Publications

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2023

Methods for computer-assisted PROTAC design.

Rovers E, Schapira M

Methods Enzymol. 690:311-340. doi: 10.1016/bs.mie.2023.06.020

Publication date: October 20, 2023

PMID: 37858533

Structure of LRRK1 and mechanisms of autoinhibition and activation.

Reimer JM, Dickey AM, Lin YX, Abrisch RG, Mathea S, Chatterjee D, Fay EJ, Knapp S, Daugherty MD, Reck-Peterson SL, Leschziner AE

Nat Struct Mol Biol. doi: 10.1038/s41594-023-01109-1

Publication date: October 19, 2023

PMID: 37857821

Improving data quality in chemical biology.

Knapp S, Müller S

Nat Chem Biol. doi: 10.1038/s41589-023-01449-5

Publication date: October 16, 2023

PMID: 37845552

DARPins detect the formation of hetero-tetramers of p63 and p73 in epithelial tissues and in squamous cell carcinoma.

Strubel A, Münick P, Hartmann O, Chaikuad A, Dreier B, Schaefer JV, Gebel J, Osterburg C, Tuppi M, Schäfer B, Buck V, Rosenfeldt M, Knapp S, Plückthun A, Diefenbacher ME, Dötsch V

Cell Death Dis. 14(10):674. doi: 10.1038/s41419-023-06213-0

Publication date: October 12, 2023

PMID: 37828008

Identification of potential inhibitors of casein kinase 2 alpha of Plasmodium falciparum with potent in vitro activity.

Tomaz KCP, Tavella TA, Borba JVB, Salazar-Alvarez LC, Levandoski JE, Mottin M, Sousa BKP, Moreira-Filho JT, Almeida VM, Clementino LC, Bourgard C, Massirer KB, Couñago RM, Andrade CH, Sunnerhagen P, Bilsland E, Cassiano GC, Costa FTM

Antimicrob Agents Chemother. e0058923. doi: 10.1128/aac.00589-23

Publication date: October 11, 2023

PMID: 37819090

Structural Basis for Highly Selective Class II Alpha Phosphoinositide-3-Kinase Inhibition.

Kücükdisli M, Bel-Abed H, Cirillo D, Lo WT, Efrém NL, Horatscheck A, Perepelittchenko L, Prokofeva P, Ehret TAL, Radetzki S, Neuenschwander M, Specker E, Médard G, Müller S, Wilhelm S, Kuster B, von Kries JP, Haucke V, Nazaré M

J Med Chem. doi: 10.1021/acs.jmedchem.3c01319

Publication date: October 11, 2023

PMID: 37819647

Antagonistic roles of canonical and Alternative-RPA in disease-associated tandem CAG repeat instability.

Gall-Duncan T, Luo J, Jurkovic CM, Fischer LA, Fujita K, Deshmukh AL, Harding RJ, Tran S, Mehkary M, Li V, Leib DE, Chen R, Tanaka H, Mason AG, Lévesque D, Khan M, Razzaghi M, Prasolava T, Lanni S, Sato N, Caron MC, Panigrahi GB, Wang P, Lau R, Castel AL, Masson JY, Tippett L, Turner C, Spies M, La Spada AR, Campos EI, Curtis MA, Boisvert FM, Faull RLM, Davidson BL, Nakamori M, Okazawa H, Wold MS, Pearson CE

Cell. doi: 10.1016/j.cell.2023.09.008

Publication date: October 5, 2023

PMID: 37827155

Discovery of a 53BP1 Small Molecule Antagonist Using a Focused DNA-Encoded Library Screen.

Shell DJ, Foley CA, Wang Q, Smith CM, Guduru SKR, Zeng H, Dong A, Norris-Drouin JL, Axtman M, Hardy PB, Gupta G, Halabelian L, Frye SV, James LI, Pearce KH

J Med Chem. doi: 10.1021/acs.jmedchem.3c01192

Publication date: October 2, 2023

PMID: 37782247

A machine learning and live-cell imaging tool kit uncovers small molecules induced phospholipidosis.

