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For: Arkin MR, Randal M, DeLano WL, Hyde J, Luong TN, Oslob JD, Raphael DR, Taylor L, Wang J, McDowell RS, Wells JA, Braisted AC. Binding of small molecules to an adaptive protein-protein interface. Proc Natl Acad Sci U S A 2003;100:1603-8. [PMID: 12582206 PMCID: PMC149879 DOI: 10.1073/pnas.252756299] [Citation(s) in RCA: 280] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/10/2002] [Indexed: 11/18/2022]  Open
Number Cited by Other Article(s)
1
Tong B, Leong SG, Jian T, Niu G, Gai Y, Meng X, Lv H, Dong X, Ding X, Chen J. Site-specific pegylated IL2 mutein with biased IL2 receptor binding for cancer immunotherapy. Int Immunopharmacol 2024;136:112359. [PMID: 38815348 DOI: 10.1016/j.intimp.2024.112359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 05/06/2024] [Accepted: 05/24/2024] [Indexed: 06/01/2024]
2
Deal PE, Lee H, Mondal A, Lolicato M, Mendonça PRFD, Black H, Jang S, El-Hilali X, Bryant C, Isacoff EY, Renslo AR, Minor DL. Development of covalent chemogenetic K2P channel activators. Cell Chem Biol 2024;31:1305-1323.e9. [PMID: 39029456 DOI: 10.1016/j.chembiol.2024.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 04/19/2024] [Accepted: 06/19/2024] [Indexed: 07/21/2024]
3
Takahashi M, Chong HB, Zhang S, Yang TY, Lazarov MJ, Harry S, Maynard M, Hilbert B, White RD, Murrey HE, Tsou CC, Vordermark K, Assaad J, Gohar M, Dürr BR, Richter M, Patel H, Kryukov G, Brooijmans N, Alghali ASO, Rubio K, Villanueva A, Zhang J, Ge M, Makram F, Griesshaber H, Harrison D, Koglin AS, Ojeda S, Karakyriakou B, Healy A, Popoola G, Rachmin I, Khandelwal N, Neil JR, Tien PC, Chen N, Hosp T, van den Ouweland S, Hara T, Bussema L, Dong R, Shi L, Rasmussen MQ, Domingues AC, Lawless A, Fang J, Yoda S, Nguyen LP, Reeves SM, Wakefield FN, Acker A, Clark SE, Dubash T, Kastanos J, Oh E, Fisher DE, Maheswaran S, Haber DA, Boland GM, Sade-Feldman M, Jenkins RW, Hata AN, Bardeesy NM, Suvà ML, Martin BR, Liau BB, Ott CJ, Rivera MN, Lawrence MS, Bar-Peled L. DrugMap: A quantitative pan-cancer analysis of cysteine ligandability. Cell 2024;187:2536-2556.e30. [PMID: 38653237 PMCID: PMC11143475 DOI: 10.1016/j.cell.2024.03.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 01/15/2024] [Accepted: 03/19/2024] [Indexed: 04/25/2024]
4
Song L, Xu J, Shi Y, Zhao H, Zhang M, Wang Y, Cui Y, Chai X. An integrated strategy of UPLC-Q-TOF-MS analysis, network pharmacology, and molecular docking to explore the chemical constituents and mechanism of Zixue Powder against febrile seizures. Heliyon 2024;10:e23865. [PMID: 38192830 PMCID: PMC10772254 DOI: 10.1016/j.heliyon.2023.e23865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 12/14/2023] [Accepted: 12/14/2023] [Indexed: 01/10/2024]  Open
5
Takahashi M, Chong HB, Zhang S, Lazarov MJ, Harry S, Maynard M, White R, Murrey HE, Hilbert B, Neil JR, Gohar M, Ge M, Zhang J, Durr BR, Kryukov G, Tsou CC, Brooijmans N, Alghali ASO, Rubio K, Vilanueva A, Harrison D, Koglin AS, Ojeda S, Karakyriakou B, Healy A, Assaad J, Makram F, Rachman I, Khandelwal N, Tien PC, Popoola G, Chen N, Vordermark K, Richter M, Patel H, Yang TY, Griesshaber H, Hosp T, van den Ouweland S, Hara T, Bussema L, Dong R, Shi L, Rasmussen MQ, Domingues AC, Lawless A, Fang J, Yoda S, Nguyen LP, Reeves SM, Wakefield FN, Acker A, Clark SE, Dubash T, Fisher DE, Maheswaran S, Haber DA, Boland G, Sade-Feldman M, Jenkins R, Hata A, Bardeesy N, Suva ML, Martin B, Liau B, Ott C, Rivera MN, Lawrence MS, Bar-Peled L. DrugMap: A quantitative pan-cancer analysis of cysteine ligandability. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.20.563287. [PMID: 37961514 PMCID: PMC10634688 DOI: 10.1101/2023.10.20.563287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
6
