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For: Pan X, Wang H, Li C, Zhang JZH, Ji C. MolGpka: A Web Server for Small Molecule pKa Prediction Using a Graph-Convolutional Neural Network. J Chem Inf Model 2021;61:3159-3165. [PMID: 34251213 DOI: 10.1021/acs.jcim.1c00075] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Number Cited by Other Article(s)
1
Pronkin PG, Sorokina ON, Tatikolov AS. Spectral-fluorescent study of substituted trimethine cyanine dyes in solutions and in complexes with DNA. Effects of aggregation, moderate heating, and decreasing pH. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024;320:124611. [PMID: 38852304 DOI: 10.1016/j.saa.2024.124611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 04/12/2024] [Accepted: 06/04/2024] [Indexed: 06/11/2024]
2
Xu Y, Liu X, Xia W, Ge J, Ju CW, Zhang H, Zhang JZH. ChemXTree: A Feature-Enhanced Graph Neural Network-Neural Decision Tree Framework for ADMET Prediction. J Chem Inf Model 2024. [PMID: 39497657 DOI: 10.1021/acs.jcim.4c01186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2024]
3
Roth O, Yechezkel S, Serero O, Eliyahu A, Vints I, Tzeela P, Carignano A, Janacek DP, Peters V, Kessel A, Dwivedi V, Carmeli-Weissberg M, Shaya F, Faigenboim-Doron A, Ung KL, Pedersen BP, Riov J, Klavins E, Dawid C, Hammes UZ, Ben-Tal N, Napier R, Sadot E, Weinstain R. Slow release of a synthetic auxin induces formation of adventitious roots in recalcitrant woody plants. Nat Biotechnol 2024;42:1705-1716. [PMID: 38267759 DOI: 10.1038/s41587-023-02065-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 11/15/2023] [Indexed: 01/26/2024]
4
Lemmink IB, Willemsen L, Beij E, Bovee TFH, Zuilhof H, Salentijn GIJ. Modular Point-of-Need Tropane Alkaloid Detection at Regulatory Levels: Combining Solid-Liquid Extraction from Buckwheat with a Paper-Immobilized Liquid-Phase Microextraction and Immuno-Detection in Interconnectable 3D-Printed Devices. Anal Chem 2024;96:16462-16468. [PMID: 39365091 PMCID: PMC11483449 DOI: 10.1021/acs.analchem.4c04811] [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] [Received: 09/06/2024] [Revised: 09/19/2024] [Accepted: 09/20/2024] [Indexed: 10/05/2024]
5
Collins JW, Ebrahimkhani M, Ramirez D, Deiloff J, Gonzalez M, Abedi M, Philippe-Venec L, Cole BM, Moore B, Nwankwo JO. Attentive graph neural network models for the prediction of blood brain barrier permeability. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.12.617907. [PMID: 39463958 PMCID: PMC11507759 DOI: 10.1101/2024.10.12.617907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/29/2024]
6
Terzani F, Wang C, Rostami S, Desmet R, Snella B, Sénéchal M, Wiltschi B, Vicogne J, Melnyk O, Agouridas V. Protocol for protein modification using oxalyl thioester-mediated chemoselective ligation. STAR Protoc 2024;5:103390. [PMID: 39412993 PMCID: PMC11525222 DOI: 10.1016/j.xpro.2024.103390] [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: 07/01/2024] [Revised: 08/27/2024] [Accepted: 09/24/2024] [Indexed: 10/18/2024]  Open
7
Patient G, Bedart C, Khan NA, Renault N, Farce A. Distinct binding hotspots for natural and synthetic agonists of FFA4 from in silico approaches. Mol Inform 2024;43:e202400046. [PMID: 39046372 DOI: 10.1002/minf.202400046] [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: 02/05/2024] [Revised: 05/13/2024] [Accepted: 05/14/2024] [Indexed: 07/25/2024]
8
