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Journal articles on the topic 'Covalent approaches'

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Author: Grafiati

Published: 10 December 2022

Last updated: 28 January 2023

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1

Tang, Bohan, Jiantao Zhao, Jiang-Fei Xu, and Xi Zhang. "Tuning the stability of organic radicals: from covalent approaches to non-covalent approaches." Chemical Science 11, no. 5 (2020): 1192–204. http://dx.doi.org/10.1039/c9sc06143f.

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2

van Maarseveen, Jan H., Milo D. Cornelissen, and Simone Pilon. "Covalently Templated Syntheses of Mechanically Interlocked Molecules." Synthesis 53, no. 24 (October 8, 2021): 4527–48. http://dx.doi.org/10.1055/a-1665-4650.

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AbstractMechanically interlocked molecules (MiMs), such as catenanes and rotaxanes, exhibit unique properties due to the mechanical bond which unites their components. The translational and rotational freedom present in these compounds may be harnessed to create stimuli-responsive MiMs, which find potential application as artificial molecular machines. Mechanically interlocked structures such as lasso peptides have also been found in nature, making MiMs promising albeit elusive targets for drug discovery. Although the first syntheses of MiMs were based on covalent strategies, approaches based on non-covalent interactions rose to prominence thereafter and have remained dominant. Non-covalent strategies are generally short and efficient, but do require particular structural motifs which are difficult to alter. In a covalent approach, MiMs can be more easily modified while the components may have increased rotational and translational freedom. Both approaches have complementary merits and combining the unmatched efficiency of non-covalent approaches with the scope of covalent syntheses may open up vast opportunities. In this review, recent covalently templated syntheses of MiMs are discussed to show their complementarity and anticipate future developments in this field.1 Introduction2 Tetrahedral Templates2.1 A Carbonate Template for Non-Rusty Catenanes2.2 All-Benzene Catenanes on a Silicon Template2.3 Backfolding from Quaternary Carbon3 Planar Templates3.1 Rotaxanes Constructed in a Ring3.2 Hydrindacene as a Dynamic Covalent Template3.3 Templating on Tri- and Tetrasubstituted Benzenes4 Conclusion

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3

Georgakilas, Vasilios, Michal Otyepka, Athanasios B. Bourlinos, Vimlesh Chandra, Namdong Kim, K. Christian Kemp, Pavel Hobza, Radek Zboril, and Kwang S. Kim. "Functionalization of Graphene: Covalent and Non-Covalent Approaches, Derivatives and Applications." Chemical Reviews 112, no. 11 (September 25, 2012): 6156–214. http://dx.doi.org/10.1021/cr3000412.

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4

Bjij, Imane, Pritika Ramharack, Shama Khan, Driss Cherqaoui, and Mahmoud E. S. Soliman. "Tracing Potential Covalent Inhibitors of an E3 Ubiquitin Ligase through Target-Focused Modelling." Molecules 24, no. 17 (August 28, 2019): 3125. http://dx.doi.org/10.3390/molecules24173125.

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The Nedd4-1 E3 Ubiquitin ligase has been implicated in multiple disease conditions due its overexpression. Although the enzyme may be targeted both covalently and non-covalently, minimal studies provide effective inhibitors against it. Recently, research has focused on covalent inhibitors based on their characteristic, highly-selective warheads and ability to prevent drug resistance. This prompted us to screen for new covalent inhibitors of Nedd4-1 using a combination of computational approaches. However, this task proved challenging due to the limited number of electrophilic moieties available in virtual libraries. Therefore, we opted to divide an existing covalent Nedd4-1 inhibitor into two parts: a non-covalent binding group and a pre-selected α, β-unsaturated ester that forms the covalent linkage with the protein. A non-covalent pharmacophore model was built based on molecular interactions at the binding site. The pharmacophore was then subjected to virtual screening to identify structurally similar hit compounds. Multiple filtrations were implemented prior to selecting four hits, which were validated with a covalent conjugation and later assessed by molecular dynamic simulations. The results showed that, of the four hit molecules, Zinc00937975 exhibited advantageous molecular groups, allowing for favourable interactions with one of the characteristic cysteine residues. Predictive pharmacokinetic analysis further justified the compound as a potential lead molecule, prompting its recommendation for confirmatory biological evaluation. Our inhouse, refined, pharmacophore model approach serves as a robust method that will encourage screening for novel covalent inhibitors in drug discovery.