Hu H, Tjaden A, Knapp S, Antolin AA, Müller S

Cell Chem Biol. doi: 10.1016/j.chembiol.2023.09.003

Publication date: September 27, 2023

PMID: 37797617

Development of LM-41 and AF-2112, two flufenamic acid-derived TEAD inhibitors obtained through the replacement of the trifluoromethyl group by aryl rings.

Fnaiche A, Mélin L, Suárez NG, Paquin A, Vu V, Li F, Allali-Hassani A, Bolotokova A, Allemand F, Gelin M, Cotelle P, Woo S, LaPlante SR, Barsyte-Lovejoy D, Santhakumar V, Vedadi M, Guichou JF, Annabi B, Gagnon A

Bioorg Med Chem Lett. 129488. doi: 10.1016/j.bmcl.2023.129488

Publication date: September 26, 2023

PMID: 37770003

Discovery of Nedd4 auto-ubiquitination inhibitors.

Yong D, Green SR, Ghiabi P, Santhakumar V, Vedadi M

Sci Rep. 13(1):16057. doi: 10.1038/s41598-023-42997-z

Publication date: September 25, 2023

PMID: 37749144

Discovery of a Druggable, Cryptic Pocket in SARS-CoV-2 nsp16 Using Allosteric Inhibitors.

Inniss NL, Kozic J, Li F, Rosas-Lemus M, Minasov G, Rybáček J, Zhu Y, Pohl R, Shuvalova L, Rulíšek L, Brunzelle JS, Bednárová L, Štefek M, Kormaník JM, Andris E, Šebestík J, Li ASM, Brown PJ, Schmitz U, Saikatendu K, Chang E, Nencka R, Vedadi M, Satchell KJF

ACS Infect Dis. doi: 10.1021/acsinfecdis.3c00203

Publication date: September 20, 2023

PMID: 37728236

RNF8 ubiquitylation of XRN2 facilitates R-loop resolution and restrains genomic instability in BRCA1 mutant cells.

Krishnan R, Lapierre M, Gautreau B, Nixon KCJ, El Ghamrasni S, Patel PS, Hao J, Yerlici VT, Guturi KKN, St-Germain J, Mateo F, Saad A, Algouneh A, Earnshaw R, Shili D, Seitova A, Miller J, Khosraviani N, Penn A, Ho B, Sanchez O, Hande MP, Masson JY, Brown GW, Alaoui-Jamali M, Reynolds JJ, Arrowsmith C, Raught B, Pujana MA, Mekhail K, Stewart GS, Hakem A, Hakem R

Nucleic Acids Res. doi: 10.1093/nar/gkad733

Publication date: September 11, 2023

PMID: 37697435

Structure-Reactivity Studies of 2-Sulfonylpyrimidines Allow Selective Protein Arylation.

Pichon MM, Drelinkiewicz D, Lozano D, Moraru R, Hayward LJ, Jones M, McCoy MA, Allstrum-Graves S, Balourdas DI, Joerger AC, Whitby RJ, Goldup SM, Wells N, Langley GJ, Herniman JM, Baud MGJ

Bioconjug Chem. doi: 10.1021/acs.bioconjchem.3c00322

Publication date: September 1, 2023

PMID: 37657082

The RavA-ViaA chaperone complex modulates bacterial persistence through its association with the fumarate reductase enzyme.

Bhandari V, Reichheld SE, Houliston S, Lemak A, Arrowsmith CH, Sharpe S, Houry WA

J Biol Chem. 105199. doi: 10.1016/j.jbc.2023.105199

Publication date: September 1, 2023

PMID: 37660904

How many kinases are druggable? A review of our current understanding.

Anderson B, Rosston P, Ong HW, Hossain MA, Davis-Gilbert ZW, Drewry DH

Biochem J. 480(16):1331-1363. doi: 10.1042/BCJ20220217

Publication date: August 30, 2023

PMID: 37642371

Investigation of the Host Kinome Response to Coronavirus Infection Reveals PI3K/mTOR Inhibitors as Betacoronavirus Antivirals.