Luo W, Zhou G, Zhu Z, Yuan Y, Ke G, Wei Z, Gao Z, Zheng H. Bridging Machine Learning and Thermodynamics for Accurate pK a Prediction. JACS AU 2024;4:3451-3465. [PMID: 39328749 PMCID: PMC11423309 DOI: 10.1021/jacsau.4c00271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 07/07/2024] [Accepted: 07/10/2024] [Indexed: 09/28/2024]
9
Warren MT, Biggs CI, Bissoyi A, Gibson MI, Sosso GC. Data-driven discovery of potent small molecule ice recrystallisation inhibitors. Nat Commun 2024;15:8082. [PMID: 39278938 PMCID: PMC11402961 DOI: 10.1038/s41467-024-52266-w] [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: 12/22/2023] [Accepted: 08/27/2024] [Indexed: 09/18/2024]  Open
10
Lee KM, Jaeger VW. Adsorption of Staphylococcus aureus biofilm associated compounds on silica probed with molecular dynamics simulations. Biointerphases 2024;19:051006. [PMID: 39422496 DOI: 10.1116/6.0003870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Accepted: 09/20/2024] [Indexed: 10/19/2024]  Open
11
Rahebi P, Aryapour H. Reconstruction of the unbinding pathways of new inhibitors of the SARS-CoV-2 papain-like protease using molecular dynamics simulation. J Biomol Struct Dyn 2024;42:7501-7514. [PMID: 37505097 DOI: 10.1080/07391102.2023.2240424] [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: 05/12/2023] [Accepted: 07/18/2023] [Indexed: 07/29/2023]
12
Vautrin L, Lambert A, Mahdhaoui F, El Abed R, Boubaker T, Ingrosso F. Structural and Electronic Properties of Novel Azothiophene Dyes: A Multilevel Study Incorporating Explicit Solvation Effects. Molecules 2024;29:4053. [PMID: 39274901 PMCID: PMC11397383 DOI: 10.3390/molecules29174053] [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: 07/30/2024] [Revised: 08/20/2024] [Accepted: 08/23/2024] [Indexed: 09/16/2024]  Open
13
Abarbanel OD, Hutchison GR. QupKake: Integrating Machine Learning and Quantum Chemistry for Micro-pKa Predictions. J Chem Theory Comput 2024;20:6946-6956. [PMID: 38832803 PMCID: PMC11325546 DOI: 10.1021/acs.jctc.4c00328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
14
Kozak F, Brandis D, Pötzl C, Epasto LM, Reichinger D, Obrist D, Peterlik H, Polyansky A, Zagrovic B, Daus F, Geyer A, Becker CFW, Kurzbach D. An Atomistic View on the Mechanism of Diatom Peptide-Guided Biomimetic Silica Formation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024;11:e2401239. [PMID: 38874418 PMCID: PMC11321707 DOI: 10.1002/advs.202401239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 05/23/2024] [Indexed: 06/15/2024]
15
Ribeiro IC, de Moraes JVB, Mariotini-Moura C, Polêto MD, da Rocha Torres Pavione N, de Castro RB, Miranda IL, Sartori SK, Alves KLS, Bressan GC, de Souza Vasconcellos R, Meyer-Fernandes JR, Diaz-Muñoz G, Fietto JLR. Synthesis of new non-natural L-glycosidic flavonoid derivatives and their evaluation as inhibitors of Trypanosoma cruzi ecto-nucleoside triphosphate diphosphohydrolase 1 (TcNTPDase1). Purinergic Signal 2024;20:399-419. [PMID: 37975950 PMCID: PMC11303637 DOI: 10.1007/s11302-023-09974-7] [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: 05/03/2023] [Accepted: 10/20/2023] [Indexed: 11/19/2023]  Open
16
Miao R, Liu D, Mao L, Chen X, Zhang L, Yuan Z, Shi S, Li H, Li S. GR-pKa: a message-passing neural network with retention mechanism for pKa prediction. Brief Bioinform 2024;25:bbae408. [PMID: 39171986 PMCID: PMC11339865 DOI: 10.1093/bib/bbae408] [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: 04/24/2024] [Revised: 07/26/2024] [Accepted: 08/01/2024] [Indexed: 08/23/2024]  Open
