@article{WeiserCuiDewhurstetal.2023,
  author    = {Weiser, Jonas and Cui, Jingjing and Dewhurst, Rian D. and Braunschweig, Holger and Engels, Bernd and Fantuzzi, Felipe},
  title     = {Structure and bonding of proximity-enforced main-group dimers stabilized by a rigid naphthyridine diimine ligand},
  series = {Journal of Computational Chemistry},
  volume    = {44},
  journal   = {Journal of Computational Chemistry},
  number    = {3},
  doi       = {10.1002/jcc.26994},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-312586},
  pages     = {456 -- 467},
  year      = {2023},
  abstract  = {The development of ligands capable of effectively stabilizing highly reactive main-group species has led to the experimental realization of a variety of systems with fascinating properties. In this work, we computationally investigate the electronic, structural, energetic, and bonding features of proximity-enforced group 13-15 homodimers stabilized by a rigid expanded pincer ligand based on the 1,8-naphthyridine (napy) core. We show that the redox-active naphthyridine diimine (NDI) ligand enables a wide variety of structural motifs and element-element interaction modes, the latter ranging from isolated, element-centered lone pairs (e.g., E = Si, Ge) to cases where through-space π bonds (E = Pb), element-element multiple bonds (E = P, As) and biradical ground states (E = N) are observed. Our results hint at the feasibility of NDI-E2 species as viable synthetic targets, highlighting the versatility and potential applications of napy-based ligands in main-group chemistry.},
  language  = {en}
}
@article{WelkerKerstenMuelleretal.2021,
  author    = {Welker, Armin and Kersten, Christian and M{\"u}ller, Christin and Madhugiri, Ramakanth and Zimmer, Collin and M{\"u}ller, Patrick and Zimmermann, Robert and Hammerschmidt, Stefan and Maus, Hannah and Ziebuhr, John and Sotriffer, Christoph and Schirmeister, Tanja},
  title     = {Structure-Activity Relationships of Benzamides and Isoindolines Designed as SARS-CoV Protease Inhibitors Effective against SARS-CoV-2},
  series = {ChemMedChem},
  volume    = {16},
  journal   = {ChemMedChem},
  number    = {2},
  doi       = {10.1002/cmdc.202000548},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-225700},
  pages     = {340 -- 354},
  year      = {2021},
  abstract  = {Inhibition of coronavirus (CoV)-encoded papain-like cysteine proteases (PL\(^{pro}\)) represents an attractive strategy to treat infections by these important human pathogens. Herein we report on structure-activity relationships (SAR) of the noncovalent active-site directed inhibitor (R)-5-amino-2-methyl-N-(1-(naphthalen-1-yl)ethyl) benzamide (2 b), which is known to bind into the S3 and S4 pockets of the SARS-CoV PL\(^{pro}\). Moreover, we report the discovery of isoindolines as a new class of potent PL\(^{pro}\) inhibitors. The studies also provide a deeper understanding of the binding modes of this inhibitor class. Importantly, the inhibitors were also confirmed to inhibit SARS-CoV-2 replication in cell culture suggesting that, due to the high structural similarities of the target proteases, inhibitors identified against SARS-CoV PL\(^{pro}\) are valuable starting points for the development of new pan-coronaviral inhibitors.},
  language  = {en}
}
@article{LindlGuoKrummenacheretal.2021,
  author    = {Lindl, Felix and Guo, Xueying and Krummenacher, Ivo and Rauch, Florian and Rempel, Anna and Paprocki, Valerie and Dellermann, Theresa and Stennett, Tom E. and Lamprecht, Anna and Br{\"u}ckner, Tobias and Radacki, Krzysztof and B{\´e}langer-Chabot, Guillaume and Marder, Todd B. and Lin, Zhenyang and Braunschweig, Holger},
  title     = {Rethinking Borole Cycloaddition Reactivity},
  series = {Chemistry—A European Journal},
  volume    = {27},
  journal   = {Chemistry—A European Journal},
  number    = {43},
  doi       = {10.1002/chem.202101290},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-256888},
  pages     = {11226-11233},
  year      = {2021},