Deal PE, Lee H, Mondal A, Lolicato M, de Mendonca PRF, Black H, El-Hilali X, Bryant C, Isacoff EY, Renslo AR, Minor DL. Development of covalent chemogenetic K2P channel activators. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.15.561774. [PMID: 37905049 PMCID: PMC10614804 DOI: 10.1101/2023.10.15.561774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
7
Mushtaq M, Usmani S, Jabeen A, Nur-E-Alam M, Ahmed S, Ahmad A, Ul-Haq Z. Identification of potent anti-immunogenic agents through virtual screening, 3D-QSAR studies, and in vitro experiments. Mol Divers 2023:10.1007/s11030-023-10709-4. [PMID: 37550601 DOI: 10.1007/s11030-023-10709-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 07/30/2023] [Indexed: 08/09/2023]
8
Walker K, Baravalle R, Holyfield R, Kalms J, Wright H, Seewooruthun C, Muskett FW, Scott-Tucker A, Merritt A, Henry A, Lawson ADG, Hall G, Prosser C, Carr MD. Identification and characterisation of anti-IL-13 inhibitory single domain antibodies provides new insights into receptor selectivity and attractive opportunities for drug discovery. Front Immunol 2023;14:1216967. [PMID: 37483614 PMCID: PMC10359924 DOI: 10.3389/fimmu.2023.1216967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 06/19/2023] [Indexed: 07/25/2023]  Open
9
Peña-Guerrero J, Fernández-Rubio C, García-Sosa AT, Nguewa PA. BRCT Domains: Structure, Functions, and Implications in Disease-New Therapeutic Targets for Innovative Drug Discovery against Infections. Pharmaceutics 2023;15:1839. [PMID: 37514027 PMCID: PMC10386641 DOI: 10.3390/pharmaceutics15071839] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/12/2023] [Accepted: 06/22/2023] [Indexed: 07/30/2023]  Open
10
Yu W, Weber DJ, MacKerell AD. Integrated Covalent Drug Design Workflow Using Site Identification by Ligand Competitive Saturation. J Chem Theory Comput 2023;19:3007-3021. [PMID: 37115781 PMCID: PMC10205696 DOI: 10.1021/acs.jctc.3c00232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
11
Thompson AA, Harbut MB, Kung PP, Karpowich NK, Branson JD, Grant JC, Hagan D, Pascual HA, Bai G, Zavareh RB, Coate HR, Collins BC, Côte M, Gelin CF, Damm-Ganamet KL, Gholami H, Huff AR, Limon L, Lumb KJ, Mak PA, Nakafuku KM, Price EV, Shih AY, Tootoonchi M, Vellore NA, Wang J, Wei N, Ziff J, Berger SB, Edwards JP, Gardet A, Sun S, Towne JE, Venable JD, Shi Z, Venkatesan H, Rives ML, Sharma S, Shireman BT, Allen SJ. Identification of small-molecule protein-protein interaction inhibitors for NKG2D. Proc Natl Acad Sci U S A 2023;120:e2216342120. [PMID: 37098070 PMCID: PMC10160951 DOI: 10.1073/pnas.2216342120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Accepted: 03/10/2023] [Indexed: 04/26/2023]  Open
12
Rehman AU, Khurshid B, Ali Y, Rasheed S, Wadood A, Ng HL, Chen HF, Wei Z, Luo R, Zhang J. Computational approaches for the design of modulators targeting protein-protein interactions. Expert Opin Drug Discov 2023;18:315-333. [PMID: 36715303 PMCID: PMC10149343 DOI: 10.1080/17460441.2023.2171396] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 01/18/2023] [Indexed: 01/31/2023]
13
Zhou AL, Jensen DR, Peterson FC, Thomas MA, Schlimgen RR, Dwinell MB, Smith BC, Volkman BF. Fragment-based drug discovery of small molecule ligands for the human chemokine CCL28. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2023:S2472-5552(23)00019-9. [PMID: 36841432 DOI: 10.1016/j.slasd.2023.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 02/17/2023] [Accepted: 02/21/2023] [Indexed: 02/25/2023]
14
Shin WH, Kumazawa K, Imai K, Hirokawa T, Kihara D. Quantitative comparison of protein-protein interaction interface using physicochemical feature-based descriptors of surface patches. Front Mol Biosci 2023;10:1110567. [PMID: 36814641 PMCID: PMC9939524 DOI: 10.3389/fmolb.2023.1110567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 01/24/2023] [Indexed: 02/09/2023]  Open
15
Bum-Erdene K, Yeh IJ, Gonzalez-Gutierrez G, Ghozayel MK, Pollok K, Meroueh SO. Small-Molecule Cyanamide Pan-TEAD·YAP1 Covalent Antagonists. J Med Chem 2023;66:266-284. [PMID: 36562717 DOI: 10.1021/acs.jmedchem.2c01189] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