17
An H, Liu X, Cai W, Shao X. AttenGpKa: A Universal Predictor of Solvation Acidity Using Graph Neural Network and Molecular Topology. J Chem Inf Model 2024;64:5480-5491. [PMID: 38982757 DOI: 10.1021/acs.jcim.4c00449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/11/2024]
18
Fu Z, Treacy JW, Hosier BM, Houk KN, Maynard HD. Controlling rates and reversibilities of elimination reactions of hydroxybenzylammoniums by tuning dearomatization energies. Chem Sci 2024;15:10448-10454. [PMID: 38994402 PMCID: PMC11234877 DOI: 10.1039/d4sc02985b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 05/23/2024] [Indexed: 07/13/2024]  Open
19
Hoffer L, Charifi-Hoareau G, Barelier S, Betzi S, Miller T, Morelli X, Roche P. ChemoDOTS: a web server to design chemistry-driven focused libraries. Nucleic Acids Res 2024;52:W461-W468. [PMID: 38686808 PMCID: PMC11223810 DOI: 10.1093/nar/gkae326] [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] [Received: 03/11/2024] [Revised: 04/08/2024] [Accepted: 04/16/2024] [Indexed: 05/02/2024]  Open
20
Mou Z, Zhu Y, Zhang L, Ma M, Li Z, Guo Y, Zheng J, Zhao Z, Zhang K, Chen X, Li Z. "AquaF" Building Blocks for Water-Compatible SN2 18F-Fluorination of Small-Molecule Radiotracers. J Am Chem Soc 2024;146:17517-17529. [PMID: 38869959 DOI: 10.1021/jacs.4c05854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2024]
21
Bera A, Mukherjee S, Patra N. Exploring transmembrane allostery in the MexB: DB08385 variant as a promising inhibitor-like candidate against Pseudomonas aeruginosa antibiotic resistance: a computational study. Phys Chem Chem Phys 2024;26:17011-17027. [PMID: 38835320 DOI: 10.1039/d4cp01620c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
22
Nardi AN, Olivieri A, D'Abramo M, Salvio R. Unveiling the Cleavage Mechanism of an RNA Model Compound on the whole pH Scale: Computations Meet Experiments in the Determination of Reaction Rates. Chemphyschem 2024;25:e202300873. [PMID: 38526551 DOI: 10.1002/cphc.202300873] [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: 11/16/2023] [Revised: 02/29/2024] [Accepted: 03/24/2024] [Indexed: 03/26/2024]
23
Kersten C, Archambault P, Köhler LP. Assessment of Nucleobase Protomeric and Tautomeric States in Nucleic Acid Structures for Interaction Analysis and Structure-Based Ligand Design. J Chem Inf Model 2024;64:4485-4499. [PMID: 38766733 DOI: 10.1021/acs.jcim.4c00520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
24
He Y, Qian X, da Silva GCQ, Gabellini C, Lucherelli MA, Biagiotti G, Richichi B, Ménard-Moyon C, Gao H, Posocco P, Bianco A. Unveiling Liquid-Phase Exfoliation of Graphite and Boron Nitride Using Fluorescent Dyes Through Combined Experiments and Simulations. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024;20:e2307817. [PMID: 38267819 DOI: 10.1002/smll.202307817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 01/04/2024] [Indexed: 01/26/2024]
25
Lewis JA, Jacobo EP, Palmer N, Vermerris W, Sattler SE, Brozik JA, Sarath G, Kang C. Structural and Interactional Analysis of the Flavonoid Pathway Proteins: Chalcone Synthase, Chalcone Isomerase and Chalcone Isomerase-like Protein. Int J Mol Sci 2024;25:5651. [PMID: 38891840 PMCID: PMC11172311 DOI: 10.3390/ijms25115651] [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: 04/04/2024] [Revised: 05/16/2024] [Accepted: 05/18/2024] [Indexed: 06/21/2024]  Open
26