Fritch EJ, Mordant AL, Gilbert TSK, Wells CI, Yang X, Barker NK, Madden EA, Dinnon KH, Hou YJ, Tse LV, Castillo IN, Sims AC, Moorman NJ, Lakshmanane P, Willson TM, Herring LE, Graves LM, Baric RS

J Proteome Res. doi: 10.1021/acs.jproteome.3c00182

Publication date: August 27, 2023

PMID: 37634194

The chromatin and single-cell transcriptional landscapes of CD4 T cells in inflammatory bowel disease link risk loci with a proinflammatory Th17 cell population.

Medina TS, Murison A, Smith M, Kinker GS, Chakravarthy A, Vitiello GAF, Turpin W, Shen SY, Yau HL, Sarmento OF, Faubion W, Lupien M, Silverberg MS, Arrowsmith CH, De Carvalho DD

Front Immunol. 14:1161901. doi: 10.3389/fimmu.2023.1161901

Publication date: August 21, 2023

PMID: 37600767

SETD7 functions as a transcription repressor in prostate cancer via methylating FOXA1.

Wang Z, Petricca J, Liu M, Zhang S, Chen S, Li M, Besschetnova A, Patalano S, Venkataramani K, Siegfried KR, Macoska JA, Han D, Gao S, Vedadi M, Arrowsmith CH, He HH, Cai C

Proc Natl Acad Sci U S A. 120(33):e2220472120. doi: 10.1073/pnas.2220472120

Publication date: August 15, 2023

PMID: 37549269

Autoantibodies against the melanoma differentiation-associated protein 5 in patients with dermatomyositis target the helicase domains.

Van Gompel E, Demirdal D, Fernandes-Cerqueira C, Horuluoglu B, Galindo-Feria A, Wigren E, Gräslund S, De Langhe E, Benveniste O, Notarnicola A, Chemin K, Lundberg IE

Rheumatology (Oxford). doi: 10.1093/rheumatology/kead400

Publication date: August 12, 2023

PMID: 37572295

3D Spheroid Invasion Assay for High-Throughput Screening of Small-Molecule Libraries.

Karve K, Poon S, Prinos P, Ailles L

Methods Mol Biol. 2706:201-214. doi: 10.1007/978-1-0716-3397-7_15

Publication date: August 10, 2023

PMID: 37558951

Annotation of the Effect of Chemogenomic Compounds on Cell Health Using High-Content Microscopy in Live-Cell Mode.

Tjaden A, Knapp S, Müller S

Methods Mol Biol. 2706:59-73. doi: 10.1007/978-1-0716-3397-7_5

Publication date: August 10, 2023

PMID: 37558941

Characterization of Cellular Viability Using Label-Free Brightfield Live-Cell Imaging.

Elson L, Tjaden A, Knapp S, Müller S

Methods Mol Biol. 2706:75-88. doi: 10.1007/978-1-0716-3397-7_6

Publication date: August 10, 2023

PMID: 37558942

Developing a Kinase Chemogenomic Set: Facilitating Investigation into Kinase Biology by Linking Phenotypes to Targets.

Wells CI, Drewry DH

Methods Mol Biol. 2706:11-24. doi: 10.1007/978-1-0716-3397-7_2

Publication date: August 10, 2023

PMID: 37558938

Development of selective class I protein arginine methyltransferase inhibitors through fragment-based drug design approach.

Bhattacharya D, Shi Ming Li A, Paul B, Ghosh Dastidar U, Santhakumar V, Sarkar D, Chau I, Li F, Ghosh T, Vedadi M, Talukdar A

Eur J Med Chem. 260:115713. doi: 10.1016/j.ejmech.2023.115713

Publication date: August 10, 2023

PMID: 37597437

HiBiT Cellular Thermal Shift Assay (HiBiT CETSA).

