Featured
-
-
Article
| Open AccessProspective de novo drug design with deep interactome learning
The use of data-driven generative models for drug design is challenging due to the scarcity of data. Here, the authors introduce a “zero-shot" generative deep model to enable the generation of molecules by both structure- and ligand-based drug design and apply it to design PPARγ agonists with desired properties.
- Kenneth Atz
- , Leandro Cotos
- & Gisbert Schneider
-
Article
| Open AccessHomo-BacPROTAC-induced degradation of ClpC1 as a strategy against drug-resistant mycobacteria
Antimicrobial resistance is a global health threat and the development of alternative strategies to overcome it is of high interest. Here, the authors report proteolysis targeting chimeras active in bacteria (BacPROTACs) that bind to ClpC1, a component of the mycobacterial protein degradation machinery, and apply them for targeting a range of mycobacterial strains, including antibiotic-resistant ones.
- Lukas Junk
- , Volker M. Schmiedel
- & Guido Boehmelt
-
Article
| Open AccessCyclic peptides discriminate BCL-2 and its clinical mutants from BCL-XL by engaging a single-residue discrepancy
Pro-survival B-cell lymphoma-2 (BCL-2) family proteins BCL-2 and BCL-XL are the targets of anti-tumour drugs, but resistance is emerging. The authors present cyclic peptides against BCL-2 and BCL-XL, with a distinct mechanism of targeting characterised.
- Fengwei Li
- , Junjie Liu
- & Dalei Wu
-
Article
| Open AccessSQM2.20: Semiempirical quantum-mechanical scoring function yields DFT-quality protein–ligand binding affinity predictions in minutes
The paper presents the universal QM-based scoring function that accurately and rapidly predicts protein-ligand binding affinities, outperforming current computational tools. This is demonstrated on the PL-REX experimental benchmark dataset.
- Adam Pecina
- , Jindřich Fanfrlík
- & Jan Řezáč
-
Article
| Open AccessAvapritinib-based SAR studies unveil a binding pocket in KIT and PDGFRA
Avapritinib, a potent inhibitor, offers hope for D842V-mutant GIST patients with high response rates; however, resistance and side effects remain challenges. Here, crystal structures shed light on this and reveal a Gα-pocket for drug development.
- A. Teuber
- , T. Schulz
- & D. Rauh
-
Article
| Open AccessStructure-based design of a phosphotyrosine-masked covalent ligand targeting the E3 ligase SOCS2
SH2 domains are challenging to target using small molecules. Here, the authors develop phosphotyrosine-based covalent ligands of the E3 ligase SOCS2 using structure-based design. A pro-drug approach yields cell active inhibitors that block SOCS2 substrate recruitment.
- Sarath Ramachandran
- , Nikolai Makukhin
- & Alessio Ciulli
-
Article
| Open AccessDiscovery of a selective and biologically active low-molecular weight antagonist of human interleukin-1β
Interleukin-1β is a pro-inflammatory cytokine of medical importance. Here the authors describe the discovery of a low-molecular weight compound that antagonizes hIL-1β function in cells, demonstrating the relevance of this discovery for future development of hIL-1β directed therapeutics.
- Ulrich Hommel
- , Konstanze Hurth
- & Frédéric Bornancin
-
Article
| Open AccessStructural basis of lipid-droplet localization of 17-beta-hydroxysteroid dehydrogenase 13
Hydroxysteroid 17-beta-dehydrogenase 13 (HSD17B13) is a hepatic lipid droplet-associated enzyme that is upregulated in patients with non-alcoholic fatty liver disease. Here, the authors report crystal structures of HSD17B13 and its complexes with two series of inhibitors.
- Shenping Liu
- , Ruth F. Sommese
- & Michelle F. Clasquin
-
Article
| Open AccessNon-covalent inhibitors of thioredoxin glutathione reductase with schistosomicidal activity in vivo
Only praziquantel is available for treating schistosomiasis, a disease affecting >200 million people. Here, the authors identify compounds active against schistosome infections meeting the criteria for lead progression indicated by WHO with better activity against juvenile worms than praziquantel.