Silva IR, Souza MACE, Machado RR, Oliveira RBD, Leite EA, César IDC. Enhancing oral bioavailability of an antifungal thiazolylhydrazone derivative: Development and characterization of a self-emulsifying drug delivery system. Int J Pharm 2024;655:124011. [PMID: 38493843 DOI: 10.1016/j.ijpharm.2024.124011] [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: 02/06/2024] [Revised: 03/14/2024] [Accepted: 03/14/2024] [Indexed: 03/19/2024]
27
Li Q, Joshi D, Sanghvi YS, Yan H. Difluoroacetic acid: an alternative acid in the detritylation reaction for the solid-phase synthesis of oligonucleotides. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2024:1-9. [PMID: 38602371 DOI: 10.1080/15257770.2024.2337145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 03/20/2024] [Indexed: 04/12/2024]
28
Glass S, Schmidt M, Merten P, Abdul Latif A, Fischer K, Schulze A, Friederich P, Filiz V. Design of Modified Polymer Membranes Using Machine Learning. ACS APPLIED MATERIALS & INTERFACES 2024;16. [PMID: 38600824 PMCID: PMC11056926 DOI: 10.1021/acsami.3c18805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 03/19/2024] [Accepted: 03/21/2024] [Indexed: 04/12/2024]
29
An H, Liu X, Cai W, Shao X. Explainable Graph Neural Networks with Data Augmentation for Predicting pKa of C-H Acids. J Chem Inf Model 2024;64:2383-2392. [PMID: 37706462 DOI: 10.1021/acs.jcim.3c00958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/15/2023]
30
Kemas AM, Zandi Shafagh R, Taebnia N, Michel M, Preiss L, Hofmann U, Lauschke VM. Compound Absorption in Polymer Devices Impairs the Translatability of Preclinical Safety Assessments. Adv Healthc Mater 2024;13:e2303561. [PMID: 38053301 PMCID: PMC11469150 DOI: 10.1002/adhm.202303561] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Indexed: 12/07/2023]
31
Mehta MJ, Kim HJ, Lim SB, Naito M, Miyata K. Recent Progress in the Endosomal Escape Mechanism and Chemical Structures of Polycations for Nucleic Acid Delivery. Macromol Biosci 2024;24:e2300366. [PMID: 38226723 DOI: 10.1002/mabi.202300366] [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: 08/10/2023] [Revised: 12/22/2023] [Indexed: 01/17/2024]
32
Lee KH, Won SJ, Oyinloye P, Shi L. Unlocking the Potential of High-Quality Dopamine Transporter Pharmacological Data: Advancing Robust Machine Learning-Based QSAR Modeling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.06.583803. [PMID: 38558976 PMCID: PMC10979915 DOI: 10.1101/2024.03.06.583803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
33
Sokolova AS, Yarovaya OI, Artyushin OI, Sharova EV, Baev DS, Mordvinova ED, Shcherbakov DN, Shnaider TA, Nikitina TV, Esaulkova IL, Ilyina PA, Zarubaev VV, Brel VK, Tolstikova TG, Salakhutdinov NF. Design, synthesis and antiviral evaluation of novel conjugates of the 1,7,7-trimethylbicyclo[2.2.1]heptane scaffold and saturated N-heterocycles via 1,2,3-triazole linker. Arch Pharm (Weinheim) 2024;357:e2300549. [PMID: 38036303 DOI: 10.1002/ardp.202300549] [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: 09/29/2023] [Revised: 11/08/2023] [Accepted: 11/10/2023] [Indexed: 12/02/2023]
34
Sanchez AJ, Maier S, Raghavachari K. Leveraging DFT and Molecular Fragmentation for Chemically Accurate pKa Prediction Using Machine Learning. J Chem Inf Model 2024;64:712-723. [PMID: 38301279 DOI: 10.1021/acs.jcim.3c01923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
35
