Publications

You can search the extensive SGC publications list with keywords from the title, authors or journal name. Your search results can be exported to an Excel file by clicking the orange XLS button next to the search filters

2022

Generative and reinforcement learning approaches for the automated de novo design of bioactive compounds.

Korshunova M, Huang N, Capuzzi S, Radchenko DS, Savych O, Moroz YS, Wells CI, Willson TM, Tropsha A, Isayev O

Commun Chem. 5(1):129. doi: 10.1038/s42004-022-00733-0

Publication date: October 18, 2022

PMID: 36697952

PBRM1, SETD2 and BAP1 - the trinity of 3p in clear cell renal cell carcinoma.

Walton J, Lawson K, Prinos P, Finelli A, Arrowsmith C, Ailles L

Nat Rev Urol. doi: 10.1038/s41585-022-00659-1

Publication date: October 17, 2022

PMID: 36253570

Dissecting the stability determinants of a challenging de novo protein fold using massively parallel design and experimentation.

Kim TE, Tsuboyama K, Houliston S, Martell CM, Phoumyvong CM, Lemak A, Haddox HK, Arrowsmith CH, Rocklin GJ

Proc Natl Acad Sci U S A. 119(41):e2122676119. doi: 10.1073/pnas.2122676119

Publication date: October 11, 2022

PMID: 36191185

A Screening of Epigenetic Therapeutic Targets for Non-Small Cell Lung Cancer Reveals PADI4 and KDM6B as Promising Candidates.

Lesbon JCC, Garnica TK, Xavier PLP, Rochetti AL, Reis RM, Müller S, Fukumasu H

Int J Mol Sci. 23(19):. doi: 10.3390/ijms231911911

Publication date: October 7, 2022

PMID: 36233212

De novo design of immunoglobulin-like domains.

Chidyausiku TM, Mendes SR, Klima JC, Nadal M, Eckhard U, Roel-Touris J, Houliston S, Guevara T, Haddox HK, Moyer A, Arrowsmith CH, Gomis-Rüth FX, Baker D, Marcos E

Nat Commun. 13(1):5661. doi: 10.1038/s41467-022-33004-6

Publication date: October 3, 2022

PMID: 36192397

Covalent Modification of Bromodomain Proteins by Peptides Containing a DNA Damage-Induced, Histone Post-Translational Modification.

Jacinto MP, Heidenreich D, Müller S, Greenberg MM

Chembiochem. e202200373. doi: 10.1002/cbic.202200373

Publication date: September 29, 2022

PMID: 36173930

ChemBioPort: an online portal to navigate the structure, function and chemical inhibition of the human proteome.

Liu L, Rovers E, Schapira M

Database (Oxford). 2022:. doi: 10.1093/database/baac088

Publication date: September 27, 2022

PMID: 36164975

Identification of Novel 2,4,5-Trisubstituted Pyrimidines as Potent Dual Inhibitors of Plasmodial PfGSK3/PfPK6 with Activity against Blood Stage Parasites In Vitro.

Galal KA, Truong A, Kwarcinski F, de Silva C, Avalani K, Havener TM, Chirgwin ME, Merten E, Ong HW, Willis C, Abdelwaly A, Helal MA, Derbyshire ER, Zutshi R, Drewry DH

J Med Chem. doi: 10.1021/acs.jmedchem.2c00996

Publication date: September 27, 2022

PMID: 36166733

Development and Characterization of Type I, Type II, and Type III LIM-Kinase Chemical Probes.

Hanke T, Mathea S, Woortman J, Salah E, Berger BT, Tumber A, Kashima R, Hata A, Kuster B, Müller S, Knapp S

J Med Chem. doi: 10.1021/acs.jmedchem.2c01106

Publication date: September 22, 2022

PMID: 36136092

Fragment-based discovery of orphan nuclear receptor Nur77/NGFI-B ligands.

Arifi S, Zaienne D, Heering J, Wein T, Zhubi R, Chaikuad A, Knapp S, Marschner JA, Merk D

Bioorg Chem. 129:106164. doi: 10.1016/j.bioorg.2022.106164

Publication date: September 17, 2022

PMID: 36162288

A small molecule antagonist of SMN disrupts the interaction between SMN and RNAP II.

Liu Y, Iqbal A, Li W, Ni Z, Wang Y, Ramprasad J, Abraham KJ, Zhang M, Zhao DY, Qin S, Loppnau P, Jiang H, Guo X, Brown PJ, Zhen X, Xu G, Mekhail K, Ji X, Bedford MT, Greenblatt JF, Min J

Nat Commun. 13(1):5453. doi: 10.1038/s41467-022-33229-5

Publication date: September 16, 2022

PMID: 36114190

Identification and Utilization of a Chemical Probe to Interrogate the Roles of PIKfyve in the Lifecycle of β-Coronaviruses.

Drewry DH, Potjewyd FM, Bayati A, Smith JL, Dickmander RJ, Howell S, Taft-Benz S, Min SM, Hossain MA, Heise M, McPherson PS, Moorman NJ, Axtman AD

J Med Chem. doi: 10.1021/acs.jmedchem.2c00697

Publication date: September 16, 2022

PMID: 36111834

CDK11 regulates pre-mRNA splicing by phosphorylation of SF3B1.

Hluchý M, Gajdušková P, Ruiz de Los Mozos I, Rájecký M, Kluge M, Berger BT, Slabá Z, Potěšil D, Weiß E, Ule J, Zdráhal Z, Knapp S, Paruch K, Friedel CC, Blazek D

Nature. doi: 10.1038/s41586-022-05204-z

Publication date: September 14, 2022

PMID: 36104565

Identification of Histone Peptide Binding Specificity and Small-Molecule Ligands for the TRIM33α and TRIM33β Bromodomains.

Sekirnik AR, Reynolds JK, See L, Bluck JP, Scorah AR, Tallant C, Lee B, Leszczynska KB, Grimley RL, Storer RI, Malattia M, Crespillo S, Caria S, Duclos S, Hammond EM, Knapp S, Morris GM, Duarte F, Biggin PC, Conway SJ

ACS Chem Biol. doi: 10.1021/acschembio.2c00266

Publication date: September 13, 2022

PMID: 36098557

Combinatorial Anticancer Drug Screen Identifies Off-Target Effects of Epigenetic Chemical Probes.

Barghout SH, Mann MK, Aman A, Yu Y, Alteen MG, Schimmer AD, Schapira M, Arrowsmith CH, Barsyte-Lovejoy D

ACS Chem Biol. doi: 10.1021/acschembio.2c00451

Publication date: September 9, 2022

PMID: 36084291

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

Displaying 201 - 250 of 1744
Download XLS