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5

Sotriffer, Christoph. "Docking of Covalent Ligands: Challenges and Approaches." Molecular Informatics 37, no. 9-10 (June 21, 2018): 1800062. http://dx.doi.org/10.1002/minf.201800062.

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6

Kizior, Beata, Mariusz Michalczyk, Jarosław J. Panek, Wiktor Zierkiewicz, and Aneta Jezierska. "Unraveling the Nature of Hydrogen Bonds of “Proton Sponges” Based on Car-Parrinello and Metadynamics Approaches." International Journal of Molecular Sciences 24, no. 2 (January 12, 2023): 1542. http://dx.doi.org/10.3390/ijms24021542.

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The nature of intra- and intermolecular non-covalent interactions was studied in four naphthalene derivatives commonly referred to as “proton sponges”. Special attention was paid to an intramolecular hydrogen bond present in the protonated form of the compounds. The unsubstituted “proton sponge” served as a reference structure to study the substituent influence on the hydrogen bond (HB) properties. We selected three compounds substituted by methoxy, amino, and nitro groups. The presence of the substituents either retained the parent symmetry or rendered the compounds asymmetric. In order to reveal the non-covalent interaction properties, the Hirshfeld surface (HS) was computed for the crystal structures of the studied compounds. Next, quantum-chemical simulations were performed in vacuo and in the crystalline phase. Car–Parrinello molecular dynamics (CPMD), Path Integral Molecular Dynamics (PIMD), and metadynamics were employed to investigate the time-evolution changes of metric parameters and free energy profile in both phases. Additionally, for selected snapshots obtained from the CPMD trajectories, non-covalent interactions and electronic structure were studied. Quantum theory of atoms in molecules (QTAIM) and the Density Overlap Regions Indicator (DORI) were applied for this purpose. It was found based on Hirshfeld surfaces that, besides intramolecular hydrogen bonds, other non-covalent interactions are present and have a strong impact on the crystal structure organization. The CPMD results obtained in both phases showed frequent proton transfer phenomena. The proton was strongly delocalized in the applied time-scale and temperature, especially in the PIMD framework. The use of metadynamics allowed for tracing the free energy profiles and confirming that the hydrogen bonds present in “proton sponges” are Low-Barrier Hydrogen Bonds (LBHBs). The electronic and topological analysis quantitatively described the temperature dependence and time-evolution changes of the electronic structure. The covalency of the hydrogen bonds was estimated based on QTAIM analysis. It was found that strong hydrogen bonds show greater covalency, which is additionally determined by the proton position in the hydrogen bridge.

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7

Sainz-Urruela, Carlos, Soledad Vera-López, María Paz San Andrés, and Ana M. Díez-Pascual. "Surface functionalization of graphene oxide with tannic acid: Covalent vs non-covalent approaches." Journal of Molecular Liquids 357 (July 2022): 119104. http://dx.doi.org/10.1016/j.molliq.2022.119104.

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8

Sakamaki, Daisuke, Samrat Ghosh, and Shu Seki. "Dynamic covalent bonds: approaches from stable radical species." Materials Chemistry Frontiers 3, no. 11 (2019): 2270–82. http://dx.doi.org/10.1039/c9qm00488b.

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9

Gautam, Chandkiram, and Selvam Chelliah. "Methods of hexagonal boron nitride exfoliation and its functionalization: covalent and non-covalent approaches." RSC Advances 11, no. 50 (2021): 31284–327. http://dx.doi.org/10.1039/d1ra05727h.

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10

Nigel-Etinger, Izana, Atif Mahammed, and Zeev Gross. "Covalent versus non-covalent (biocatalytic) approaches for enantioselective sulfoxidation catalyzed by corrole metal complexes." Catalysis Science & Technology 1, no. 4 (2011): 578. http://dx.doi.org/10.1039/c1cy00046b.

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11

Hussein, Omar A., Khairul Habib, R. Saidur, Ali S. Muhsan, Syed Shahabuddin, and Omer A. Alawi. "The influence of covalent and non-covalent functionalization of GNP based nanofluids on its thermophysical, rheological and suspension stability properties." RSC Advances 9, no. 66 (2019): 38576–89. http://dx.doi.org/10.1039/c9ra07811h.