Ramachandran S, Szewczyk M, Barghout SH, Ciulli A, Barsyte-Lovejoy D, Vu V

Methods Mol Biol. 2706:149-165. doi: 10.1007/978-1-0716-3397-7_11

Publication date: August 10, 2023

PMID: 37558947

Measuring Protein-Protein Interactions in Cells using Nanoluciferase Bioluminescence Resonance Energy Transfer (NanoBRET) Assay.

Szewczyk MM, Owens DDG, Barsyte-Lovejoy D

Methods Mol Biol. 2706:137-148. doi: 10.1007/978-1-0716-3397-7_10

Publication date: August 10, 2023

PMID: 37558946

Quality Control of Chemogenomic Library Using LC-MS.

Němec V, Knapp S

Methods Mol Biol. 2706:51-58. doi: 10.1007/978-1-0716-3397-7_4

Publication date: August 10, 2023

PMID: 37558940

SETDB1 Triple Tudor Domain Ligand, (R,R)-59, Promotes Methylation of Akt1 in Cells.

Uguen M, Deng Y, Li F, Shell DJ, Norris-Drouin JL, Stashko MA, Ackloo S, Arrowsmith CH, James LI, Liu P, Pearce KH, Frye SV

ACS Chem Biol. doi: 10.1021/acschembio.3c00280

Publication date: August 9, 2023

PMID: 37556795

The identification of high-performing antibodies for transmembrane protein 106B (TMEM106B) for use in Western blot, immunoprecipitation, and immunofluorescence.

Ayoubi R, Fotouhi M, Southern K, Bhajiawala R, Fanti R, Prinos P, McPherson PS, Laflamme C

F1000Res. 12:308. doi: 10.12688/f1000research.131333.1

Publication date: August 7, 2023

PMID: 37545650

Discovery and Characterization of a Chemical Probe Targeting the Zinc-Finger Ubiquitin-Binding Domain of HDAC6.

Harding RJ, Franzoni I, Mann MK, Szewczyk MM, Mirabi B, Ferreira de Freitas R, Owens DDG, Ackloo S, Scheremetjew A, Juarez-Ornelas KA, Sanichar R, Baker RJ, Dank C, Brown PJ, Barsyte-Lovejoy D, Santhakumar V, Schapira M, Lautens M, Arrowsmith CH

J Med Chem. doi: 10.1021/acs.jmedchem.3c00314

Publication date: July 27, 2023

PMID: 37499118

Reaction hijacking inhibition of Plasmodium falciparum asparagine tRNA synthetase.

Tilley L, Xie S, Wang Y, Morton C, Metcalfe R, Dogovski C, Pasaje CF, Dunn E, Luth M, Kumpornsin K, Istvan E, Park J, Fairhurst K, Yeo T, Yildirim O, Bhebhe M, Klug D, Rutledge P, Godoy L, Dey S, De Souza M, Siqueira-Neto J, Ketprasit N, Du Y, Amini M, Shami G, Nie S, Williamson N, Jana G, Maity B, Thomson P, Foley T, Loesbanluechai D, Puhalovich T, Tan D, Niles J, Han BW, Goldberg D, Burrows J, Fidock D, Lee M, Winzeler E, Griffin M, Todd M

Res Sq. doi: 10.21203/rs.3.rs-3198291/v1

Publication date: July 27, 2023

PMID: 37546892

The Canadian Open Neuroscience Platform-An open science framework for the neuroscience community.

Harding RJ, Bermudez P, Bernier A, Beauvais M, Bellec P, Hill S, Karakuzu A, Knoppers BM, Pavlidis P, Poline JB, Roskams J, Stikov N, Stone J, Strother S, Evans AC

PLoS Comput Biol. 19(7):e1011230. doi: 10.1371/journal.pcbi.1011230

Publication date: July 27, 2023

PMID: 37498959

5-Iodotubercidin sensitizes cells to RIPK1-dependent necroptosis by interfering with NFκB signaling.

