular mechanisms of allostery, and understand the communication between topologically independent binding sites in protein structures. The establishment of an evolutionary relationship between different binding centers within protein superfamilies and the discovery of new functional and allosteric (regulatory) sites using computational approaches can improve our understanding of the structure-function relationship in proteins and provide new opportunities for drug design and enzyme engineering.

ChemInform Abstract: Synthesis of Spiro Compounds as Medicinal Agents; New Opportunities for Drug Design and Discovery. Part I: A Review

AbstractReview: 109 refs.

Preclinical characterization of acyl sulfonimidamides: potential carboxylic acid bioisosteres with tunable properties.

Herein we present the preclinical characterization of novel compounds containing the linear acyl sulfonimidamide functionality. Specifically, we studied the pKa , lipophilicity, in vitro metabolic stability, plasma protein binding, Caco-2 permeability, and aqueous solubility for nine aryl acyl sulfonimidamides. In comparison with widely used carboxylic acid bioisosteres, the acyl sulfonimidamides were found to be less acidic and more lipophilic depending on the substitution pattern in the studied compounds. Importantly, the pKa values (5.9-7.6) were significantly influenced by substituents on the nitrogen atom and the aryl substituents. Moreover, the acyl sulfonimidamides displayed membrane permeabilities ranging from moderate to very high, which correlated with decreased pKa and low to negligible efflux ratios. We foresee that the chiral sulfur center and the two handles for structural diversity of linear acyl sulfonimidamides will offer new opportunities for drug design and for improving the oral bioavailability of acidic drug candidates.

G-protein-coupled receptors oligomerization: emerging signaling units and new opportunities for drug design.

G-protein-coupled receptors (GPCRs) are a widespread family of transmembrane receptors with different physiologically relevant functions. Alterations in the structure and function of these receptors at different levels (ligand binding, signaling and trafficking) may result in a number of pathological conditions which represent a major health problem. Mutations in these receptors are also linked to different inherited diseases for which there is no cure to date. Rationale design, based on receptor structural knowledge, is needed for the discovery of novel drugs with higher selectivity and less side effects. In fact, about 50% of the drugs currently under development target this kind of receptors. Oligomerization among GPCRs has been clearly established from experimental, particularly in vitro, studies. Moreover, homo and heterodimerization provide new unexpected clues for explaining the molecular mechanisms underlying some diseases in which GPCRs signaling might be affected. In this review we will analyze GPCRs structure and function for a better understanding of the dimerization process and the experimental approaches currently used to detect such interactions. Furthermore, how drugs targeting heteromers can represent new opportunities to tackle novel and safer treatments of some pathologies will be described. Recent results, in this regard, will be reported as encouraging examples in the field. Finally, the newest technologies available for developing drugs targeting heteromers will also be reviewed highlighting the importance of bivalent ligands that emerge as very powerful molecules interacting with heteromers.

Quantification of free ligand conformational preferences by NMR and their relationship to the bioactive conformation

Accurate unbound solution 3D-structures of ligands provide unique opportunities for medicinal chemistry and, in particular, a context to understand binding thermodynamics and kinetics. Previous methods of deriving these 3D-structures have had neither the accuracy nor resolution needed for drug design and have not yet realized their potential. Here, we describe and apply a NMR methodology to the aminoglycoside streptomycin that can accurately quantify accessible 3D-space and rank the occupancy of observed conformers to a resolution that enables medicinal chemistry understanding and design. Importantly, it is based upon conventional small molecule NMR techniques and can be performed in physiologically-relevant solvents. The methodology uses multiple datasets, an order of magnitude more experimental data than previous NMR approaches and a dynamic model during refinement, is independent of computational chemistry and avoids the problem of virtual conformations. The refined set of solution 3D-shapes for streptomycin can be grouped into two major families, of which the most populated is almost identical to the 30S ribosomal subunit bioactive shape. We therefore propose that accurate unbound ligand solution conformations may, in some cases, provide a subsidiary route to bioactive shape without crystallography. This experimental technique opens up new opportunities for drug design and more so when complemented with protein co-crystal structures, SAR data and pharmacophore modeling.