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12

Fairhurst, Robin A., Thomas Knoepfel, Catherine Leblanc, Nicole Buschmann, Christoph Gaul, Jutta Blank, Inga Galuba, et al. "Approaches to selective fibroblast growth factor receptor 4 inhibition through targeting the ATP-pocket middle-hinge region." MedChemComm 8, no. 8 (2017): 1604–13. http://dx.doi.org/10.1039/c7md00213k.

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13

Aleman, Elvin A., Heidi S. Pedini, and David Rueda. "Covalent-Bond-Based Immobilization Approaches for Single-Molecule Fluorescence." Biophysical Journal 98, no. 3 (January 2010): 185a. http://dx.doi.org/10.1016/j.bpj.2009.12.990.

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14

AlemÃ¡n, Elvin A., Heidi S. Pedini, and David Rueda. "Covalent-Bond-Based Immobilization Approaches for Single-Molecule Fluorescence." ChemBioChem 10, no. 18 (December 14, 2009): 2862–66. http://dx.doi.org/10.1002/cbic.200900640.

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15

Gottfried, Anna, and Elmar Weinhold. "Sequence-specific covalent labelling of DNA." Biochemical Society Transactions 39, no. 2 (March 22, 2011): 623–28. http://dx.doi.org/10.1042/bst0390623.

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Sequence-specific DNA modification is of significance for applications in bio- and nano-technology, medical diagnostics and fundamental life sciences research. Preferentially, labelling should be performed covalently, which avoids doubts about label dissociation from the DNA under various conditions. Several methods to label native DNA have been developed in the last two decades. Triple-helix-forming oligodeoxynucleotides and hairpin polyamides that bind DNA sequences specifically in the major and minor groove respectively were used as targeting devices for subsequent covalent labelling. In addition, enzyme-directed labelling approaches utilizing nicking endonucleases in combination with DNA polymerases or DNA methyltransferases have been employed. This review summarizes various techniques useful for functionalization of long native DNA.

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16

Nunes, Charneira, Morello, Rodrigues, Pereira, and Antunes. "Mass Spectrometry-Based Methodologies for Targeted and Untargeted Identification of Protein Covalent Adducts (Adductomics): Current Status and Challenges." High-Throughput 8, no. 2 (April 23, 2019): 9. http://dx.doi.org/10.3390/ht8020009.

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Protein covalent adducts formed upon exposure to reactive (mainly electrophilic) chemicals may lead to the development of a wide range of deleterious health outcomes. Therefore, the identification of protein covalent adducts constitutes a huge opportunity for a better understanding of events underlying diseases and for the development of biomarkers which may constitute effective tools for disease diagnosis/prognosis, for the application of personalized medicine approaches and for accurately assessing human exposure to chemical toxicants. The currently available mass spectrometry (MS)-based methodologies, are clearly the most suitable for the analysis of protein covalent modifications, providing accuracy, sensitivity, unbiased identification of the modified residue and conjugates along with quantitative information. However, despite the huge technological advances in MS instrumentation and bioinformatics tools, the identification of low abundant protein covalent adducts is still challenging. This review is aimed at summarizing the MS-based methodologies currently used for the identification of protein covalent adducts and the strategies developed to overcome the analytical challenges, involving not only sample pre-treatment procedures but also distinct MS and data analysis approaches.

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17

Cuesta, Adolfo, and Jack Taunton. "Lysine-Targeted Inhibitors and Chemoproteomic Probes." Annual Review of Biochemistry 88, no. 1 (June 20, 2019): 365–81. http://dx.doi.org/10.1146/annurev-biochem-061516-044805.

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Covalent inhibitors are widely used in drug discovery and chemical biology. Although covalent inhibitors are frequently designed to react with noncatalytic cysteines, many ligand binding sites lack an accessible cysteine. Here, we review recent advances in the chemical biology of lysine-targeted covalent inhibitors and chemoproteomic probes. By analyzing crystal structures of proteins bound to common metabolites and enzyme cofactors, we identify a large set of mostly unexplored lysines that are potentially targetable with covalent inhibitors. In addition, we describe mass spectrometry–based approaches for determining proteome-wide lysine ligandability and lysine-reactive chemoproteomic probes for assessing drug–target engagement. Finally, we discuss the design of amine-reactive inhibitors that form reversible covalent bonds with their protein targets.

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18

Jin, Yinghua, Qi Wang, Philip Taynton, and Wei Zhang. "Dynamic Covalent Chemistry Approaches Toward Macrocycles, Molecular Cages, and Polymers." Accounts of Chemical Research 47, no. 5 (April 16, 2014): 1575–86. http://dx.doi.org/10.1021/ar500037v.