- Valentina Z. Petukhova
- , Sammy Y. Aboagye
- & Pavel A. Petukhov
-
Article
| Open AccessFrom a drug repositioning to a structure-based drug design approach to tackle acute lymphoblastic leukemia
Deoxycytidine kinase is the rate-limiting enzyme of the salvage pathway and it has recently emerged as a target for antiproliferative therapies for cancers where it is essential. Here, the authors develop a potent inhibitor applying an iterative multidisciplinary approach, which relies on computational design coupled with experimental evaluations.
- Magali Saez-Ayala
- , Laurent Hoffer
- & Xavier Morelli
-
Article
| Open AccessA covalent BTK ternary complex compatible with targeted protein degradation
Bridging covalent ligand discovery with chimeric degrader design has emerged as a mechanism to target proteins that lack enzymatic activity or are intractable. Here, the authors use biochemical and cellular tools to deconvolute the role of covalent modification in targeted protein degradation using Bruton’s tyrosine kinase.
- James Schiemer
- , Andrew Maxwell
- & Matthew F. Calabrese
-
Article
| Open AccessSynthesis of macrocyclic nucleoside antibacterials and their interactions with MraY
MraY is a membrane enzyme required for bacterial cell wall synthesis. Here, the authors modify sphaerimicins as antibacterials targeting it via structure-based design and synthesis through two key reactions, showing a platform for further development of MraY inhibitors as antibacterials.
- Takeshi Nakaya
- , Miyuki Yabe
- & Satoshi Ichikawa
-
Article
| Open AccessChemoenzymatic synthesis of sulfur-linked sugar polymers as heparanase inhibitors
Heparin is a family of complex carbohydrates binding to proteins to modulate cell activities. Here the authors report the synthesis, and conformations simulations of S-linked hemi-A heparosan [GlcA-S-GlcNAc]n, a thio-glycosidic uncleavable polysaccharide, and test it as human heparanase inhibitor.
- Peng He
- , Xing Zhang
- & Paul L. DeAngelis
-
Article
| Open AccessGenerative deep learning enables the discovery of a potent and selective RIPK1 inhibitor
Retrieval of a new starting active compound with a novel scaffold during early drug development is an important but challenging task. Here, the authors propose a generative deep learning model and by applying this model they discover a potent and highly selective RIPK1 inhibitor with a previously unreported scaffold.
- Yueshan Li
- , Liting Zhang
- & Shengyong Yang
-
Article
| Open AccessChemical space docking enables large-scale structure-based virtual screening to discover ROCK1 kinase inhibitors
Virtual screening of huge libraries is successful in identifying drug leads. Here, the authors describe a computational strategy, Chemical Space Docking, which combines docking with a reaction-based search of compounds, thereby enabling the exploration of billions of compounds and beyond.
- Paul Beroza
- , James J. Crawford
- & Christian Lemmen
-
Article
| Open AccessLysyl-tRNA synthetase, a target for urgently needed M. tuberculosis drugs
Tuberculosis is a major cause of mortality, and the rise of drug-resistant strains of Mycobacterium tuberculosis requires the urgent development of safe and effective treatments. In this work, the authors develop a compound against lysyl-tRNA synthetase, demonstrating on-target mechanism of action and efficacy in vivo.
- Simon R. Green
- , Susan H. Davis
- & Laura A. T. Cleghorn
-
Article
| Open AccessA selective and orally bioavailable VHL-recruiting PROTAC achieves SMARCA2 degradation in vivo
Protein degraders are an emerging drug modality; however, their properties lie beyond typical drug-like space. Here the authors report optimisation via structure-based exit vector and linker design towards the VHL-recruiting PROTAC ACBI2, an orally bioavailable and selective degrader of SMARCA2.
