Medicinal chemistry articles within Nature Chemistry

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  • Research Briefing |

    A protein-templated selection approach has been developed for the discovery of full ligands from dual-pharmacophore DNA-encoded libraries by incorporating fragment linking into the selection process. The performance of this method was demonstrated with selections against protein–protein interaction and protein–DNA interaction targets, through which potent and selective inhibitors were identified.

  • Article |

    Dual-pharmacophore DNA-encoded chemical libraries enable the identification of two synergistic binders for a biological target, but subsequent linking of this pair is required to obtain a full ligand, which can be challenging. Here we report a protein-templated selection of DNA-encoded dynamic library that can identify full ligands from fragment libraries without the need for subsequent fragment linking.

    • Yu Zhou
    • , Wenyin Shen
    •  & Xiaoyu Li

  • In Your Element |

    Thomas Kruse and Søren Østergaard reflect on the development of the GLP-1 analogue, semaglutide, which is reshaping peptide therapeutics in type 2 diabetes, weight management, and beyond.

    • Thomas Kruse
    •  & Søren Østergaard

  • Thesis |

    Given the fraught history of fluorine, Michelle Francl wonders what made medicinal chemists consider fluorine derivatives?

    • Michelle Francl

  • Article |

    In contrast to photothermal therapy requiring high powers over extended times and photodynamic therapy being abrogated by inhibitors of reactive oxygen species, actuation of vibronic modes in single molecules—molecular jackhammers—can now induce efficient cancer cell death. Here, the mechanical disassembly of cell membranes is characterized as the underlying mechanism by which this vibronic-driven action promotes necrotic cell death.

    • Ciceron Ayala-Orozco
    • , Diego Galvez-Aranda
    •  & James M. Tour

  • Article
    | Open Access

    Late-stage functionalization of complex drug molecules is challenging. To address this problem, a discovery platform based on geometric deep learning and high-throughput experimentation was developed. The computational model predicts binary reaction outcome, reaction yield and regioselectivity with low error margins, enabling the functionalization of complex molecules without de novo synthesis.

    • David F. Nippa
    • , Kenneth Atz
    •  & Gisbert Schneider

  • Research Briefing |

    To develop covalent inhibitors with high potency and low off-target effects, combinatorial approaches that search for candidates from large libraries are desired. Here, sulfur(VI) fluoride exchange (SuFEx) in vitro selection is established for the evolution of covalent aptamers from trillions of SuFEx-modified oligonucleotides. Through this technique, covalent aptamers with optimally balanced selectivity and reactivity are identified.

  • Article |

    The bicyclo[1.1.1]pentane (BCP) motif has drawn increasing attention recently in drug discovery. Now, a programmable bis-functionalization strategy has been developed to modularly access bridge-substituted BCP scaffolds, based on the inherent chemoselectivity of BCP bis-boronates (3° > 2°). This strategy should enable further structure–activity relationship studies of BCP-containing drug candidates and open the door to unexplored chemical space.

    • Yangyang Yang
    • , Jet Tsien
    •  & Tian Qin

  • Article |

    Covalent inhibitors offer high potency but their potential is hindered by off-target reactivity. Now, an in vitro selection method has been developed to enable the discovery of covalent inhibitors from trillions of oligonucleotides endowed with the sulfur(VI) fluoride exchange chemistry. This strategy generates covalent inhibitors of protein–protein interactions with optimally balanced selectivity and reactivity.

    • Zichen Qin
    • , Kaining Zhang
    •  & Yu Xiang

  • Article |

    Now a reactivity-based RNA profiling strategy can measure the global off-target transcriptome interactions of small-molecule drugs at single-nucleotide resolution. Using this approach, three FDA-approved drugs were evaluated, uncovering pervasive drug–RNA interactions and interactions that perturb RNA functions in cells.

    • Linglan Fang
    • , Willem A. Velema
    •  & Eric T. Kool

  • News & Views |

    Pharmacologically inactive prodrugs that can be activated by near-infrared light are attractive candidates for clinical applications. Now, platinum-based photo-oxidants have been shown to eradicate tumours in mice with a new mode of action.

    • Gloria Vigueras
    •  & Gilles Gasser

  • Article |

    The design and construction of a stereo-defined DNA-encoded chemical library, featuring the four different 4-amino-proline stereoisomers as a central scaffold, has now enabled the discovery of potent ligands to proteins of pharmaceutical interest. Parallel screening with closely related isoforms (anti-targets) facilitated the isolation of hits with high selectivity ratios.