Xin X, Zhou J, He Q, Peng Y, Wei Y, Zhao H, Tong T. Resolution of trans-1,2-cyclohexanedicarboxylic acid containing two carboxylic groups by forming diastereomeric salts based on feeding molar ratio control. Chirality 2024;36:e23634. [PMID: 38057950 DOI: 10.1002/chir.23634] [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: 04/14/2023] [Accepted: 11/15/2023] [Indexed: 12/08/2023]
36
Makhaeva GF, Kovaleva NV, Rudakova EV, Boltneva NP, Lushchekina SV, Astakhova TY, Timokhina EN, Serkov IV, Proshin AN, Soldatova YV, Poletaeva DA, Faingold II, Mumyatova VA, Terentiev AA, Radchenko EV, Palyulin VA, Bachurin SO, Richardson RJ. Combining Experimental and Computational Methods to Produce Conjugates of Anticholinesterase and Antioxidant Pharmacophores with Linker Chemistries Affecting Biological Activities Related to Treatment of Alzheimer's Disease. Molecules 2024;29:321. [PMID: 38257233 PMCID: PMC10820264 DOI: 10.3390/molecules29020321] [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: 11/01/2023] [Revised: 12/19/2023] [Accepted: 12/27/2023] [Indexed: 01/24/2024]  Open
37
Dunkelmann DL, Piedrafita C, Dickson A, Liu KC, Elliott TS, Fiedler M, Bellini D, Zhou A, Cervettini D, Chin JW. Adding α,α-disubstituted and β-linked monomers to the genetic code of an organism. Nature 2024;625:603-610. [PMID: 38200312 PMCID: PMC10794150 DOI: 10.1038/s41586-023-06897-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 11/23/2023] [Indexed: 01/12/2024]
38
Cui Q, Huang C, Liu JY, Zhang JT. Small Molecule Inhibitors Targeting the "Undruggable" Survivin: The Past, Present, and Future from a Medicinal Chemist's Perspective. J Med Chem 2023;66:16515-16545. [PMID: 38092421 DOI: 10.1021/acs.jmedchem.3c01130] [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: 12/29/2023]
39
Bhanja KK, Sharma M, Patra N. Uncovering the Structural and Binding Insights of Dual Inhibitors Simultaneously Targeting Two Distinct Sites on EGFR Kinase. J Phys Chem B 2023;127:10749-10765. [PMID: 38055900 DOI: 10.1021/acs.jpcb.3c04337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
40
Chen J, Zhao S, Wesseling S, Kramer NI, Rietjens IM, Bouwmeester H. Acetylcholinesterase Inhibition in Rats and Humans Following Acute Fenitrothion Exposure Predicted by Physiologically Based Kinetic Modeling-Facilitated Quantitative In Vitro to In Vivo Extrapolation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023;57:20521-20531. [PMID: 38008925 PMCID: PMC10720383 DOI: 10.1021/acs.est.3c07077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 11/11/2023] [Accepted: 11/14/2023] [Indexed: 11/28/2023]
41
Sharma V, Giammona M, Zubarev D, Tek A, Nugyuen K, Sundberg L, Congiu D, La YH. Formulation Graphs for Mapping Structure-Composition of Battery Electrolytes to Device Performance. J Chem Inf Model 2023;63:6998-7010. [PMID: 37948621 PMCID: PMC10685446 DOI: 10.1021/acs.jcim.3c01030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 10/21/2023] [Accepted: 10/24/2023] [Indexed: 11/12/2023]
42
Khramtsov P, Minin A, Galaeva Z, Mukhlynina E, Kropaneva M, Rayev M. Optimizing the Composition of the Substrate Enhances the Performance of Peroxidase-like Nanozymes in Colorimetric Assays: A Case Study of Prussian Blue and 3,3'-Diaminobenzidine. Molecules 2023;28:7622. [PMID: 38005344 PMCID: PMC10674554 DOI: 10.3390/molecules28227622] [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: 09/26/2023] [Revised: 11/10/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023]  Open
