Publications

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2022

Structural basis for Gemin5 decamer-mediated mRNA binding.

Guo Q, Zhao S, Francisco-Velilla R, Zhang J, Embarc-Buh A, Abellan S, Lv M, Tang P, Gong Q, Shen H, Sun L, Yao X, Min J, Shi Y, Martínez-Salas E, Zhang K, Xu C

Nat Commun. 13(1):5166. doi: 10.1038/s41467-022-32883-z

Publication date: September 2, 2022

PMID: 36056043

Crystal structure of SARS-CoV-2 nsp10-nsp16 in complex with small molecule inhibitors, SS148 and WZ16.

Klima M, Khalili Yazdi A, Li F, Chau I, Hajian T, Bolotokova A, Kaniskan HÜ, Han Y, Wang K, Li D, Luo M, Jin J, Boura E, Vedadi M

Protein Sci. 31(9):e4395. doi: 10.1002/pro.4395

Publication date: August 31, 2022

PMID: 36040262

PKC isoforms activate LRRK1 kinase by phosphorylating conserved residues (Ser1064, Ser1074 and Thr1075) within the CORB GTPase domain.

Malik AU, Karapetsas A, Nirujogi RS, Chatterjee D, Phung TK, Wightman M, Gourlay R, Morrice NA, Mathea S, Knapp S, Alessi DR

Biochem J. doi: 10.1042/BCJ20220308

Publication date: August 30, 2022

PMID: 36040231

PROTAC degraders as chemical probes for studying target biology and target validation.

Němec V, Schwalm MP, Müller S, Knapp S

Chem Soc Rev. doi: 10.1039/d2cs00478j

Publication date: August 25, 2022

PMID: 36004812

Pharmacokinetic Optimization of Small Molecule Janus Kinase 3 Inhibitors to Target Immune Cells.

Laux J, Forster M, Riexinger L, Schwamborn A, Guezguez J, Pokoj C, Kudolo M, Berger LM, Knapp S, Schollmeyer D, Guse J, Burnet M, Laufer SA

ACS Pharmacol Transl Sci. 5(8):573-602. doi: 10.1021/acsptsci.2c00054

Publication date: August 12, 2022

PMID: 35983274

Discovery of novel druggable pockets on polyomavirus VP1 through crystallographic fragment-based screening to develop capsid assembly inhibitors.

Osipov EM, Munawar AH, Beelen S, Fearon D, Douangamath A, Wild C, Weeks SD, Van Aerschot A, von Delft F, Strelkov SV

RSC Chem Biol. 3(8):1013-1027. doi: 10.1039/d2cb00052k

Publication date: August 3, 2022

PMID: 35974998

Compilation and evaluation of a fatty acid mimetics screening library.

Ehrler JHM, Brunst S, Tjaden A, Kilu W, Heering J, Hernandez-Olmos V, Krommes A, Kramer JS, Steinhilber D, Schubert-Zsilavecz M, Müller S, Merk D, Proschak E

Biochem Pharmacol. 204:115191. doi: 10.1016/j.bcp.2022.115191

Publication date: July 27, 2022

PMID: 35907497

Enzymatic nucleosome acetylation selectively affects activity of histone methyltransferases in vitro.

Trush VV, Feller C, Li ASM, Allali-Hassani A, Szewczyk MM, Chau I, Eram MS, Jiang B, Luu R, Zhang F, Barsyte-Lovejoy D, Aebersold R, Arrowsmith CH, Vedadi M

Biochim Biophys Acta Gene Regul Mech. 194845. doi: 10.1016/j.bbagrm.2022.194845

Publication date: July 27, 2022

PMID: 35907431

Cryo-EM structure of the human Kv3.1 channel reveals gating control by the cytoplasmic T1 domain.