Chauhan C, Kraemer A, Knapp S, Windheim M, Kotlyarov A, Menon MB, Gaestel M

Cell Death Discov. 9(1):262. doi: 10.1038/s41420-023-01576-x

Publication date: July 26, 2023

PMID: 37495567

Discovery and characterization of a specific inhibitor of serine-threonine kinase cyclin dependent kinase-like 5 (CDKL5) demonstrates role in hippocampal CA1 physiology.

Castano A, Silvestre M, Wells CI, Sanderson JL, Ferrer CA, Ong HW, Lang Y, Richardson W, Silvaroli JA, Bashore FM, Smith JL, Genereux IM, Dempster K, Drewry DH, Pabla NS, Bullock AN, Benke TA, Ultanir S, Axtman AD

Elife. 12:. doi: 10.7554/eLife.88206

Publication date: July 25, 2023

PMID: 37490324

Leucettinibs, a Class of DYRK/CLK Kinase Inhibitors Inspired by the Marine Sponge Natural Product Leucettamine B.

Deau E, Lindberg MF, Miege F, Roche D, George N, George P, Krämer A, Knapp S, Meijer L

J Med Chem. doi: 10.1021/acs.jmedchem.3c00884

Publication date: July 24, 2023

PMID: 37487467

Targeting the Alternative Vitamin E Metabolite Binding Site Enables Noncanonical PPARγ Modulation.

Arifi S, Marschner JA, Pollinger J, Isigkeit L, Heitel P, Kaiser A, Obeser L, Höfner G, Proschak E, Knapp S, Chaikuad A, Heering J, Merk D

J Am Chem Soc. doi: 10.1021/jacs.3c03417

Publication date: June 29, 2023

PMID: 37385602

CaMKK2 is not involved in contraction-stimulated AMPK activation and glucose uptake in skeletal muscle.

Negoita F, Addinsall AB, Hellberg K, Bringas CF, Hafen PS, Sermersheim TJ, Agerholm M, Lewis CTA, Ahwazi D, Ling NXY, Larsen JK, Deshmukh AS, Hossain MA, Oakhill JS, Ochala J, Brault JJ, Sankar U, Drewry DH, Scott JW, Witczak CA, Sakamoto K

Mol Metab. 101761. doi: 10.1016/j.molmet.2023.101761

Publication date: June 26, 2023

PMID: 37380024

Discovery of a Novel DCAF1 Ligand Using a Drug-Target Interaction Prediction Model: Generalizing Machine Learning to New Drug Targets.

Kimani SW, Owen J, Green SR, Li F, Li Y, Dong A, Brown PJ, Ackloo S, Kuter D, Yang C, MacAskill M, MacKinnon SS, Arrowsmith CH, Schapira M, Shahani V, Halabelian L

J Chem Inf Model. doi: 10.1021/acs.jcim.3c00082

Publication date: June 23, 2023

PMID: 37350740

Target 2035 - an update on private sector contributions.

Ackloo S, Antolin AA, Bartolome JM, Beck H, Bullock A, Betz UAK, Böttcher J, Brown PJ, Chaturvedi M, Crisp A, Daniels D, Dreher J, Edfeldt K, Edwards AM, Egner U, Elkins J, Fischer C, Glendorf T, Goldberg S, Hartung IV, Hillisch A, Homan E, Knapp S, Köster M, Krämer O, Llaveria J, Lessel U, Lindemann S, Linderoth L, Matsui H, Michel M, Montel F, Mueller-Fahrnow A, Müller S, Owen DR, Saikatendu KS, Santhakumar V, Sanderson W, Scholten C, Schapira M, Sharma S, Shireman B, Sundström M, Todd MH, Tredup C, Venable J, Willson TM, Arrowsmith CH

RSC Med Chem. 14(6):1002-1011. doi: 10.1039/d2md00441k

Publication date: June 22, 2023

PMID: 37360399

Delineation of functional subdomains of Huntingtin protein and their interaction with HAP40.