16
Lerma Romero JA, Kolmar H. Accessing Transient Binding Pockets by Protein Engineering and Yeast Surface Display Screening. Methods Mol Biol 2023;2681:249-274. [PMID: 37405652 DOI: 10.1007/978-1-0716-3279-6_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2023]
17
Ozdemir ES, Nussinov R. Pathogen-driven cancers from a structural perspective: Targeting host-pathogen protein-protein interactions. Front Oncol 2023;13:1061595. [PMID: 36910650 PMCID: PMC9997845 DOI: 10.3389/fonc.2023.1061595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 02/06/2023] [Indexed: 02/25/2023]  Open
18
Li X, Guo Y, Li J, Yu Z, Cheng J, Ren F, Jia H, Zhang Y, Cui S, Zhang T, Shi W. Discovery and Structural Explorations of G-Protein Biased μ-Opioid Receptor Agonists. ChemMedChem 2022;17:e202200416. [PMID: 36210341 DOI: 10.1002/cmdc.202200416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 10/04/2022] [Indexed: 01/14/2023]
19
Boike L, Henning NJ, Nomura DK. Advances in covalent drug discovery. Nat Rev Drug Discov 2022;21:881-898. [PMID: 36008483 PMCID: PMC9403961 DOI: 10.1038/s41573-022-00542-z] [Citation(s) in RCA: 214] [Impact Index Per Article: 107.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/26/2022] [Indexed: 01/04/2023]
20
IL-2 Flexible Loops Might Play a Role in IL-2 Interaction with the High-Affinity IL-2 Receptor: A Molecular Dynamics (MD) Study. J CHEM-NY 2022. [DOI: 10.1155/2022/3646375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]  Open
21
Sarma H, Sastry GN. A Computational Study on the Interaction of NSP10 and NSP14: Unraveling the RNA Synthesis Proofreading Mechanism in SARS-CoV-2, SARS-CoV, and MERS-CoV. ACS OMEGA 2022;7:30003-30022. [PMID: 36035077 PMCID: PMC9397572 DOI: 10.1021/acsomega.2c03007] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 08/03/2022] [Indexed: 06/15/2023]
22
Therapeutic Mechanism and Key Active Ingredients of Shenfu Injection in Sepsis: A Network Pharmacology and Molecular Docking Approach. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022;2022:9686149. [PMID: 36062176 PMCID: PMC9439916 DOI: 10.1155/2022/9686149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 07/12/2022] [Accepted: 07/15/2022] [Indexed: 11/17/2022]
23
Human endogenous retrovirus-K (HERV-K) reverse transcriptase (RT) structure and biochemistry reveals remarkable similarities to HIV-1 RT and opportunities for HERV-K-specific inhibition. Proc Natl Acad Sci U S A 2022;119:e2200260119. [PMID: 35771941 PMCID: PMC9271190 DOI: 10.1073/pnas.2200260119] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
24
Sarma H, Jamir E, Sastry GN. Protein-protein interaction of RdRp with its co-factor NSP8 and NSP7 to decipher the interface hotspot residues for drug targeting: A comparison between SARS-CoV-2 and SARS-CoV. J Mol Struct 2022;1257:132602. [PMID: 35153334 PMCID: PMC8824464 DOI: 10.1016/j.molstruc.2022.132602] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 02/03/2022] [Accepted: 02/07/2022] [Indexed: 02/09/2023]
25
Structure-based assessment and druggability classification of protein-protein interaction sites. Sci Rep 2022;12:7975. [PMID: 35562538 PMCID: PMC9106675 DOI: 10.1038/s41598-022-12105-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 04/20/2022] [Indexed: 11/08/2022]  Open
26
Einsiedel J, Schmidt MF, Hübner H, Gmeiner P. Development of disulfide-functionalized peptides covalently binding G protein-coupled receptors. Bioorg Med Chem 2022;61:116720. [PMID: 35334449 DOI: 10.1016/j.bmc.2022.116720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/15/2022] [Accepted: 03/17/2022] [Indexed: 11/29/2022]
27
Rehman AU, Lu S, Khan AA, Khurshid B, Rasheed S, Wadood A, Zhang J. Hidden allosteric sites and De-Novo drug design. Expert Opin Drug Discov 2021;17:283-295. [PMID: 34933653 DOI: 10.1080/17460441.2022.2017876] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
28