43
Elsanhoury R, Alasmari A, Parupathi P, Jumaa M, Al-Fayoumi S, Kumar A, Khashan R, Nazzal S, Fayyad AA. AI & experimental-based discovery and preclinical IND-enabling studies of selective BMX inhibitors for development of cancer therapeutics. Int J Pharm 2023;645:123384. [PMID: 37678472 DOI: 10.1016/j.ijpharm.2023.123384] [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: 06/13/2023] [Revised: 08/14/2023] [Accepted: 09/04/2023] [Indexed: 09/09/2023]
44
Murillo-Gelvez J, Dmitrenko O, Torralba-Sanchez TL, Tratnyek PG, Di Toro DM. pKa prediction of per- and polyfluoroalkyl acids in water using in silico gas phase stretching vibrational frequencies and infrared intensities. Phys Chem Chem Phys 2023;25:24745-24760. [PMID: 37671434 DOI: 10.1039/d3cp01390a] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/07/2023]
45
Tous-Granados AM, Hernandez-Maldonado AJ. A SIFSIX-MOF constructed from a metalloligand yields enhanced stability for selective CO2 adsorption. Chem Commun (Camb) 2023;59:10020-10023. [PMID: 37525956 DOI: 10.1039/d3cc02683c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
46
Hagg A, Kirschner KN. Open-Source Machine Learning in Computational Chemistry. J Chem Inf Model 2023;63:4505-4532. [PMID: 37466636 PMCID: PMC10430767 DOI: 10.1021/acs.jcim.3c00643] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Indexed: 07/20/2023]
47
Makhaeva GF, Kovaleva NV, Rudakova EV, Boltneva NP, Lushchekina SV, Astakhova TY, Timokhina EN, Serebryakova OG, Shchepochkin AV, Averkov MA, Utepova IA, Demina NS, Radchenko EV, Palyulin VA, Fisenko VP, Bachurin SO, Chupakhin ON, Charushin VN, Richardson RJ. Derivatives of 9-phosphorylated acridine as butyrylcholinesterase inhibitors with antioxidant activity and the ability to inhibit β-amyloid self-aggregation: potential therapeutic agents for Alzheimer's disease. Front Pharmacol 2023;14:1219980. [PMID: 37654616 PMCID: PMC10466253 DOI: 10.3389/fphar.2023.1219980] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 07/18/2023] [Indexed: 09/02/2023]  Open
48
Bhat-Ambure J, Ambure P, Serrano-Candelas E, Galiana-Roselló C, Gil-Martínez A, Guerrero M, Martin M, González-García J, García-España E, Gozalbes R. G4-QuadScreen: A Computational Tool for Identifying Multi-Target-Directed Anticancer Leads against G-Quadruplex DNA. Cancers (Basel) 2023;15:3817. [PMID: 37568632 PMCID: PMC10416877 DOI: 10.3390/cancers15153817] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/16/2023] [Accepted: 07/21/2023] [Indexed: 08/13/2023]  Open
49
Szabó ZI, Boda F, Fiser B, Dobó M, Szőcs L, Tóth G. Chiral Separation of Oxazolidinone Analogs by Capillary Electrophoresis Using Anionic Cyclodextrins as Chiral Selectors: Emphasis on Enantiomer Migration Order. Molecules 2023;28:molecules28114530. [PMID: 37299005 DOI: 10.3390/molecules28114530] [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: 04/27/2023] [Revised: 05/28/2023] [Accepted: 06/01/2023] [Indexed: 06/12/2023]  Open
50
Pais JP, Antoniuk O, Freire R, Pires D, Valente E, Anes E, Constantino L. Nitrobenzoates and Nitrothiobenzoates with Activity against M. tuberculosis. Microorganisms 2023;11:microorganisms11040969. [PMID: 37110393 PMCID: PMC10142844 DOI: 10.3390/microorganisms11040969] [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: 02/27/2023] [Revised: 04/01/2023] [Accepted: 04/04/2023] [Indexed: 04/29/2023]  Open
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