Alteen MG, Deme JC, Alvarez CP, Loppnau P, Hutchinson A, Seitova A, Chandrasekaran R, Silva Ramos E, Secker C, Alqazzaz M, Wanker EE, Lea SM, Arrowsmith CH, Harding RJ

Structure. doi: 10.1016/j.str.2023.06.002

Publication date: June 20, 2023

PMID: 37390814

Tracking the PROTAC degradation pathway in living cells highlights the importance of ternary complex measurement for PROTAC optimization.

Schwalm MP, Krämer A, Dölle A, Weckesser J, Yu X, Jin J, Saxena K, Knapp S

Cell Chem Biol. doi: 10.1016/j.chembiol.2023.06.002

Publication date: June 20, 2023

PMID: 37354907

Structure-Based Discovery of Inhibitors of the SARS-CoV-2 Nsp14 N7-Methyltransferase.

Singh I, Li F, Fink EA, Chau I, Li A, Rodriguez-Hernández A, Glenn I, Zapatero-Belinchón FJ, Rodriguez ML, Devkota K, Deng Z, White K, Wan X, Tolmachova NA, Moroz YS, Kaniskan HÜ, Ott M, García-Sastre A, Jin J, Fujimori DG, Irwin JJ, Vedadi M, Shoichet BK

J Med Chem. doi: 10.1021/acs.jmedchem.2c02120

Publication date: June 9, 2023

PMID: 37294077

Design and Synthesis of Pyrazole-Based Macrocyclic Kinase Inhibitors Targeting BMPR2.

Amrhein JA, Wang G, Berger BT, Berger LM, Kalampaliki AD, Krämer A, Knapp S, Hanke T

ACS Med Chem Lett. 14(6):833-840. doi: 10.1021/acsmedchemlett.3c00127

Publication date: June 8, 2023

PMID: 37312836

Structural insights into a regulatory mechanism of FIR RRM1-FUSE interaction.

Ni X, Joerger AC, Chaikuad A, Knapp S

Open Biol. 13(5):230031. doi: 10.1098/rsob.230031

Publication date: May 31, 2023

PMID: 37253421

Mutation in the Common Docking Domain Affects MAP Kinase ERK2 Catalysis and Stability.

Novak L, Petrosino M, Pasquo A, Chaikuad A, Chiaraluce R, Knapp S, Consalvi V

Cancers (Basel). 15(11):. doi: 10.3390/cancers15112938

Publication date: May 26, 2023

PMID: 37296900

Identification of inhibitors for the trans-membrane Trypanosoma cruzi eIF2α kinase relevant for parasite proliferation.

Marcelino TP, Fala AM, da Silva MM, Souza-Melo N, Malvezzi AM, Klippel AH, Zoltner M, Padilla-Mejia N, Kosto S, Field MC, Burle Caldas GA, Teixeira SMR, Couñago RM, Massirer KB, Schenkman S

J Biol Chem. 104857. doi: 10.1016/j.jbc.2023.104857

Publication date: May 23, 2023

PMID: 37230387

Open drug discovery in Alzheimer's disease.

Axtman AD, Brennan PE, Frappier-Brinton T, Betarbet R, Carter GW, Fu H, Gileadi O, Greenwood AK, Leal K, Longo FM, Mangravite LM, Edwards AM, Levey AI

Alzheimers Dement (N Y). 9(2):e12394. doi: 10.1002/trc2.12394

Publication date: May 22, 2023

PMID: 37215505

Structure-Based Development of Isoform-Selective Inhibitors of Casein Kinase 1ε vs Casein Kinase 1δ.

Choi JY, Noguchi Y, Alburger JM, Bayle S, Chung E, Grant W, Chaikuad A, Knapp S, Duckett DR, Roush WR

J Med Chem. doi: 10.1021/acs.jmedchem.2c01180

Publication date: May 19, 2023

PMID: 37204207

Targeting the Divergent Roles of STK3 Inhibits Breast Cancer Cell Growth and Opposes Doxorubicin-Induced Cardiotoxicity In Vitro.

Nam J, Schirmer AU, Loh C, Drewry DH, Macias E

Cancers (Basel). 15(10):. doi: 10.3390/cancers15102817

Publication date: May 18, 2023

PMID: 37345153

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