Gironda-Martínez A, Gorre ÉMD, Prati L, Gosalbes JF, Dakhel S, Cazzamalli S, Samain F, Donckele EJ, Neri D. Identification and Validation of New Interleukin-2 Ligands Using DNA-Encoded Libraries. J Med Chem 2021;64:17496-17510. [PMID: 34821503 DOI: 10.1021/acs.jmedchem.1c01693] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
29
Sannigrahi A, Chattopadhyay K. Pore formation by pore forming membrane proteins towards infections. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2021;128:79-111. [PMID: 35034727 DOI: 10.1016/bs.apcsb.2021.09.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
30
Kamalinia G, Grindel BJ, Takahashi TT, Millward SW, Roberts RW. Directing evolution of novel ligands by mRNA display. Chem Soc Rev 2021;50:9055-9103. [PMID: 34165126 PMCID: PMC8725378 DOI: 10.1039/d1cs00160d] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
31
Small organic molecules accelerate the expansion of regulatory T cells. Bioorg Chem 2021;111:104908. [PMID: 33895604 DOI: 10.1016/j.bioorg.2021.104908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 04/04/2021] [Accepted: 04/07/2021] [Indexed: 11/21/2022]
32
Kim J, Lee JY, Park SY, Lee YJ, Kim MS. Crystal structure of human interleukin-2 in complex with TCB2, a new antibody-drug candidate with antitumor activity. Oncoimmunology 2021;10:1899671. [PMID: 33796411 PMCID: PMC7971329 DOI: 10.1080/2162402x.2021.1899671] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 02/24/2021] [Indexed: 10/31/2022]  Open
33
In silico data mining of large-scale databases for the virtual screening of human interleukin-2 inhibitors. ACTA PHARMACEUTICA (ZAGREB, CROATIA) 2021;71:33-56. [PMID: 32697741 DOI: 10.2478/acph-2021-0002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/08/2020] [Indexed: 01/19/2023]
34
Bansia H, Mahanta P, Yennawar NH, Ramakumar S. Small Glycols Discover Cryptic Pockets on Proteins for Fragment-Based Approaches. J Chem Inf Model 2021;61:1322-1333. [PMID: 33570386 DOI: 10.1021/acs.jcim.0c01126] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
35
Lu W, Kostic M, Zhang T, Che J, Patricelli MP, Jones LH, Chouchani ET, Gray NS. Fragment-based covalent ligand discovery. RSC Chem Biol 2021;2:354-367. [PMID: 34458789 PMCID: PMC8341086 DOI: 10.1039/d0cb00222d] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 02/22/2021] [Accepted: 01/20/2021] [Indexed: 12/15/2022]  Open
36
Dehbashi M, Hojati Z, Motovali-Bashi M, Ganjalikhani-Hakemi M, Shimosaka A, Cho WC. Computational study for suppression of CD25/IL-2 interaction. Biol Chem 2021;402:167-178. [PMID: 33544473 DOI: 10.1515/hsz-2020-0326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 10/22/2020] [Indexed: 02/05/2023]
37
In Silico Identification of Potential Druggable Binding Sites on CIN85 SH3 Domain. Int J Mol Sci 2021;22:ijms22020534. [PMID: 33430321 PMCID: PMC7825788 DOI: 10.3390/ijms22020534] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 01/03/2021] [Accepted: 01/04/2021] [Indexed: 02/01/2023]  Open
38
Simien JM, Haglund E. Topological Twists in Nature. Trends Biochem Sci 2021;46:461-471. [PMID: 33419636 DOI: 10.1016/j.tibs.2020.12.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 11/24/2020] [Accepted: 12/03/2020] [Indexed: 11/25/2022]
39
Gerak CAN, Cho SY, Kolesnikov M, Okon M, Murphy MEP, Sessions RB, Roberge M, McIntosh LP. Biophysical characterization of the ETV6 PNT domain polymerization interfaces. J Biol Chem 2021;296:100284. [PMID: 33450226 PMCID: PMC7949025 DOI: 10.1016/j.jbc.2021.100284] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 12/22/2020] [Accepted: 01/11/2021] [Indexed: 11/21/2022]  Open
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Karakus U, Sahin D, Mittl PRE, Mooij P, Koopman G, Boyman O. Receptor-gated IL-2 delivery by an anti-human IL-2 antibody activates regulatory T cells in three different species. Sci Transl Med 2020;12:12/574/eabb9283. [DOI: 10.1126/scitranslmed.abb9283] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 09/25/2020] [Indexed: 12/11/2022]
