How modern enzymes evolved as complex catalytic machineries to facilitate diverse chemical transformations is an open question for the emerging field of systems chemistry. Inspired by Nature's ingenuity in creating complex catalytic structures for exotic functions, short peptide-based cross β amyloid sequences have been shown to access intricate binding surfaces demonstrating the traits of extant enzymes and proteins. Based on their catalytic proficiencies reported recently, these amyloid assemblies have been argued as the earliest protein folds. Herein, we map out the recent progress made by our laboratory and other research groups that demonstrate the catalytic diversity of cross β amyloid assemblies. The important role of morphology and specific mutations in peptide sequences has been underpinned in this review. We have divided the feature article into different sections where examples from biology have been covered demonstrating the mechanism of extant biocatalysts and compared with recent works on cross β amyloid folds showing covalent catalysis, aldolase, hydrolase, peroxidase-like activities and complex cascade catalysis. Beyond equilibrium, we have extended our discussion towards transient catalytic amyloid phases mimicking the energy driven cytoskeleton polymerization. Finally, a future outlook has been provided on the way ahead for short peptide-based systems chemistry approaches that can lead to the development of robust catalytic networks with improved enzyme-like proficiencies and higher complexities. The discussed examples along with the rationale behind selecting specific amino acids sequence will benefit readers to design systems for achieving catalytic reactivity similar to natural complex enzymes.Structural data on the SARS-CoV-2 main protease in complex with a zinc-containing organic inhibitor are already present in the literature and gave hints on the presence of a zinc binding site involving the catalytically relevant cysteine and histidine residues. https://www.selleckchem.com/Bcl-2.html In this paper, the structural basis of ionic zinc binding to the SARS-CoV-2 main protease has been elucidated by X-ray crystallography. The zinc binding affinity and its ability to inhibit the SARS-CoV-2 main protease have been investigated. These findings provide solid ground for the design of potent and selective metal-conjugated inhibitors of the SARS-CoV-2 main protease.Relativistic quantum chemical calculations are performed based on one of two physical pictures, namely the Dirac picture and the Schrödinger picture. With regard to the latter, the so-called picture-change effect (PCE) and picture-change correction (PCC) have been studied. The PCE, which is the change in the expectation value associated with the transformation, is not commonly a minor effect. The electron density, which is given by the expectation value of the density operator, is a fundamental variable in relativistic density functional theory (RDFT). Thus, performing the PCC in RDFT calculations is essential not only in terms of numerical agreement with the Dirac picture, but also from the viewpoint of fundamental theory. This paper explains theories and numerical studies of PCE and PCC in RDFT after overviewing those in properties, which involves the authors' works on the development of RDFT in the Schrödinger picture and relativistic exchange-correlation functionals based on picture-change-corrected variables.A series of novel bis-acenaphthoquinone diimides featuring a highly electron-deficient bis-acenaphthoquinone core are facilely synthesized via Knoevenagel condensation reaction. The diimides show high electron deficiency and good coplanar conformation, together with one of them having a maximum electron mobility up to 0.038 cm2 V-1 s-1.The waveguide layer of diffraction-based leaky waveguides (LWs) must be made of materials that have low refractive index, are permeable to analytes, can be deposited by spin coating, and can be functionalised and crosslinked. These requirements are fulfilled by thin films of chitosan hydrogels. In this work, we studied the reproducibility of diffraction-based LWs with chitosan waveguides. The average refractive index sensitivity (RIS) and RI limit of detection (LOD) of the eight devices investigated herein were 125.5 ± 3.8 deg RIU-1 and 1.9 × 10-6 ± 1.3 × 10-6 RIU, respectively. While several challenges associated with the realisation of reproducible chitosan LWs have been addressed, reducing the variations in RI LOD requires improving the adhesion of chitosan films to glass substrates, minimising bubbles trapped in microfluidic channels, and using pumps with minimal pulsations. We showed that the buffer baseline of LWs with unmodified chitosan before and after introducing 750 μM bovine serum albumin (BSA), which is equal to the physiological levels of serum albumin, was different by 3.6%. Nevertheless, using biotin, anti-biotin antibody and BSA as exemplar recognition element, analyte and interferent, respectively, we demonstrated that diffraction-based chitosan LWs were suitable for monitoring analyte-RE binding in the presence of 750 μM BSA.Complexes trans,trans,trans-[Pt(N3)2(OH)(OCOR)(py)2] where py = pyridine and where OCOR = succinate (1); 4-oxo-4-propoxybutanoate (2) and N-methylisatoate (3) have been synthesized by derivation of trans,trans,trans-[Pt(OH)2(N3)2(py)2] (4) and characterised by NMR and EPR spectroscopy, ESI-MS and X-ray crystallography. Irradiation of 1-3 with green (517 nm) light initiated photoreduction to Pt(ii) and release of the axial ligands at a 3-fold faster rate than for 4. TD-DFT calculations showed dissociative transitions at longer wavelengths for 1 compared to 4. Complexes 1 and 2 showed greater photocytotoxicity than 4 when irradiated with 420 nm light (A2780 cell line IC50 values 2.7 and 3.7 μM) and complex 2 was particularly active towards the cisplatin-resistant cell line A2780cis (IC50 3.7 μM). Unlike 4, complexes 1-3 were phototoxic under green light irradiation (517 nm), with minimal toxicity in the dark. A pKa(H2O) of 5.13 for the free carboxylate group was determined for 1, corresponding to an overall negative charge during biological experiments, which crucially, did not appear to impede cellular accumulation and photocytotoxicity.