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19

Liu, Chuan-Zhi, Meng Yan, Hui Wang, Dan-Wei Zhang, and Zhan-Ting Li. "Making Molecular and Macromolecular Helical Tubes: Covalent and Noncovalent Approaches." ACS Omega 3, no. 5 (May 11, 2018): 5165–76. http://dx.doi.org/10.1021/acsomega.8b00681.

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20

Hossam, Monia, Deena S. Lasheen, and Khaled A. M. Abouzid. "Covalent EGFR Inhibitors: Binding Mechanisms, Synthetic Approaches, and Clinical Profiles." Archiv der Pharmazie 349, no. 8 (June 3, 2016): 573–93. http://dx.doi.org/10.1002/ardp.201600063.

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21

Wang, Lei, Jinkyu Han, Jessica Hoy, Fang Hu, Haiqing Liu, Molly M. Gentleman, Matthew Y. Sfeir, James A. Misewich, and Stanislaus S. Wong. "Probing differential optical and coverage behavior in nanotube–nanocrystal heterostructures synthesized by covalent versus non-covalent approaches." Dalton Transactions 43, no. 20 (2014): 7480. http://dx.doi.org/10.1039/c3dt53405g.

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22

Bjij, Imane, Fisayo A. Olotu, Clement Agoni, Emmanuel Adeniji, Shama Khan, Ahmed El Rashedy, Driss Cherqaoui, and Mahmoud E. S. Soliman. "Covalent Inhibition in Drug Discovery: Filling the Void in Literature." Current Topics in Medicinal Chemistry 18, no. 13 (October 4, 2018): 1135–45. http://dx.doi.org/10.2174/1568026618666180731161438.

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The serendipitous discovery of covalent inhibitors and their characteristic potency of inducing irreversible and complete inhibition in therapeutic targets have caused a paradigm shift from the use of non-covalent drugs in disease treatment. This has caused a significant evolution in the field of covalent targeting to understand their inhibitory mechanisms and facilitate the systemic design of novel covalent modifiers for ‘undruggable’ targets. Computational techniques have evolved over the years and have significantly contributed to the process of drug discovery by mirroring the pattern of biological occurrences thereby providing insights into the dynamics and conformational transitions associated with biomolecular interactions. Moreover, our previous contributions towards the systematic design of selective covalent modifiers have revealed the various setbacks associated with the use of these conventional techniques in the study of covalent systems, hence there is a need for distinct approaches. In this review, we highlight the modifications and development of computational techniques suitable for covalent systems, their lapses, shortcomings and recent advancements.

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23

Zhang, Weiwei, Linjiang Chen, Sheng Dai, Chengxi Zhao, Cheng Ma, Lei Wei, Minghui Zhu, et al. "Reconstructed covalent organic frameworks." Nature 604, no. 7904 (April 6, 2022): 72–79. http://dx.doi.org/10.1038/s41586-022-04443-4.

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AbstractCovalent organic frameworks (COFs) are distinguished from other organic polymers by their crystallinity1–3, but it remains challenging to obtain robust, highly crystalline COFs because the framework-forming reactions are poorly reversible4,5. More reversible chemistry can improve crystallinity6–9, but this typically yields COFs with poor physicochemical stability and limited application scope5. Here we report a general and scalable protocol to prepare robust, highly crystalline imine COFs, based on an unexpected framework reconstruction. In contrast to standard approaches in which monomers are initially randomly aligned, our method involves the pre-organization of monomers using a reversible and removable covalent tether, followed by confined polymerization. This reconstruction route produces reconstructed COFs with greatly enhanced crystallinity and much higher porosity by means of a simple vacuum-free synthetic procedure. The increased crystallinity in the reconstructed COFs improves charge carrier transport, leading to sacrificial photocatalytic hydrogen evolution rates of up to 27.98 mmol h−1 g−1. This nanoconfinement-assisted reconstruction strategy is a step towards programming function in organic materials through atomistic structural control.

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24

Salah, Lakhdar Sidi, Nassira Ouslimani, Dalila Bousba, Isabelle Huynen, Yann Danlée, and Hammouche Aksas. "Carbon Nanotubes (CNTs) from Synthesis to Functionalized (CNTs) Using Conventional and New Chemical Approaches." Journal of Nanomaterials 2021 (September 20, 2021): 1–31. http://dx.doi.org/10.1155/2021/4972770.