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Mukhatayev Z, Dellacecca ER, Cosgrove C, Shivde R, Jaishankar D, Pontarolo-Maag K, Eby JM, Henning SW, Ostapchuk YO, Cedercreutz K, Issanov A, Mehrotra S, Overbeck A, Junghans RP, Leventhal JR, Le Poole IC. Antigen Specificity Enhances Disease Control by Tregs in Vitiligo. Front Immunol 2020;11:581433. [PMID: 33335528 PMCID: PMC7736409 DOI: 10.3389/fimmu.2020.581433] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 10/27/2020] [Indexed: 12/19/2022]  Open
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Khalil R, Usmani S, Nur-E-Alam M, Ahmed S, Ul-Haq Z. Site-directed Fragnomics and MD Simulations Approaches to Identify Interleukin-2 Inhibitors. Med Chem 2020;17:407-417. [PMID: 33191887 DOI: 10.2174/1573406416999201113104501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 09/28/2020] [Accepted: 10/05/2020] [Indexed: 11/22/2022]
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Mitoma S, El-Khaiat HM, Uto T, Sato K, Sekiguchi S, Norimine J. Characterization of bovine interleukin-2 stably expressed in HEK-293 cells. J Vet Med Sci 2020;83:134-141. [PMID: 33177289 PMCID: PMC7870392 DOI: 10.1292/jvms.20-0423] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]  Open
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Iida S, Nakamura HK, Mashimo T, Fukunishi Y. Structural Fluctuations of Aromatic Residues in an Apo-Form Reveal Cryptic Binding Sites: Implications for Fragment-Based Drug Design. J Phys Chem B 2020;124:9977-9986. [PMID: 33140952 DOI: 10.1021/acs.jpcb.0c04963] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Han Y, Cheng L, Sun W. Analysis of Protein-Protein Interaction Networks through Computational Approaches. Protein Pept Lett 2020;27:265-278. [PMID: 31692419 DOI: 10.2174/0929866526666191105142034] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 05/08/2019] [Accepted: 09/26/2019] [Indexed: 01/02/2023]
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Tan YS, Verma CS. Straightforward Incorporation of Multiple Ligand Types into Molecular Dynamics Simulations for Efficient Binding Site Detection and Characterization. J Chem Theory Comput 2020;16:6633-6644. [PMID: 32810406 DOI: 10.1021/acs.jctc.0c00405] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Computational methods-guided design of modulators targeting protein-protein interactions (PPIs). Eur J Med Chem 2020;207:112764. [PMID: 32871340 DOI: 10.1016/j.ejmech.2020.112764] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/09/2020] [Accepted: 08/16/2020] [Indexed: 12/15/2022]
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Dolbois A, Batiste L, Wiedmer L, Dong J, Brütsch M, Huang D, Deerain NM, Spiliotopoulos D, Cheng-Sánchez I, Laul E, Nevado C, Śledź P, Caflisch A. Hitting a Moving Target: Simulation and Crystallography Study of ATAD2 Bromodomain Blockers. ACS Med Chem Lett 2020;11:1573-1580. [PMID: 32832026 DOI: 10.1021/acsmedchemlett.0c00080] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 06/30/2020] [Indexed: 12/15/2022]  Open
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Brooks BD, Closmore A, Yang J, Holland M, Cairns T, Cohen GH, Bailey-Kellogg C. Characterizing Epitope Binding Regions of Entire Antibody Panels by Combining Experimental and Computational Analysis of Antibody: Antigen Binding Competition. Molecules 2020;25:molecules25163659. [PMID: 32796656 PMCID: PMC7464469 DOI: 10.3390/molecules25163659] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 07/27/2020] [Accepted: 07/28/2020] [Indexed: 11/16/2022]  Open
50
Keeley A, Petri L, Ábrányi-Balogh P, Keserű GM. Covalent fragment libraries in drug discovery. Drug Discov Today 2020;25:983-996. [PMID: 32298798 DOI: 10.1016/j.drudis.2020.03.016] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/07/2020] [Accepted: 03/23/2020] [Indexed: 12/20/2022]
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