Chi G, Liang Q, Sridhar A, Cowgill JB, Sader K, Radjainia M, Qian P, Castro-Hartmann P, Venkaya S, Singh NK, McKinley G, Fernandez-Cid A, Mukhopadhyay SMM, Burgess-Brown NA, Delemotte L, Covarrubias M, Dürr KL

Nat Commun. 13(1):4087. doi: 10.1038/s41467-022-29594-w

Publication date: July 15, 2022

PMID: 35840580

A New Chemotype of Chemically Tractable Nonsteroidal Estrogens Based on a Thieno[2,3-d]pyrimidine Core.

Sammeta VR, Norris JD, Artham S, Torrice CD, Byemerwa J, Joiner C, Fanning SW, McDonnell DP, Willson TM

ACS Med Chem Lett. 13(7):1151-1158. doi: 10.1021/acsmedchemlett.2c00180

Publication date: July 14, 2022

PMID: 35859859

Kinetic Characterization of SARS-CoV-2 nsp13 ATPase Activity and Discovery of Small-Molecule Inhibitors.

Yazdi AK, Pakarian P, Perveen S, Hajian T, Santhakumar V, Bolotokova A, Li F, Vedadi M

ACS Infect Dis. doi: 10.1021/acsinfecdis.2c00165

Publication date: July 13, 2022

PMID: 35822715

Binding adaptation of GS-441524 diversifies macro domains and downregulate SARS-CoV-2 de-MARylation capacity.

Tsika AC, Gallo A, Fourkiotis NK, Argyriou AI, Sreeramulu S, Löhr F, Rogov VV, Richter C, Linhard V, Gande SL, Altincekic N, Krishnathas R, Elamri I, Schwalbe H, Wollenhaupt J, Weiss MS, Spyroulias GA

J Mol Biol. 167720. doi: 10.1016/j.jmb.2022.167720

Publication date: July 12, 2022

PMID: 35839840

A Target Engagement Assay to Assess Uptake, Potency, and Retention of Antibiotics in Living Bacteria.

Fanti RC, Vasconcelos SNS, Catta-Preta CMC, Sullivan JR, Riboldi GP, Dos Reis CV, Ramos PZ, Edwards AM, Behr MA, Couñago RM

ACS Infect Dis. doi: 10.1021/acsinfecdis.2c00073

Publication date: July 11, 2022

PMID: 35815896

CACHE (Critical Assessment of Computational Hit-finding Experiments): A public-private partnership benchmarking initiative to enable the development of computational methods for hit-finding.

Ackloo S, Al-Awar R, Amaro RE, Arrowsmith CH, Azevedo H, Batey RA, Bengio Y, Betz UAK, Bologa CG, Chodera JD, Cornell WD, Dunham I, Ecker GF, Edfeldt K, Edwards AM, Gilson MK, Gordijo CR, Hessler G, Hillisch A, Hogner A, Irwin JJ, Jansen JM, Kuhn D, Leach AR, Lee AA, Lessel U, Morgan MR, Moult J, Muegge I, Oprea TI, Perry BG, Riley P, Rousseaux SAL, Saikatendu KS, Santhakumar V, Schapira M, Scholten C, Todd MH, Vedadi M, Volkamer A, Willson TM

Nat Rev Chem. 6(4):287-295. doi: 10.1038/s41570-022-00363-z

Publication date: July 6, 2022

PMID: 35783295

Multiparameter phenotypic screening for endogenous TFEB and TFE3 translocation identifies novel chemical series modulating lysosome function.

Carling PJ, Ryan BJ, McGuinness W, Kataria S, Humble SW, Milde S, Duce JA, Kapadia N, Zuercher WJ, Davis JB, Di Daniel E, Wade-Martins R

Autophagy. doi: 10.1080/15548627.2022.2095834

Publication date: July 4, 2022

PMID: 35786165

Human Diacylglycerol Kinase ε N-Terminal Segment Regulates the Phosphatidylinositol Cycle, Controlling the Rate but Not the Acyl Chain Composition of Its Lipid Intermediates.