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Carbon nanotubes (CNTs) have emerged worldwide because of their remarkable properties enlarging their field of applications. Functionalization of CNTs is a convenient strategy to tackle low dispersion and solubilization of CNTs in many solvents or polymers. It can be done by covalent or noncovalent surface functionalization that is briefly discussed regarding the current literature. Endohedral and exohedral are conventional methods based on covalent and van der Waals bonding forces that are created through CNT functionalization by various materials. In this paper, a review of new approaches and mechanisms of functionalization of CNTs is proposed, including amidation, fluorination, bromination, chlorination, hydrogenation, and electrophilic addition. Our analysis is supported by several characterization methods highlighting recent improvements hence extending the range of applicability of CNTs.

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25

Vilímová, Iveta, Katel Hervé-Aubert, and Igor Chourpa. "Formation of miRNA Nanoprobes—Conjugation Approaches Leading to the Functionalization." Molecules 27, no. 23 (December 2, 2022): 8428. http://dx.doi.org/10.3390/molecules27238428.

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Recently, microRNAs (miRNA) captured the interest as novel diagnostic and prognostic biomarkers, with their potential for early indication of numerous pathologies. Since miRNA is a short, non-coding RNA sequence, the sensitivity and selectivity of their detection remain a cornerstone of scientific research. As such, methods based on nanomaterials have emerged in hopes of developing fast and facile approaches. At the core of the detection method based on nanotechnology lie nanoprobes and other functionalized nanomaterials. Since miRNA sensing and detection are generally rooted in the capture of target miRNA with the complementary sequence of oligonucleotides, the sequence needs to be attached to the nanomaterial with a specific conjugation strategy. As each nanomaterial has its unique properties, and each conjugation approach presents its drawbacks and advantages, this review offers a condensed overview of the conjugation approaches in nanomaterial-based miRNA sensing. Starting with a brief recapitulation of specific properties and characteristics of nanomaterials that can be used as a substrate, the focus is then centered on covalent and non-covalent bonding chemistry, leading to the functionalization of the nanomaterials, which are the most commonly used in miRNA sensing methods.

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26

Kim, Mi-Sun, Lauriane A. Buisson, Dean A. Heathcote, Haipeng Hu, D. Christopher Braddock, Anthony G. M. Barrett, Philip G. Ashton-Rickardt, and James P. Snyder. "Approaches to design non-covalent inhibitors for human granzyme B (hGrB)." Org. Biomol. Chem. 12, no. 44 (September 23, 2014): 8952–65. http://dx.doi.org/10.1039/c4ob01874e.

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27

Zhang, Yanmin, Danfeng Zhang, Haozhong Tian, Yu Jiao, Zhihao Shi, Ting Ran, Haichun Liu, et al. "Identification of Covalent Binding Sites Targeting Cysteines Based on Computational Approaches." Molecular Pharmaceutics 13, no. 9 (August 10, 2016): 3106–18. http://dx.doi.org/10.1021/acs.molpharmaceut.6b00302.

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28

Economopoulos, Solon P., and Nikos Tagmatarchis. "Multichromophores Onto Graphene: Supramolecular Non-Covalent Approaches for Efficient Light Harvesting." Journal of Physical Chemistry C 119, no. 15 (April 6, 2015): 8046–53. http://dx.doi.org/10.1021/acs.jpcc.5b00731.

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29

Setaro, Antonio, Alphonse Fiebor, Mohsen Adeli, and Stephanie Reich. "Novel Covalent Approaches to Control the Doping Level within Carbon Nanotubes." ECS Meeting Abstracts MA2020-01, no. 7 (May 1, 2020): 701. http://dx.doi.org/10.1149/ma2020-017701mtgabs.

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30

Pikabea, Aintzane, and Jacqueline Forcada. "Novel approaches for the preparation of magnetic nanogels via covalent bonding." Journal of Polymer Science Part A: Polymer Chemistry 55, no. 21 (August 3, 2017): 3573–86. http://dx.doi.org/10.1002/pola.28740.

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31

Martínez‐Abadía, Marta, and Aurelio Mateo‐Alonso. "Structural Approaches to Control Interlayer Interactions in 2D Covalent Organic Frameworks." Advanced Materials 32, no. 40 (August 30, 2020): 2002366. http://dx.doi.org/10.1002/adma.202002366.