- Christiane Kofink
- , Nicole Trainor
- & William Farnaby
-
Article
| Open AccessInsight into mode-of-action and structural determinants of the compstatin family of clinical complement inhibitors
Therapeutic modulation of the complement system has gained interest over the past two decades. Here, the authors provide molecular-level insight into the mode-of-action, target selectivity and species specificity of the compstatin family of complement inhibitors, which entered the clinic in 2021.
- Christina Lamers
- , Xiaoguang Xue
- & Daniel Ricklin
-
Article
| Open AccessStructure of the active Gi-coupled human lysophosphatidic acid receptor 1 complexed with a potent agonist
LPA1 is one of the GPCRs that are drug targets for various diseases. Here the authors report a cryo-EM structure of the active human LPA1-Gi complex bound to an LPA analog with more potent activity against LPA1 and clarified the ligand recognition mechanism.
- Hiroaki Akasaka
- , Tatsuki Tanaka
- & Osamu Nureki
-
Article
| Open AccessIdentification of a binding site on soluble RANKL that can be targeted to inhibit soluble RANK-RANKL interactions and treat osteoporosis
Huang et al. discover a binding site on soluble RANKL that is not found on its membrane-bound homologue. A drug screening identified a small molecule (S3-15) that can target this binding site and has anti-osteoporotic but not immunosuppressive effects.
- Dane Huang
- , Chao Zhao
- & Jun Xu
-
Article
| Open AccessRational design of a sensitivity-enhanced tracer for discovering efficient APC–Asef inhibitors
The adenomatous polyposis coli (APC)–Asef protein interaction is essential for colorectal cancer metastasis. Here, the authors present the rational design of a sensitivity-enhanced tracer for fluorescence polarization assays, enabling them to discover more efficient APC–Asef interaction inhibitors.
- Jie Zhong
- , Yuegui Guo
- & Jian Zhang
-
Article
| Open AccessAn LNA-amide modification that enhances the cell uptake and activity of phosphorothioate exon-skipping oligonucleotides
Oligonucleotides targeting mRNA are promising therapeutic agents but suffer from poor bioavailability. Here, the authors develop reduced-charge oligonucleotides with artificial LNA-amide linkages with improved cell uptake and minimal structural deviation to the DNA:RNA duplex.
- Ysobel R. Baker
- , Cameron Thorpe
- & Tom Brown
-
Article
| Open AccessCovalent narlaprevir- and boceprevir-derived hybrid inhibitors of SARS-CoV-2 main protease
Three covalent hybrid inhibitors of SARS-CoV-2 main protease (Mpro) have been designed and compared to Pfizer’s nirmatrelvir (PF-07321332), providing atomic and thermodynamic details of their binding to the enzyme, and antiviral potency.
- Daniel W. Kneller
- , Hui Li
- & Andrey Kovalevsky
-
Article
| Open AccessAn unexpected strategy to alleviate hypoxia limitation of photodynamic therapy by biotinylation of photosensitizers
Type I photodynamic therapy (PDT) sensitizers show good hypoxia tolerance but only few strategies are available for the design of purely organic Type I photosensitizers (PS). Here, the authors use biotinylation as design strategy to obtain PS-Biotin sensitizers with high efficiency for the generation of superoxide anion radicals and singlet oxygen.
- Jing An
- , Shanliang Tang
- & Wen-Heng Zheng
-
Article
| Open AccessSmall molecule SWELL1 complex induction improves glycemic control and nonalcoholic fatty liver disease in murine Type 2 diabetes
Type 2 diabetes is associated with insulin resistance, impaired insulin secretion and liver steatosis. Here the authors report a proof-of-concept study for small molecule SWELL1 modulators as a therapeutic approach to treat diabetes and associated liver steatosis by enhancing systemic insulin-sensitivity and insulin secretion in mice.