    • Sebastian Oehler
    • , Laura Lucaroni
    •  & Gabriele Bassi

  • Article
    | Open Access

    The ortho-substituted phenyl ring is a basic structural element in chemistry. Now, 2-oxabicyclo[2.1.1]hexanes have been developed as saturated bioisosteres of the ortho-substituted phenyl ring with improved physicochemical properties. Replacement of the phenyl ring with 2-oxabicyclo[2.1.1]hexanes in marketed agrochemicals fluxapyroxad and boscalid improved water solubility, reduced lipophilicity and retained bioactivity.

    • Aleksandr Denisenko
    • , Pavel Garbuz
    •  & Pavel K. Mykhailiuk

  • Article |

    Water-soluble, cell-permeable, inert fluorescent tags called OregonFluors have been developed to withstand environmental changes while resistant towards non-specific binding with subcellular structures. These tags enable quantitative imaging of drug target availability in cells and tissues, providing a route for the future assessment of personalized therapies.

    • Lei G. Wang
    • , Antonio R. Montaño
    •  & Summer L. Gibbs

  • Article |

    Tigilanol tiglate is a therapeutic lead for the treatment of a broad range of cancers. Now, it has been shown that tigilanol tiglate can be synthesized in a time and step economical fashion from phorbol—its naturally abundant biosynthetic precursor. This synthesis provides rapid access to analogues with unprecedented protein kinase C binding activity.

    • Paul A. Wender
    • , Zachary O. Gentry
    •  & Edward Njoo

  • Article |

    General synthetic methods to access pleuromutilin antibiotics are limited due to their complex carbocyclic skeleton. Now, a synthetic platform has been developed to access structurally diverse pleuromutilins with variations at the quaternary C12 position and hydrindanone cores. Seventeen structurally distinct derivatives were prepared and evaluated against a panel of Gram-positive and -negative bacteria.

    • Olivia Goethe
    • , Mikaela DiBello
    •  & Seth B. Herzon

  • News & Views |

    Malleicyprols are highly reactive polyketides responsible for virulence in some pathogenic bacteria. Now, the enzyme that constructs the cyclopropanol warhead of malleicyprols has been identified. This enzyme could represent a useful target for developing new antivirulence therapeutics.

    • Elijah Abraham
    •  & Rebecca A. Butcher

  • News & Views |

    Antibody-mediated delivery of therapeutics has been primarily limited to agents containing amine, alcohol or thiol functional groups. Now, an approach has been developed to create stable and bio-reversible prodrugs that mask ortho-quinones. Drug release requires both protease activation followed by acid-assisted elimination.

    • Thomas Pillow

  • Article
    | Open Access

    A strategy for protecting redox-active ortho-quinones, which show promise as anticancer agents but suffer from redox-cycling behaviour and systemic toxicity, has been developed. The ortho-quinones are derivatized to redox-inactive para-aminobenzyl ketols. Upon amine deprotection, an acid-promoted, self-immolative C–C bond-cleaving 1,6-elimination releases the redox-active hydroquinone. The strategy also enables conjugation to a carrier for targeted delivery of ortho-quinone species.

    • Lavinia Dunsmore
    • , Claudio D. Navo
    •  & Gonçalo J. L. Bernardes

  • Review Article |

    Enzymes, either purified or as whole-cell biocatalysts, can be concatenated into catalytic cascades and used to produce pharmaceutically relevant molecules. This Review discusses the advantages and requirements of multistep enzyme cascades and also highlights how they can be harnessed to achieve highly sustainable and cost-efficient syntheses.

    • Ana I. Benítez-Mateos
    • , David Roura Padrosa
    •  & Francesca Paradisi

  • Perspective |

    DNA-encoded libraries can be applied in a diverse range of applications beyond simple binding assays. This Perspective covers the recent progress in using DNA-encoded chemical libraries to investigate complex biological targets and discusses their potential to identify structures that elicit function or possess other useful properties.

    • Yiran Huang
    • , Yizhou Li
    •  & Xiaoyu Li

  • News & Views |

    Aryl aminooxetanes are used as amide bioisosteres in drug discovery but there are limited strategies for synthesizing them. Now, an approach has been developed that simplifies the synthesis of these privileged motifs, enabling a broad range of amines to be used.

    • Malcolm P. Huestis
    •  & Jack A. Terrett

  • News & Views |

    It is extremely difficult to design a broad-spectrum inhibitor for metallo-β-lactamases (MBLs) due to the diversity in the active site. Now, indole-2-carboxylates have been developed as broad-spectrum inhibitors for MBLs. These inhibitors take advantage of key elements of both MBL substrates and products and work by locking a hydroxide.