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32

Jamshidiha, Mostafa, Thomas Lanyon-Hogg, Charlotte L. Sutherell, Gregory B. Craven, Montse Tersa, Elena De Vita, Delia Brustur, et al. "Identification of the first structurally validated covalent ligands of the small GTPase RAB27A." RSC Medicinal Chemistry 13, no. 2 (2022): 150–55. http://dx.doi.org/10.1039/d1md00225b.

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33

Bartkowski, Michał, and Silvia Giordani. "Supramolecular chemistry of carbon nano-onions." Nanoscale 12, no. 17 (2020): 9352–58. http://dx.doi.org/10.1039/d0nr01713b.

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34

Hoyas Pérez, Nadia, and James E. M. Lewis. "Synthetic strategies towards mechanically interlocked oligomers and polymers." Organic & Biomolecular Chemistry 18, no. 35 (2020): 6757–80. http://dx.doi.org/10.1039/d0ob01583k.

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35

Dzhardimalieva, Gulzhian I., Bal C. Yadav, Sarkyt E. Kudaibergenov, and Igor E. Uflyand. "Basic Approaches to the Design of Intrinsic Self-Healing Polymers for Triboelectric Nanogenerators." Polymers 12, no. 11 (November 4, 2020): 2594. http://dx.doi.org/10.3390/polym12112594.

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Triboelectric nanogenerators (TENGs) as a revolutionary system for harvesting mechanical energy have demonstrated high vitality and great advantage, which open up great prospects for their application in various areas of the society of the future. The past few years have seen exponential growth in many new classes of self-healing polymers (SHPs) for TENGs. This review presents and evaluates the SHP range for TENGs, and also attempts to assess the impact of modern polymer chemistry on the development of advanced materials for TENGs. Among the most widely used SHPs for TENGs, the analysis of non-covalent (hydrogen bond, metal–ligand bond), covalent (imine bond, disulfide bond, borate bond) and multiple bond-based SHPs in TENGs has been performed. Particular attention is paid to the use of SHPs with shape memory as components of TENGs. Finally, the problems and prospects for the development of SHPs for TENGs are outlined.

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36

Gorka, Alexander P., Roger R. Nani, and Martin J. Schnermann. "Cyanine polyene reactivity: scope and biomedical applications." Organic & Biomolecular Chemistry 13, no. 28 (2015): 7584–98. http://dx.doi.org/10.1039/c5ob00788g.

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37

Nicholls, Robert A., Robbie P. Joosten, Fei Long, Marcin Wojdyr, Andrey Lebedev, Eugene Krissinel, Lucrezia Catapano, Marcus Fischer, Paul Emsley, and Garib N. Murshudov. "Modelling covalent linkages in CCP4." Acta Crystallographica Section D Structural Biology 77, no. 6 (May 19, 2021): 712–26. http://dx.doi.org/10.1107/s2059798321001753.

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In this contribution, the current protocols for modelling covalent linkages within the CCP4 suite are considered. The mechanism used for modelling covalent linkages is reviewed: the use of dictionaries for describing changes to stereochemistry as a result of the covalent linkage and the application of link-annotation records to structural models to ensure the correct treatment of individual instances of covalent linkages. Previously, linkage descriptions were lacking in quality compared with those of contemporary component dictionaries. Consequently, AceDRG has been adapted for the generation of link dictionaries of the same quality as for individual components. The approach adopted by AceDRG for the generation of link dictionaries is outlined, which includes associated modifications to the linked components. A number of tools to facilitate the practical modelling of covalent linkages available within the CCP4 suite are described, including a new restraint-dictionary accumulator, the Make Covalent Link tool and AceDRG interface in Coot, the 3D graphical editor JLigand and the mechanisms for dealing with covalent linkages in the CCP4i2 and CCP4 Cloud environments. These integrated solutions streamline and ease the covalent-linkage modelling workflow, seamlessly transferring relevant information between programs. Current recommended practice is elucidated by means of instructive practical examples. By summarizing the different approaches to modelling linkages that are available within the CCP4 suite, limitations and potential pitfalls that may be encountered are highlighted in order to raise awareness, with the intention of improving the quality of future modelled covalent linkages in macromolecular complexes.

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38

Brogi, Simone, Roberta Ibba, Sara Rossi, Stefania Butini, Vincenzo Calderone, Sandra Gemma, and Giuseppe Campiani. "Covalent Reversible Inhibitors of Cysteine Proteases Containing the Nitrile Warhead: Recent Advancement in the Field of Viral and Parasitic Diseases." Molecules 27, no. 8 (April 15, 2022): 2561. http://dx.doi.org/10.3390/molecules27082561.