- Susheel K. Gunasekar
- , Litao Xie
- & Rajan Sah
-
Article
| Open AccessDifferential activation mechanisms of lipid GPCRs by lysophosphatidic acid and sphingosine 1-phosphate
Liu et al. report structures of human sphingosine 1-phosphate (S1P) receptor 1 (S1P1) in complex with Gi and S1P or the multiple sclerosis (MS) drug Siponimod, as well as human lysophosphatidic acid (LPA) receptor 1 (LPA1) in complex with Gi and LPA, revealing distinct conformations of the lysophospholipids interacting with their cognate GPCRs.
- Shian Liu
- , Navid Paknejad
- & Xin-Yun Huang
-
Article
| Open AccessDecisive role of water and protein dynamics in residence time of p38α MAP kinase inhibitors
The molecular determinants of the residence time of a small molecule inhibitor at its target protein are not well understood. Here, Pantsar et al. show that the target protein’s conformational stability and solvent exposure are key factors governing the target residence time of kinase inhibitors.
- Tatu Pantsar
- , Philipp D. Kaiser
- & Stefan A. Laufer
-
Article
| Open AccessSliding of HIV-1 reverse transcriptase over DNA creates a transient P pocket – targeting P-pocket by fragment screening
Here the authors observe a transient P-pocket created when HIV reverse transcriptase slides over DNA substrate, identify fragments targeting this pocket, and develop a cryo-EM platform for lead optimization.
- Abhimanyu K. Singh
- , Sergio E. Martinez
- & Kalyan Das
-
Article
| Open AccessDevelopment of a BCL-xL and BCL-2 dual degrader with improved anti-leukemic activity,
Simultaneous targeting of BCL-xL and BCL-2 is an attractive approach for cancer treatment. Based on information gained by computational structure modelling, the authors develop a PROTAC that induces degradation of both BCL-xL and BCL-2 and effectively targets BCL-xL/2-dependent leukaemia cells.
- Dongwen Lv
- , Pratik Pal
- & Daohong Zhou
-
Article
| Open AccessStructure of PDE3A–SLFN12 complex and structure-based design for a potent apoptosis inducer of tumor cells
Anagrelide, nauclefine and DNMDP induce apoptosis by forming complexes with phosphodiesterase 3A (PDE3A) and Schlafen 12 protein (SLFN12). Here, the authors present the cryo-EM structures of PDE3A-SLFN12 complexes with these compounds as molecular glues. Based on the complex structure, they developed an anagrelide analog that shows a higher potency in inducing apoptosis in cultured cells and also promotes tumor growth inhibition in tumor xenografts, which is of interest for cancer drug development.
- Jie Chen
- , Nan Liu
- & Xiaodong Wang
-
Article
| Open AccessCellular model system to dissect the isoform-selectivity of Akt inhibitors
Elucidating specific effects of protein kinase Akt isoforms remains challenging. Here, the authors establish an Akt isoform-dependent cellular model system and use it, together with X-ray crystallography and structure-based ligand design, to develop isoform-selective covalent-allosteric Akt inhibitors
- Lena Quambusch
- , Laura Depta
- & Daniel Rauh
-
Article
| Open AccessProtein mimetic amyloid inhibitor potently abrogates cancer-associated mutant p53 aggregation and restores tumor suppressor function
Amyloid aggregation of mutant p53 contributes to its loss of tumor suppressor function and oncogenic gain-of-function. Here, the authors use a protein mimetic to abrogate mutant p53 aggregation and rescue p53 function, which inhibits cancer cell proliferation in vitro and halts tumor growth in vivo.
- L. Palanikumar
- , Laura Karpauskaite
- & Mazin Magzoub
-
Article
| Open AccessDiscovery of first-in-class inhibitors of ASH1L histone methyltransferase with anti-leukemic activity
The histone methyltransferase ASH1L plays a role in various diseases, including cancer, and has been validated as a therapeutic target; however, no inhibitors of ASH1L have been reported. Here the authors present small molecule inhibitors of ASH1L and demonstrate their on-target activity in leukemia cells and a mouse model of leukemia.