New opportunities in drug design of metalloproteinase inhibitors: combination between structure–function experimental approaches and systems biology

Introduction: MMPs (matrix metalloproteinases) and ADAMs (a disintegrin and metalloproteinases) are endopeptidases central to the degradation and remodeling of the extracellular matrix. These proteases also exhibit regulatory activity in cell signaling pathways and thus tissue homeostasis under normal conditions and in many diseases. Consequently, individual members of the MMP and ADAM protein families were identified as important therapeutic targets. However, designing effective inhibitors in vivo for this class of enzymes appears to be extremely challenging. This is attributed to the broad structural similarity of their active sites and to the dynamic functional interconnectivity of MMPs with other proteases, their inhibitors, and substrates (the so-called degradome) in healthy and disease tissues.Areas covered: The article covers the progress in designing metalloproteinase inhibitors, based on recent advancements in our understanding of enzyme structures and their function as master regulators. It also discusses the potential of utilizing structure-based drug design strategies in conjunction with systems biology experimental approaches for designing potent and therapeutically effective metalloproteinase inhibitors.Expert opinion: We highlight the use of protein-based drug design strategies, for example, antibodies and protein scaffolds, targeting extracatalytic domains, which are central to proteolytic and non-proteolytic enzyme functions. Such rationally designed function-blocking inhibitors may create new opportunities in disease management and in emerging therapies that require control of dysregulated MMP activity without causing severe side effects. Importantly, the lessons learned from studying these protein-based inhibitors can be implemented to design new and effective small or medium sized synthetic antagonists.

4D-QSAR: Perspectives in Drug Design

Drug design is a process driven by innovation and technological breakthroughs involving a combination of advanced experimental and computational methods. A broad variety of medicinal chemistry approaches can be used for the identification of hits, generation of leads, as well as to accelerate the optimization of leads into drug candidates. The quantitative structure–activity relationship (QSAR) formalisms are among the most important strategies that can be applied for the successful design new molecules. This review provides a comprehensive review on the evolution and current status of 4D-QSAR, highlighting present challenges and new opportunities in drug design.

Fragment-based QSAR strategies in drug design

Recently, fragment-based drug design has been established as a crucial strategy for hit identification and lead generation, which has strongly encouraged the development of approaches to specifically recognize and evaluate molecular fragments or structural scaffolds that preferentially interact with particular sites of important biological targets. In this context, fragment-based quantitative structure–activity relationship (FB-QSAR) has emerged as a versatile tool to explore the chemical and biological space of data sets of compounds. FB-QSAR approaches have evolved from a classical use in the generation of standard QSAR models into advanced drug design tools for database mining, pharmacokinetic property prediction and optimization of multiple parameters. This paper provides a brief perspective on the evolution and current status of FB-QSAR, highlighting new opportunities in drug design.

Advances in the Structure-Based Design of the Influenza A Neuraminidase Inhibitors

Since 2003, highly pathogenic H5N1 influenza viruses have been the cause of large-scale death in poultry and the subsequent infection and death of over 140 humans. At present, there are only three licensed anti-Influenza drugs namely Relenza (Zanamivir - ZMV), Tamiflu (Oseltamivir - OTV) and Amantadine/Rimantadine. The latter targets the M2 ion channel whereas the other compounds target neuraminidase (NA) and were designed through structure-based enzyme inhibitor programmes. Some structural knowledge of the Influenza neuraminidase is now known, due to remarkable advances in crystallographic techniques. The structure of H5N1 NA is particularly attractive because it offers new opportunities for drug design. Besides a profound impact that structural biology has had on understanding the Influenza virus and the rational design of antivirals, computational methods are now a viable partner to experiment in designing NA inhibitors. We herein discuss the development of current neuraminidase inhibitors, the emergence of resistance to them, and recent research progress towards the development of new inhibitors.