    • Hongyan Li
    •  & Hongzhe Sun

  • Article |

    The efficacy of carbapenem antibiotics can be compromised by metallo-β-lactamases, but a high-throughput screen followed by optimization has now enabled the discovery of indole-2-carboxylates (InCs) as potent broad-spectrum metallo-β-lactamase inhibitors. The results highlight the potential of InC–carbapenem combinations for clinical use as well as mechanism-guided approaches to combatting globally disseminated antibiotic resistant mechanisms.

    • Jürgen Brem
    • , Tharindi Panduwawala
    •  & Christopher J. Schofield

  • Article |

    DNA-encoded libraries facilitate the discovery of ligands that interact with biomolecules but such technologies do not take full advantage of the principles of Darwinian selection. Now, libraries of conformationally constrained peptides (Dsuprabodies) have been assembled using a strategy that allows for iterative cycles of selection, amplification and diversification. This method was validated with selections against streptavidin and PD-L1.

    • Balayeshwanth R. Vummidi
    • , Lluc Farrera-Soler
    •  & Nicolas Winssinger

  • Article |

    Prodrugs offer one route to treat cancer, but they require activation once they have been delivered to the tumour. Now, a simultaneous chemo-radiotherapy strategy has been demonstrated in mice that uses gamma or X-ray irradiation to locally activate an anticancer prodrug.

    • Jin Geng
    • , Yichuan Zhang
    •  & Mark Bradley

  • News & Views |

    DNA-encoded libraries are a powerful tool to identify hit compounds for drug discovery. Now, two papers have reported new advances in this technology. One paper reports a method to screen for binders inside a living cell, and the other investigates the effects of stereo- and regiochemistry on ligand discovery.

    • Minsoo Song
    •  & Gil Tae Hwang

  • News & Views |

    The therapeutic applications of DNAzymes are limited because of their low effectiveness in vivo. Now, a promising approach for constructing DNAzymes that show high gene-silencing efficiency in mammalian cells has been developed. This approach incorporates chemical modifications into an existing DNAzyme scaffold.

    • Yifei Zhou
    •  & Chuanzheng Zhou

  • News & Views |

    Sophisticated drug delivery systems are as essential to modern medicine as drugs themselves. Now, polymer mechanochemistry in sonicated solutions has been used to activate drugs in three different systems. These results offer a promising approach that can be tailored to diverse molecular structures of modern pharmaceuticals.

    • Roman Boulatov

  • Article |

    A method to label membrane proteins with a DNA tag has been developed that enables the selection of DNA-encoded chemical libraries against endogenous membrane proteins on live cells. As a demonstration, a 30-million-compound DNA-encoded chemical library is screened against folate receptor, carbonic anhydrase 12 and epidermal growth factor receptor on live cells.

    • Yiran Huang
    • , Ling Meng
    •  & Xiaoyu Li

  • News & Views |

    Electrophilic groups that undergo sulfur-exchange chemistry with protein nucleophiles can serve as the functional basis of chemical proteomic probes. A new addition to this class, sulfuramidimidoyl fluoride (SAF), which can be included in an array of covalent small molecule probes, exhibits a unique reactivity profile with proteins.

    • Thomas E. Speltz
    •  & Raymond E. Moellering

  • Article |

    A selection-based screen has now revealed preferences in small-molecule chemotypes that bind RNA as well as preferences in the RNA motifs that bind small molecules. Analysis of these data enabled the design of a small molecule that selectively binds a non-coding microRNA and upregulates expression of vascular endothelial growth factor A.

    • Hafeez S. Haniff
    • , Laurent Knerr
    •  & Matthew D. Disney

  • Comment |

    The gap between fundamental academic research and the applied industrial research that is necessary to ensure real-world applications can be bridged by engaging in well-defined collaborative academia–industry projects and fostering better communication between the scientists involved in them.

    • Danielle Schultz
    •  & Louis-Charles Campeau

  • Article |

    Screening commercial kinase inhibitors for antibacterial activity identified the anticancer drug sorafenib as a major hit. Subsequent structure–activity optimization created a new antibacterial analogue with high potency against methicillin-resistant Staphylococcus aureus, including challenging persisters and biofilms, as well as demonstrating efficacy in an in vivo mouse model. The mode of action involves stimulation of protein secretion and inhibition of menaquinone biosynthesis.

    • Philipp Le
    • , Elena Kunold
    •  & Stephan A. Sieber

  • Article |

    A set of enantioprobes—photoreactive, clickable fragment pairs differing only in absolute stereochemistry—have been used to provide a robust and streamlined chemical proteomic map of small-molecule/protein interactions in human cells. More than 170 stereoselective fragment–protein interactions were discovered and shown to occur at functional sites on proteins from diverse classes.