Bozelli JC, Yune J, Aulakh SS, Cao Z, Fernandes A, Seitova A, Tong Y, Schreier S, Epand RM

ACS Chem Biol. doi: 10.1021/acschembio.2c00387

Publication date: June 29, 2022

PMID: 35767833

Temozolomide-induced guanine mutations create exploitable vulnerabilities of guanine-rich DNA and RNA regions in drug-resistant gliomas.

Tiek DM, Erdogdu B, Razaghi R, Jin L, Sadowski N, Alamillo-Ferrer C, Hogg JR, Haddad BR, Drewry DH, Wells CI, Pickett JE, Song X, Goenka A, Hu B, Goldlust SA, Zuercher WJ, Pertea M, Timp W, Cheng SY, Riggins RB

Sci Adv. 8(25):eabn3471. doi: 10.1126/sciadv.abn3471

Publication date: June 24, 2022

PMID: 35731869

Chemical biology and pharmacology of histone lysine methylation inhibitors.

Barghout SH, Machado RAC, Barsyte-Lovejoy D

Biochim Biophys Acta Gene Regul Mech. 194840. doi: 10.1016/j.bbagrm.2022.194840

Publication date: June 23, 2022

PMID: 35753676

A Toolbox for the Generation of Chemical Probes for Baculovirus IAP Repeat Containing Proteins.

Schwalm MP, Berger LM, Meuter MN, Vasta JD, Corona CR, Röhm S, Berger BT, Farges F, Beinert SM, Preuss F, Morasch V, Rogov VV, Mathea S, Saxena K, Robers MB, Müller S, Knapp S

Front Cell Dev Biol. 10:886537. doi: 10.3389/fcell.2022.886537

Publication date: June 21, 2022

PMID: 35721509

Host Kinase CSNK2 is a Target for Inhibition of Pathogenic SARS-like β-Coronaviruses.

Yang X, Dickmander RJ, Bayati A, Taft-Benz SA, Smith JL, Wells CI, Madden EA, Brown JW, Lenarcic EM, Yount BL, Chang E, Axtman AD, Baric RS, Heise MT, McPherson PS, Moorman NJ, Willson TM

ACS Chem Biol. doi: 10.1021/acschembio.2c00378

Publication date: June 19, 2022

PMID: 35723434

Designed Ankyrin Repeat Proteins as a tool box for analyzing p63.

Strubel A, Münick P, Chaikuad A, Dreier B, Schaefer J, Gebel J, Osterburg C, Tuppi M, Schäfer B, Knapp S, Plückthun A, Dötsch V

Cell Death Differ. doi: 10.1038/s41418-022-01030-y

Publication date: June 18, 2022

PMID: 35717504

Methylation of the Hippo effector YAP by the methyltransferase SETD7 drives myocardial ischemic injury: a translational study.

Ambrosini S, Montecucco F, Kolijn D, Pedicino D, Akhmedov A, Mohammed SA, Herwig M, Gorica E, Lujza Szabó P, Weber L, Russo G, Vinci R, Matter CM, Liuzzo G, Brown PJ, Rossi FMV, Camici GG, Sciarretta S, Paolo Beltrami A, Crea F, Podesser B, Lüscher TF, Kiss A, Ruschitzka F, Hamdani N, Costantino S, Paneni F

Cardiovasc Res. doi: 10.1093/cvr/cvac102

Publication date: June 16, 2022

PMID: 35709329

Genome-wide translation control analysis of developing human neurons.

Lins ÉM, Oliveira NCM, Reis O, Ferrasa A, Herai R, Muotri AR, Massirer KB, Bengtson MH

Mol Brain. 15(1):55. doi: 10.1186/s13041-022-00940-9

Publication date: June 15, 2022

PMID: 35706057

Structure and activity of human TMPRSS2 protease implicated in SARS-CoV-2 activation.