- David S. Rogawski
- , Jing Deng
- & Jolanta Grembecka
-
Article
| Open AccessSelective inhibition of cullin 3 neddylation through covalent targeting DCN1 protects mice from acetaminophen-induced liver toxicity
Activation of cullin-RING ligases can be inhibited by targeting DCN1, but selective DCN1 inhibitors with in vivo activity are lacking. Here, the authors develop covalent DCN1 inhibitors that selectively and potently inhibit cullin-3 activation and downstream functions in cells and in mice.
- Haibin Zhou
- , Jianfeng Lu
- & Shaomeng Wang
-
Article
| Open AccessStructure-based design of a Cortistatin analogue with immunomodulatory activity in models of inflammatory bowel disease
Inflammatory bowel disease is caused by chronic inflammation of the gastrointestinal tract and disturbed immune responses. Here the authors present examination of Cortistatin analogues that display enhanced half-life stability whilst maintaining immunomodulatory functionality.
- Álvaro Rol
- , Toni Todorovski
- & Maria J. Macias
-
Article
| Open AccessFast acting allosteric phosphofructokinase inhibitors block trypanosome glycolysis and cure acute African trypanosomiasis in mice
Glycolytic enzymes are challenging drug targets due to their highly conserved active sites and phosphorylated substrates. Here, the authors identify fast acting allosteric inhibitors of Trypanosoma brucei phosphofructokinase that block trypanosome glycolysis and provide cure evidence in murine model.
- Iain W. McNae
- , James Kinkead
- & Malcolm D. Walkinshaw
-
Article
| Open AccessDesigned CXCR4 mimic acts as a soluble chemokine receptor that blocks atherogenic inflammation by agonist-specific targeting
The development of specific anti-cytokine/chemokine therapeutic strategies for atherosclerotic disease is challenging. Here, the authors have designed a peptide-based ectodomain mimic of the chemokine receptor CXCR4 that selectively targets MIF but not CXCL12 and blocks experimental atherosclerosis in vivo.
- Christos Kontos
- , Omar El Bounkari
- & Jürgen Bernhagen
-
Article
| Open AccessAdipoR1/AdipoR2 dual agonist recovers nonalcoholic steatohepatitis and related fibrosis via endoplasmic reticulum-mitochondria axis
Nonalcoholic steatohepatitis (NASH) and associated liver fibrosis have limited therapy options. Here the authors report a novel adiponectin-based dual agonist for adiponectin receptors 1 and 2 with a longer half-life, and show that it ameliorates NASH and liver fibrosis in mouse models.
- Hongjiao Xu
- , Qian Zhao
- & Xianxing Jiang
-
Article
| Open AccessStructure-based evolution of a promiscuous inhibitor to a selective stabilizer of protein–protein interactions
Small molecule stabilizers of protein–protein interactions hold great therapeutic potential. Based on virtual screening and molecular docking, the authors here develop a strategy to evolve weak, promiscuous inhibitors of 14-3-3 interactions into selective stabilizers of the 14-3-3/ChREBP complex.
- Eline Sijbesma
- , Emira Visser
- & Christian Ottmann
-
Article
| Open AccessSmall molecules that inhibit TNF signalling by stabilising an asymmetric form of the trimer
While biologics have been successfully applied in TNF antagonist treatments, there are no clinically approved small molecules that target TNF. Here, the authors discover potent small molecule inhibitors of TNF, elucidate their molecular mechanism, and demonstrate TNF inhibition in vitro and in vivo.
- James O’Connell
- , John Porter
- & Alastair Lawson
-
Article
| Open AccessHarnessing calcineurin-FK506-FKBP12 crystal structures from invasive fungal pathogens to develop antifungal agents
FK506 is a potential antifungal compound that inhibits calcineurin, but it also has immunosuppressive activity. Here, Juvvadi et al. report the structure of FK506 in complex with the FK506-binding protein FKPB12 and calcineurin, and design a less immunosuppresive FK506 analog with antifungal activity in mice.