How modern enzymes evolved as complex catalytic machineries to facilitate diverse chemical transformations is an open question for the emerging field of systems chemistry. Inspired by Nature's ingenuity in creating complex catalytic structures for exotic functions, short peptide-based cross β amyloid sequences have been shown to access intricate binding surfaces demonstrating the traits of extant enzymes and proteins. Based on their catalytic proficiencies reported recently, these amyloid assemblies have been argued as the earliest protein folds. Herein, we map out the recent progress made by our laboratory and other research groups that demonstrate the catalytic diversity of cross β amyloid assemblies. The important role of morphology and specific mutations in peptide sequences has been underpinned in this review. We have divided the feature article into different sections where examples from biology have been covered demonstrating the mechanism of extant biocatalysts and compared with recent works on cross β amyloid folds showing covalent catalysis, aldolase, hydrolase, peroxidase-like activities and complex cascade catalysis. Beyond equilibrium, we have extended our discussion towards transient catalytic amyloid phases mimicking the energy driven cytoskeleton polymerization. Finally, a future outlook has been provided on the way ahead for short peptide-based systems chemistry approaches that can lead to the development of robust catalytic networks with improved enzyme-like proficiencies and higher complexities. The discussed examples along with the rationale behind selecting specific amino acids sequence will benefit readers to design systems for achieving catalytic reactivity similar to natural complex enzymes.Structural data on the SARS-CoV-2 main protease in complex with a zinc-containing organic inhibitor are already present in the literature and gave hints on the presence of a zinc binding site involving the catalytically relevant cysteine and histidine residues. https://www.selleckchem.com/Bcl-2.html In this paper, the structural basis of ionic zinc binding to the SARS-CoV-2 main protease has been elucidated by X-ray crystallography. The zinc binding affinity and its ability to inhibit the SARS-CoV-2 main protease have been investigated. These findings provide solid ground for the design of potent and selective metal-conjugated inhibitors of the SARS-CoV-2 main protease.Relativistic quantum chemical calculations are performed based on one of two physical pictures, namely the Dirac picture and the Schrödinger picture. With regard to the latter, the so-called picture-change effect (PCE) and picture-change correction (PCC) have been studied. The PCE, which is the change in the expectation value associated with the transformation, is not commonly a minor effect. The electron density, which is given by the expectation value of the density operator, is a fundamental variable in relativistic density functional theory (RDFT). Thus, performing the PCC in RDFT calculations is essential not only in terms of numerical agreement with the Dirac picture, but also from the viewpoint of fundamental theory. This paper explains theories and numerical studies of PCE and PCC in RDFT after overviewing those in properties, which involves the authors' works on the development of RDFT in the Schrödinger picture and relativistic exchange-correlation functionals based on picture-change-corrected variables.A series of novel bis-acenaphthoquinone diimides featuring a highly electron-deficient bis-acenaphthoquinone core are facilely synthesized via Knoevenagel condensation reaction. The diimides show high electron deficiency and good coplanar conformation, together with one of them having a maximum electron mobility up to 0.038 cm2 V-1 s-1.The waveguide layer of diffraction-based leaky waveguides (LWs) must be made of materials that have low refractive index, are permeable to analytes, can be deposited by spin coating, and can be functionalised and crosslinked. These requirements are fulfilled by thin films of chitosan hydrogels. In this work, we studied the reproducibility of diffraction-based LWs with chitosan waveguides. The average refractive index sensitivity (RIS) and RI limit of detection (LOD) of the eight devices investigated herein were 125.5 ± 3.8 deg RIU-1 and 1.9 × 10-6 ± 1.3 × 10-6 RIU, respectively. While several challenges associated with the realisation of reproducible chitosan LWs have been addressed, reducing the variations in RI LOD requires improving the adhesion of chitosan films to glass substrates, minimising bubbles trapped in microfluidic channels, and using pumps with minimal pulsations. We showed that the buffer baseline of LWs with unmodified chitosan before and after introducing 750 μM bovine serum albumin (BSA), which is equal to the physiological levels of serum albumin, was different by 3.6%. Nevertheless, using biotin, anti-biotin antibody and BSA as exemplar recognition element, analyte and interferent, respectively, we demonstrated that diffraction-based chitosan LWs were suitable for monitoring analyte-RE binding in the presence of 750 μM BSA.Complexes trans,trans,trans-[Pt(N3)2(OH)(OCOR)(py)2] where py = pyridine and where OCOR = succinate (1); 4-oxo-4-propoxybutanoate (2) and N-methylisatoate (3) have been synthesized by derivation of trans,trans,trans-[Pt(OH)2(N3)2(py)2] (4) and characterised by NMR and EPR spectroscopy, ESI-MS and X-ray crystallography. Irradiation of 1-3 with green (517 nm) light initiated photoreduction to Pt(ii) and release of the axial ligands at a 3-fold faster rate than for 4. TD-DFT calculations showed dissociative transitions at longer wavelengths for 1 compared to 4. Complexes 1 and 2 showed greater photocytotoxicity than 4 when irradiated with 420 nm light (A2780 cell line IC50 values 2.7 and 3.7 μM) and complex 2 was particularly active towards the cisplatin-resistant cell line A2780cis (IC50 3.7 μM). Unlike 4, complexes 1-3 were phototoxic under green light irradiation (517 nm), with minimal toxicity in the dark. A pKa(H2O) of 5.13 for the free carboxylate group was determined for 1, corresponding to an overall negative charge during biological experiments, which crucially, did not appear to impede cellular accumulation and photocytotoxicity.
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