Fraser BJ, Beldar S, Seitova A, Hutchinson A, Mannar D, Li Y, Kwon D, Tan R, Wilson RP, Leopold K, Subramaniam S, Halabelian L, Arrowsmith CH, Bénard F

Nat Chem Biol. doi: 10.1038/s41589-022-01059-7

Publication date: June 8, 2022

PMID: 35676539

Illuminating the Dark: Highly Selective Inhibition of Serine/Threonine Kinase 17A with Pyrazolo[1,5-a]pyrimidine-Based Macrocycles.

Kurz CG, Preuss F, Tjaden A, Cusack M, Amrhein JA, Chatterjee D, Mathea S, Berger LM, Berger BT, Krämer A, Weller M, Weiss T, Müller S, Knapp S, Hanke T

J Med Chem. doi: 10.1021/acs.jmedchem.2c00173

Publication date: May 24, 2022

PMID: 35608370

PRMT inhibition induces a viral mimicry response in triple-negative breast cancer.

Wu Q, Nie DY, Ba-Alawi W, Ji Y, Zhang Z, Cruickshank J, Haight J, Ciamponi FE, Chen J, Duan S, Shen Y, Liu J, Marhon SA, Mehdipour P, Szewczyk MM, Dogan-Artun N, Chen W, Zhang LX, Deblois G, Prinos P, Massirer KB, Barsyte-Lovejoy D, Jin J, De Carvalho DD, Haibe-Kains B, Wang X, Cescon DW, Lupien M, Arrowsmith CH

Nat Chem Biol. doi: 10.1038/s41589-022-01024-4

Publication date: May 16, 2022

PMID: 35578032

Calcium/calmodulin-dependent protein kinase kinase 2 regulates hepatic fuel metabolism.

Stork BA, Dean A, Ortiz AR, Saha P, Putluri N, Planas-Silva MD, Mahmud I, Rajapakshe K, Coarfa C, Knapp S, Lorenzi PL, Kemp BE, Turk BE, Scott JW, Means AR, York B

Mol Metab. 101513. doi: 10.1016/j.molmet.2022.101513

Publication date: May 11, 2022

PMID: 35562082

Enabling pseudokinases as potential drug targets.

Preuss F, Chatterjee D, Dederer V, Knapp S, Mathea S

Methods Enzymol. 667:663-683. doi: 10.1016/bs.mie.2022.03.050

Publication date: May 8, 2022

PMID: 35525558

AD Informer Set: Chemical tools to facilitate Alzheimer's disease drug discovery.

Potjewyd FM, Annor-Gyamfi JK, Aubé J, Chu S, Conlon IL, Frankowski KJ, Guduru SKR, Hardy BP, Hopkins MD, Kinoshita C, Kireev DB, Mason ER, Moerk CT, Nwogbo F, Pearce KH, Richardson TI, Rogers DA, Soni DM, Stashko M, Wang X, Wells C, Willson TM, Frye SV, Young JE, Axtman AD

Alzheimers Dement (N Y). 8(1):e12246. doi: 10.1002/trc2.12246

Publication date: April 28, 2022

PMID: 35475262

Protein proximity networks and functional evaluation of the Casein Kinase 1 γ family reveal unique roles for CK1γ3 in WNT signaling.

Agajanian MJ, Potjewyd FM, Bowman BM, Solomon S, LaPak KM, Bhatt DP, Smith JL, Goldfarb D, Axtman AD, Major MB

J Biol Chem. 101986. doi: 10.1016/j.jbc.2022.101986

Publication date: April 26, 2022

PMID: 35487243

BET bromodomain inhibitors.

Schwalm MP, Knapp S

Curr Opin Chem Biol. 68:102148. doi: 10.1016/j.cbpa.2022.102148

Publication date: April 21, 2022

PMID: 35462054

Use of AD Informer Set compounds to explore validity of novel targets in Alzheimer's disease pathology.