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In the field of drug discovery, the nitrile group is well represented among drugs and biologically active compounds. It can form both non-covalent and covalent interactions with diverse biological targets, and it is amenable as an electrophilic warhead for covalent inhibition. The main advantage of the nitrile group as a warhead is mainly due to its milder electrophilic character relative to other more reactive groups (e.g., -CHO), reducing the possibility of unwanted reactions that would hinder the development of safe drugs, coupled to the ease of installation through different synthetic approaches. The covalent inhibition is a well-assessed design approach for serine, threonine, and cysteine protease inhibitors. The mechanism of hydrolysis of these enzymes involves the formation of a covalent acyl intermediate, and this mechanism can be exploited by introducing electrophilic warheads in order to mimic this covalent intermediate. Due to the relevant role played by the cysteine protease in the survival and replication of infective agents, spanning from viruses to protozoan parasites, we will review the most relevant and recent examples of protease inhibitors presenting a nitrile group that have been introduced to form or to facilitate the formation of a covalent bond with the catalytic cysteine active site residue.

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39

Harris, Christopher M., Sage E. Foley, Eric R. Goedken, Mark Michalak, Sara Murdock, and Noel S. Wilson. "Merits and Pitfalls in the Characterization of Covalent Inhibitors of Bruton’s Tyrosine Kinase." SLAS DISCOVERY: Advancing the Science of Drug Discovery 23, no. 10 (July 10, 2018): 1040–50. http://dx.doi.org/10.1177/2472555218787445.

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In vitro analysis of covalent inhibitors requires special consideration, due to the time-dependent and typically irreversible nature of their target interaction. While many analyses are reported for the characterization of a final candidate, it is less clear which are most useful in the lead optimization phase of drug discovery. In the context of identifying covalent inhibitors of Bruton’s tyrosine kinase (BTK), we evaluated multiple techniques for characterizing covalent inhibitors. Several methods qualitatively support the covalent mechanism of action or support a particular aspect of interaction but were not otherwise informative to differentiate inhibitors. These include the time dependence of IC50, substrate competition, mass spectrometry, and recovery of function after inhibitor removal at the biochemical and cellular level. A change in IC50 upon mutation of the targeted BTK C481 nucleophile or upon removal of the electrophilic moiety of the inhibitor was not always a reliable indicator of covalent inhibition. Determination of kinact and KI provides a quantitative description of covalent interactions but was challenging at scale and frequently failed to provide more than the ratio of the two values, kinact/KI. Overall, a combination of approaches is required to assess time-dependent, covalent, and irreversible inhibitors in a manner suitable to reliably advance drug candidates.

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40

Ostrem, Jonathan M. L., and Kevan M. Shokat. "Targeting KRAS G12C with Covalent Inhibitors." Annual Review of Cancer Biology 6, no. 1 (April 11, 2022): 49–64. http://dx.doi.org/10.1146/annurev-cancerbio-041621-012549.

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KRAS is the most frequently mutated oncogene in cancer. Following numerous attempts to inhibit KRAS spanning multiple decades, recent efforts aimed at covalently targeting the mutant cysteine of KRAS G12C have yielded very encouraging results. Indeed, one such molecule, sotorasib, has already received accelerated US Food and Drug Administration approval with phase III clinical trials currently underway. A second molecule, adagrasib, has also progressed to phase III, and several others have entered early-phase clinical trials. The success of these efforts has inspired an array of novel approaches targeting KRAS, with some reporting extension to the two most common oncogenic KRAS mutations, G12V and G12D.

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Kumar, Sushil, Gergo Ignacz, and Gyorgy Szekely. "Synthesis of covalent organic frameworks using sustainable solvents and machine learning." Green Chemistry 23, no. 22 (2021): 8932–39. http://dx.doi.org/10.1039/d1gc02796d.

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Cui, Daling, Dmitrii F. Perepichka, Jennifer M. MacLeod, and Federico Rosei. "Surface-confined single-layer covalent organic frameworks: design, synthesis and application." Chemical Society Reviews 49, no. 7 (2020): 2020–38. http://dx.doi.org/10.1039/c9cs00456d.

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This review describes the state of the art of surface-confined single-layer covalent organic frameworks, focusing on reticular design, synthesis approaches, and exploring applications in host/guest chemistry.