    • Yujia Wang
    • , Melissa M. Dix
    •  & Benjamin F. Cravatt

  • Article |

    Current photodynamic therapy photosensitizers require oxygen; however, tumours are often hypoxic. Now, an organoiridium complex with an unusually high redox potential, which is effective in normoxia and hypoxia, has been developed. The organoiridium complex kills cancer cells by an immunogenic apoptotic mechanism involving efficient photocatalytic oxidation of NADH to NAD radicals, and reduction of cytochrome c.

    • Huaiyi Huang
    • , Samya Banerjee
    •  & Peter J. Sadler

  • Article |

    The complete biosynthesis of the fungal indole alkaloid malbrancheamide, which culminates in an intramolecular [4+2] hetero-Diels–Alder cyclization to produce the bicyclo[2.2.2]diazaoctane scaffold, has now been discovered. Chemical synthesis and protein structural analysis were used to provide mechanistic insight into this enzyme-dependent diastereo- and enantioselective cycloaddition.

    • Qingyun Dan
    • , Sean A. Newmister
    •  & Robert M. Williams

  • Perspective |

    The shape complementarity between the active site of a catalyst and a substrate influences how effectively a reaction can be catalysed. Computational tools can be used to visualize the shape around the active centre of a range of catalysts and the application of such approaches to rationalize the behaviour of known catalysts — and to design new ones — is discussed.

    • Laura Falivene
    • , Zhen Cao
    •  & Luigi Cavallo

  • News & Views |

    Methods for generating molecular diversity provide a route to screen a wider section of chemical space, to discover compounds with useful biological properties. Now, a complexity-to-diversity strategy has enabled the discovery of a multi-cyclic structure from a complex natural product that induces ferroptotic cell death in cancer cells.

    • Tatiana Cañeque
    •  & Raphaël Rodriguez

  • Article |

    A set of stereochemically complex and structurally diverse compounds were created from the diterpene natural product pleuromutilin using the complexity-to-diversity strategy. Phenotypic screening identified a compound that induces rapid ferroptotic death of cancer cells. Experiments to probe the mechanism revealed the compound to be an inhibitor of thioredoxin.

    • Evijola Llabani
    • , Robert W. Hicklin
    •  & Paul J. Hergenrother

  • Article |

    Rapamycin and FK506 are macrocycles that contain an FKBP-binding domain and an effector domain responsible for interacting with their respective targets, mTOR and calcineurin. Now, a 45,000-compound macrocycle library has been synthesized by fusing oligopeptides with synthetic FKBP-binding domains. Screening and subsequent optimization yielded a highly potent FKBP-dependent inhibitor of hENT1.

    • Zufeng Guo
    • , Sam Y. Hong
    •  & Jun O. Liu

  • Article |

    Inhibiting the interaction between amyloid-β (Aβ) and a neuronal cell surface receptor, LilrB2, could offer a potential route for treating Alzheimer’s disease. Now, binding sites between Aβ and LilrB2 have been discovered and computational selection has identified inhibitors that block this binding site. Cell-penetrating inhibitors were found to block the Aβ–LilrB2 interaction and limit Aβ-induced cytotoxicity.

    • Qin Cao
    • , Woo Shik Shin
    •  & Lin Jiang

  • News & Views |

    The structure of an antibiotic that is effective against Gram-positive bacteria, but not against Gram-negative bacteria, has now been modified to improve its effectiveness against Gram-negative bacteria. The approach could help broaden the spectrum of activity of other antibiotics.

    • Jed F. Fisher
    •  & Shahriar Mobashery

  • Article |

    New natural-product-inspired molecules are often limited by their only partial coverage of biologically relevant chemical space. Combining fragments of natural products has now been shown to yield pseudo natural products, which — while still being inspired by natural products — populate previously unexplored areas of chemical space and have novel biological activities.

    • George Karageorgis
    • , Elena S. Reckzeh
    •  & Herbert Waldmann

  • Editorial |

    Encoded chemical libraries can be used to screen a vast array of compounds against a protein target to identify potent binders. A collection of articles in this issue discuss different methods to increase the chemical space sampled by encoded macrocycle libraries and the advantages that such libraries offer for discovering new drug leads.

  • Q&A |

    Ghotas Evindar, Chemistry Group Leader at GlaxoSmithKline, talks with Nature Chemistry about the advantages of using encoded libraries in drug discovery and the challenges these technologies present.

    • Russell Johnson

  • News & Views |

    Certain drug targets have been deemed undruggable because of the difficulty in finding pharmacologically useful inhibitors. Now, two teams have developed exciting technologies for the creation of diverse collections of macrocyclic molecules and have demonstrated their usefulness for discovering macrocyclic inhibitors.

    • Emil S. Iqbal
    •  & Matthew C. T. Hartman

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