Potjewyd FM, Annor-Gyamfi JK, Aubé J, Chu S, Conlon IL, Frankowski KJ, Guduru SKR, Hardy BP, Hopkins MD, Kinoshita C, Kireev DB, Mason ER, Moerk CT, Nwogbo F, Pearce KH, Richardson TI, Rogers DA, Soni DM, Stashko M, Wang X, Wells C, Willson TM, Frye SV, Young JE, Axtman AD

Alzheimers Dement (N Y). 8(1):e12253. doi: 10.1002/trc2.12253

Publication date: April 19, 2022

PMID: 35434254

SAMPL7 protein-ligand challenge: A community-wide evaluation of computational methods against fragment screening and pose-prediction.

Grosjean H, Işık M, Aimon A, Mobley D, Chodera J, von Delft F, Biggin PC

J Comput Aided Mol Des. doi: 10.1007/s10822-022-00452-7

Publication date: April 15, 2022

PMID: 35426591

A Consensus Compound/Bioactivity Dataset for Data-Driven Drug Design and Chemogenomics.

Isigkeit L, Chaikuad A, Merk D

Molecules. 27(8):. doi: 10.3390/molecules27082513

Publication date: April 13, 2022

PMID: 35458710

Galaxy workflows for fragment-based virtual screening: a case study on the SARS-CoV-2 main protease.

Bray S, Dudgeon T, Skyner R, Backofen R, Grüning B, von Delft F

J Cheminform. 14(1):22. doi: 10.1186/s13321-022-00588-6

Publication date: April 12, 2022

PMID: 35414112

Identification of 4-anilino-quin(az)oline as a cell active Protein Kinase Novel 3 (PKN3) inhibitor chemotype.

Asquith CRM, Temme L, East MP, Laitinen T, Pickett J, Kwarcinski FE, Sinha P, Wells CI, Johnson GL, Zutshi R, Drewry DH

ChemMedChem. doi: 10.1002/cmdc.202200161

Publication date: April 11, 2022

PMID: 35403825

Synthesis and biological evaluation of Haspin inhibitors: Kinase inhibitory potency and cellular activity.

Zeinyeh W, Esvan YJ, Josselin B, Defois M, Baratte B, Knapp S, Chaikuad A, Anizon F, Giraud F, Ruchaud S, Moreau P

Eur J Med Chem. 236:114369. doi: 10.1016/j.ejmech.2022.114369

Publication date: April 9, 2022

PMID: 35447555

Validating Small Molecule Chemical Probes for Biological Discovery.

Vu V, Szewczyk MM, Nie DY, Arrowsmith CH, Barsyte-Lovejoy D

Annu Rev Biochem. doi: 10.1146/annurev-biochem-032620-105344

Publication date: April 1, 2022

PMID: 35363509

PRMT7 ablation stimulates anti-tumor immunity and sensitizes melanoma to immune checkpoint blockade.

Srour N, Villarreal OD, Hardikar S, Yu Z, Preston S, Miller WH, Szewczyk MM, Barsyte-Lovejoy D, Xu H, Chen T, Del Rincón SV, Richard S

Cell Rep. 38(13):110582. doi: 10.1016/j.celrep.2022.110582

Publication date: March 29, 2022

PMID: 35354055

Kinase domain autophosphorylation rewires the activity and substrate specificity of CK1 enzymes.

Cullati SN, Chaikuad A, Chen JS, Gebel J, Tesmer L, Zhubi R, Navarrete-Perea J, Guillen RX, Gygi SP, Hummer G, Dötsch V, Knapp S, Gould KL

Mol Cell. doi: 10.1016/j.molcel.2022.03.005

Publication date: March 21, 2022

PMID: 35353987

PRMT5 regulates ATF4 transcript splicing and oxidative stress response.