Multivalent-Based Drug Design Applied to Serotonin 5-HT4 Receptor Oligomers

Historically treated as monomeric polypeptides, G protein-coupled receptors (GPCRs) have been shown to exist and function as constitutively formed dimers or oligomers. The quaternary structure of GPCRs may modulate ligand binding properties through allosteric mechanisms offering new opportunities for drug design by exploiting multivalency. In this context, multivalent ligands versus bivalent-ligands, possessing two binding motifs connected by a linker, have been investigated and have revealed striking differences in their functional properties compared to their monovalent counterparts. These bi-functional drugs, which are able to activate the two protomers in a dimer simultaneously, emerge as novel and promising drugs for a variety of multi-factorial diseases. In this review, key requirements for the successful design and synthesis of GPCR multivalent ligands composed of pharmacophores and a linker will be discussed. We will then focus on the 5-HT(4) receptor (5-HT(4)R), whose ligands emerged as promising drugs for a variety of central nervous disorders. Upon description of biochemical and biophysical evidences of 5-HT(4)R dimerization, we will present the multivalent ligand approach, which was assisted by molecular docking experiments on the 5-HT(4)R dimer model.

Fragment-based QSAR: perspectives in drug design

Drug design is a process driven by innovation and technological breakthroughs involving a combination of advanced experimental and computational methods. A broad variety of medicinal chemistry approaches can be used for the identification of hits, generation of leads, as well as to accelerate the optimization of leads into drug candidates. Quantitative structure-activity relationship (QSAR) methods are among the most important strategies that can be applied for the successful design of small molecule modulators having clinical utility. Hologram QSAR (HQSAR) is a modern 2D fragment-based QSAR method that employs specialized molecular fingerprints. HQSAR can be applied to large data sets of compounds, as well as traditional-size sets, being a versatile tool in drug design. The HQSAR approach has evolved from a classical use in the generation of standard QSAR models for data correlation and prediction into advanced drug design tools for virtual screening and pharmacokinetic property prediction. This paper provides a brief perspective on the evolution and current status of HQSAR, highlighting present challenges and new opportunities in drug design.

Bivalent Ligands as Specific Pharmacological Tools for G Protein-Coupled Receptor Dimers

G protein-coupled receptors (GPCRs) are major drug targets and are organized in dimeric/oligomeric complexes. These dimers may be composed of identical (homodimer) or different (heterodimer) receptors. GPCR dimerization provides new opportunities for drug design. Different strategies have been developed to specifically target GPCR dimers. Bivalent ligands, which are composed of two functional pharmacophores linked by a spacer, are among the most promising strategies. Due to the constitutive nature of GPCR dimers, bivalent ligands are expected in most cases to bind to and stabilize preexisting dimers rather then to promote ligand-induced dimerization. Most studies on GPCR dimerization were conducted so far in heterologous expression systems. Due the development of heterodimer-specific tools such as bivalent ligands, dimerization has now been confirmed for an increasing number of receptors in native tissues. In this review, we will discuss general considerations for the design and synthesis of bivalent ligands and present the functional in vitro and in vivo properties of reported bivalent ligands.

Analogue inhibitors by modifying oseltamivir based on the crystal neuraminidase structure for treating drug-resistant H5N1 virus

The worldwide spread of H5N1 avian influenza and the increasing reports about its resistance to the existing drugs have made a priority for the development of the new anti-influenza molecules. The crystal structure of H5N1 avian influenza neuraminidase reported recently by Russell et al. [R.J. Russell, L.F. Haire, D.J. Stevens, P.J. Collins, Y. P. Lin, G.M. Blackburn, A.J. Hay, S.J. Gamblin, J.J. Skehel, The structure of H5N1 avian influenza neuraminidase suggests new opportunities for drug design, Nature 443 (2006) 45–49] have provided new opportunities for drug design in this regard. It is revealed through the structure that the active sites of the group-1 neuraminidases, which contain the N1 subtype, have a very different three-dimensional structure from those of group-2 neuraminidases. The key difference is in the 150-loop cavity adjacent to the conserved active site in neuraminidase. Based on these findings and by modifying oseltamivir, six analog inhibitors were proposed as candidates for developing inhibitors against H5N1 virus, particularly against the oseltamivir-resistant H5N1 virus strain.