  abstract  = {Boroles are attracting broad interest for their myriad and diverse applications, including in synthesis, small molecule activation and functional materials. Their properties and reactivity are closely linked to the cyclic conjugated diene system, which has been shown to participate in cycloaddition reactions, such as the Diels-Alder reaction with alkynes. The reaction steps leading to boranorbornadienes, borepins and tricyclic boracyclohexenes from the thermal reaction of boroles with alkynes are seemingly well understood as judged from the literature. Herein, we question the long-established mechanistic picture of pericyclic rearrangements by demonstrating that seven-membered borepins (i. e., heptaphenylborepin and two derivatives substituted with a thienyl and chloride substituent on boron) exist in a dynamic equilibrium with the corresponding bicyclic boranorbornadienes, the direct Diels-Alder products, but are not isolable products from the reactions. Heating gradually converts the isomeric mixtures into fluorescent tricyclic boracyclohexenes, the most stable isomers in the series. Results from mechanistic DFT calculations reveal that the tricyclic compounds derive from the boranorbornadienes and not the borepins, which were previously believed to be intermediates in purely pericyclic processes.},
  language  = {en}
}
@phdthesis{Paasche2013,
  author    = {Paasche, Alexander},
  title     = {Mechanistic Insights into SARS Coronavirus Main Protease by Computational Chemistry Methods},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-79029},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2013},
  abstract  = {The SARS virus is the etiological agent of the severe acute respiratory syndrome, a deadly disease that caused more than 700 causalities in 2003. One of its viral proteins, the SARS coronavirus main protease, is considered as a potential drug target and represents an important model system for other coronaviruses. Despite extensive knowledge about this enzyme, it still lacks an effective anti-viral drug. Furthermore, it possesses some unusual features related to its active-site region. This work gives atomistic insights into the SARS coronavirus main protease and tries to reveal mechanistic aspects that control catalysis and inhibition. Thereby, it applies state-of-the-art computational methods to develop models for this enzyme that are capable to reproduce and interpreting the experimental observations. The theoretical investigations are elaborated over four main fields that assess the accuracy of the used methods, and employ them to understand the function of the active-site region, the inhibition mechanism, and the ligand binding. The testing of different quantum chemical methods reveals that their performance depends partly on the employed model. This can be a gas phase description, a continuum solvent model, or a hybrid QM/MM approach. The latter represents the preferred method for the atomistic modeling of biochemical reactions. A benchmarking uncovers some serious problems for semi-empirical methods when applied in proton transfer reactions. To understand substrate cleavage and inhibition of SARS coronavirus main protease, proton transfer reactions between the Cys/His catalytic dyad are calculated. Results show that the switching between neutral and zwitterionic state plays a central role for both mechanisms. It is demonstrated that this electrostatic trigger is remarkably influenced by substrate binding. Whereas the occupation of the active-site by the substrate leads to a fostered zwitterion formation, the inhibitor binding does not mimic this effect for the employed example. The underlying reason is related to the coverage of the active-site by the ligand, which gives new implications for rational improvements of inhibitors. More detailed insights into reversible and irreversible inhibition are derived from in silico screenings for the class of Michael acceptors that follow a conjugated addition reaction. From the comparison of several substitution patterns it becomes obvious that different inhibitor warheads follow different mechanisms. Nevertheless, the initial formation of a zwitterionic catalytic dyad is found as a common precondition for all inhibition reactions. Finally, non-covalent inhibitor binding is investigated for the case of SARS coranavirus main protease in complex with the inhibitor TS174. A novel workflow is developed that includes an interplay between theory and experiment in terms of molecular dynamic simulation, tabu search, and X-ray structure refinement. The results show that inhibitor binding is possible for multiple poses and stereoisomers of TS174.},
  subject      = {SARS},
  language  = {en}
}