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43

Wei, Ying, Yongxia Yan, Xiaoyan Li, Linghai Xie, and Wei Huang. "Covalent nanosynthesis of fluorene-based macrocycles and organic nanogrids." Organic & Biomolecular Chemistry 20, no. 1 (2022): 73–97. http://dx.doi.org/10.1039/d1ob01558c.

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This paper presents an overview of synthetic approaches for fluorene-based cyclic compounds by examining four different connection models of fluorenes, involving 2,7-, 3,6-, 9,9-, and 2,9-linked patterns.

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Marekha, Bogdan A., Oleg N. Kalugin, and Abdenacer Idrissi. "Non-covalent interactions in ionic liquid ion pairs and ion pair dimers: a quantum chemical calculation analysis." Physical Chemistry Chemical Physics 17, no. 26 (2015): 16846–57. http://dx.doi.org/10.1039/c5cp02197a.

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Plet, Benoît, Adéline Delcambre, Stéphane Chaignepain, and Jean-Marie Schmitter. "Affinity ranking of peptide–polyphenol non-covalent assemblies by mass spectrometry approaches." Tetrahedron 71, no. 20 (May 2015): 3007–11. http://dx.doi.org/10.1016/j.tet.2015.02.015.

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Voice, Angus, Gary Tresadern, Herman van Vlijmen, and Adrian Mulholland. "Limitations of Ligand-Only Approaches for Predicting the Reactivity of Covalent Inhibitors." Journal of Chemical Information and Modeling 59, no. 10 (September 9, 2019): 4220–27. http://dx.doi.org/10.1021/acs.jcim.9b00404.

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Zhu, Congzhi, Alexander J. Kalin, and Lei Fang. "Covalent and Noncovalent Approaches to Rigid Coplanar π-Conjugated Molecules and Macromolecules." Accounts of Chemical Research 52, no. 4 (April 3, 2019): 1089–100. http://dx.doi.org/10.1021/acs.accounts.9b00022.

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Chen, Xinyi, Keyu Geng, Ruoyang Liu, Ke Tian Tan, Yifan Gong, Zhongping Li, Shanshan Tao, Qiuhong Jiang, and Donglin Jiang. "Covalent Organic Frameworks: Chemical Approaches to Designer Structures and Built‐In Functions." Angewandte Chemie International Edition 59, no. 13 (March 23, 2020): 5050–91. http://dx.doi.org/10.1002/anie.201904291.

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McAulay, Kirsten, Alan Bilsland, and Marta Bon. "Reactivity of Covalent Fragments and Their Role in Fragment Based Drug Discovery." Pharmaceuticals 15, no. 11 (November 8, 2022): 1366. http://dx.doi.org/10.3390/ph15111366.

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Fragment based drug discovery has long been used for the identification of new ligands and interest in targeted covalent inhibitors has continued to grow in recent years, with high profile drugs such as osimertinib and sotorasib gaining FDA approval. It is therefore unsurprising that covalent fragment-based approaches have become popular and have recently led to the identification of novel targets and binding sites, as well as ligands for targets previously thought to be ‘undruggable’. Understanding the properties of such covalent fragments is important, and characterizing and/or predicting reactivity can be highly useful. This review aims to discuss the requirements for an electrophilic fragment library and the importance of differing warhead reactivity. Successful case studies from the world of drug discovery are then be examined.

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González-Sálamo, Javier, Gabriel Jiménez-Skrzypek, Cecilia Ortega-Zamora, Miguel Ángel González-Curbelo, and Javier Hernández-Borges. "Covalent Organic Frameworks in Sample Preparation." Molecules 25, no. 14 (July 20, 2020): 3288. http://dx.doi.org/10.3390/molecules25143288.

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Covalent organic frameworks (COFs) can be classified as emerging porous crystalline polymers with extremely high porosity and surface area size, and good thermal stability. These properties have awakened the interests of many areas, opening new horizons of research and applications. In the Analytical Chemistry field, COFs have found an important application in sample preparation approaches since their inherent properties clearly match, in a good number of cases, with the ideal characteristics of any extraction or clean-up sorbent. The review article is meant to provide a detailed overview of the different COFs that have been used up to now for sample preparation (i.e., solid-phase extraction in its most relevant operational modes—conventional, dispersive, magnetic/solid-phase microextraction and stir-bar sorptive extraction); the extraction devices/formats in which they have been applied; and their performances and suitability for this task.

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