- Praveen R. Juvvadi
- , David Fox III
- & William J. Steinbach
-
Article
| Open AccessStructure and inhibition mechanism of the catalytic domain of human squalene epoxidase
Squalene epoxidase (SQLE) is a key enzyme in cholesterol biosynthesis and is a target for hypercholesteremia and cancer drug development. Here the authors present the crystal structures of the human SQLE catalytic domain alone and bound with small molecule inhibitors, which will facilitate the development of next-generation SQLE inhibitors.
- Anil K. Padyana
- , Stefan Gross
- & Gromoslaw A. Smolen
-
Article
| Open AccessLattice engineering enables definition of molecular features allowing for potent small-molecule inhibition of HIV-1 entry
Temsavir, a compound that inhibits HIV entry by binding envelope (Env), is currently in clinical development. Here, Lai et al. identify a more than 10-fold improved compound and, using lattice engineering, obtain crystal structures that give insights into improved inhibition between small molecules and Env.
- Yen-Ting Lai
- , Tao Wang
- & Peter D. Kwong
-
Article
| Open AccessDiscovery of Mcl-1-specific inhibitor AZD5991 and preclinical activity in multiple myeloma and acute myeloid leukemia
High expression of Mcl-1 promotes tumorigenesis and resistance to anticancer therapies. Here they report a macrocyclic molecule with high selectivity and affinity for Mcl-1 that exhibits potent anti-tumor effects as single agent and in combination with bortezomib or venetoclax in preclinical models of multiple myeloma and acute myeloid leukemia.
- Adriana E. Tron
- , Matthew A. Belmonte
- & Alexander W. Hird
-
Article
| Open AccessDesign and 22-step synthesis of highly potent D-ring modified and linker-equipped analogs of spongistatin 1
Step-economical and efficient syntheses of Spongistatin 1 analogs are desirable for the development of potent anti-proliferative agents. Here, the authors report a 22-step synthesis of a D-ring modified Spongistatin 1 analog with retained picomolar potency among a group of C(15) ester derivatives.
- Linda M. Suen
- , Makeda A. Tekle-Smith
- & James L. Leighton
-
Article
| Open AccessHigh-resolution NMR studies of antibiotics in cellular membranes
Antibiotics that target the peptidoglycan precursor lipid II are promising templates for next-generation antibiotics. Here authors use solid-state NMR and monitor lipid II-binding antibiotics, such as nisin, directly in cell membranes.
- João Medeiros-Silva
- , Shehrazade Jekhmane
- & Markus Weingarth
-
Article
| Open AccessSmall molecule inhibitors of RAS-effector protein interactions derived using an intracellular antibody fragment
Intracellular antibodies can inhibit disease-relevant protein interactions, but inefficient cellular uptake limits their utility. Using a RAS-targeting intracellular antibody as a screening tool, the authors here identify small molecules that inhibit RAS-effector interactions and readily penetrate cells.
- Camilo E. Quevedo
- , Abimael Cruz-Migoni
- & Terence H. Rabbitts
-
Article
| Open AccessStructure-guided design of an Hsp90β N-terminal isoform-selective inhibitor
The molecular chaperone Hsp90 oversees the folding of many proteins associated with cancer progression but existing small-molecule inhibitors of this pathway are not isoform-selective. Here, the authors rationally design an Hsp90 inhibitor that displays high selectivity for the Hsp90β isoform.
- Anuj Khandelwal
- , Caitlin N. Kent
- & Brian S. J. Blagg
-
Article
| Open AccessA covalent PIN1 inhibitor selectively targets cancer cells by a dual mechanism of action
PIN1 is a promising therapeutic target for cancer treatment. In this study, the authors identify a covalent inhibitor of PIN1 with anti-tumour and anti-metastatic properties thanks to PIN1 inactivation and to the release, after binding to PIN1, of a quinone-mimicking compound that elicits reactive oxygen generation and causes DNA damage.
- Elena Campaner
- , Alessandra Rustighi
- & Giannino Del Sal