Szewczyk MM, Luciani GM, Vu V, Murison A, Dilworth D, Barghout SH, Lupien M, Arrowsmith CH, Minden MD, Barsyte-Lovejoy D

Redox Biol. 51:102282. doi: 10.1016/j.redox.2022.102282

Publication date: March 11, 2022

PMID: 35305370

Stopping pandemics before they start: Lessons learned from SARS-CoV-2.

Edwards AM, Baric RS, Saphire EO, Ulmer JB

Science. 375(6585):1133-1139. doi: 10.1126/science.abn1900

Publication date: March 11, 2022

PMID: 35271333

Development of novel urea-based ATM kinase inhibitors with subnanomolar cellular potency and high kinome selectivity.

Dimitrov T, Anli C, Moschopoulou AA, Kronenberger T, Kudolo M, Geibel C, Schwalm MP, Knapp S, Zender L, Forster M, Laufer S

Eur J Med Chem. 235:114234. doi: 10.1016/j.ejmech.2022.114234

Publication date: March 8, 2022

PMID: 35325634

Resistance to kinase inhibition through shortened target engagement.

Rangwala AM, Berger BT, Robers MB, Knapp S, Seeliger MA

Mol Cell Oncol. 9(1):2029999. doi: 10.1080/23723556.2022.2029999

Publication date: March 8, 2022

PMID: 35252553

Evolutionary history of the p53 family DNA-binding domain: insights from an Alvinella pompejana homolog.

Zhang Q, Balourdas DI, Baron B, Senitzki A, Haran TE, Wiman KG, Soussi T, Joerger AC

Cell Death Dis. 13(3):214. doi: 10.1038/s41419-022-04653-8

Publication date: March 7, 2022

PMID: 35256607

The MYC oncoprotein directly interacts with its chromatin cofactor PNUTS to recruit PP1 phosphatase.

Wei Y, Redel C, Ahlner A, Lemak A, Johansson-Åkhe I, Houliston S, Kenney TMG, Tamachi A, Morad V, Duan S, Andrews DW, Wallner B, Sunnerhagen M, Arrowsmith CH, Penn LZ

Nucleic Acids Res. doi: 10.1093/nar/gkac138

Publication date: March 4, 2022

PMID: 35244724

Longitudinal assessment of reactivity and affinity profile of anti-Jo1 autoantibodies to distinct HisRS domains and a splice variant in a cohort of patients with myositis and anti-synthetase syndrome.

Notarnicola A, Preger C, Lundström SL, Renard N, Wigren E, Van Gompel E, Galindo-Feria AS, Persson H, Fathi M, Grunewald J, Jakobsson PJ, Gräslund S, Lundberg IE, Fernandes-Cerqueira C

Arthritis Res Ther. 24(1):62. doi: 10.1186/s13075-022-02745-6

Publication date: March 2, 2022

PMID: 35236390

Nanobodies as allosteric modulators of Parkinson's disease-associated LRRK2.

Singh RK, Soliman A, Guaitoli G, Störmer E, von Zweydorf F, Dal Maso T, Oun A, Van Rillaer L, Schmidt SH, Chatterjee D, David JA, Pardon E, Schwartz TU, Knapp S, Kennedy EJ, Steyaert J, Herberg FW, Kortholt A, Gloeckner CJ, Versées W

Proc Natl Acad Sci U S A. 119(9):. doi: 10.1073/pnas.2112712119

Publication date: March 1, 2022

PMID: 35217606

LRRK2 dynamics analysis identifies allosteric control of the crosstalk between its catalytic domains.

Weng JH, Aoto PC, Lorenz R, Wu J, Schmidt SH, Manschwetus JT, Kaila-Sharma P, Silletti S, Mathea S, Chatterjee D, Knapp S, Herberg FW, Taylor SS

PLoS Biol. 20(2):e3001427. doi: 10.1371/journal.pbio.3001427

Publication date: February 23, 2022

PMID: 35192607