De novo peptide design is a rapidly evolving field with significant promise for applications in both biological and biomedical sectors. Traditional peptide design methods often rely on sequence homology, which is limited to evolutionarily related proteins and fails to incorporate the key physicochemical factors necessary for proper protein folding. Generative machine learning models offer a unique opportunity to create novel peptide sequences that are inspired by existing data but are not constrained by evolutionary limitations. In this study, we developed a custom generative adversarial network (GAN) designed specifically to generate peptide sequences capable of folding into β-hairpin secondary structures. This model is built on the principles of physicochemical properties, such as hydrophobicity and residue volume, and utilizes sequence data from known structures in the PDB to guide its design process. The β-GAN model demonstrated a remarkable ability to differentiate β-hairpin structures from α-helices and disordered peptides, achieving an accuracy rate of up to 96%. Furthermore, the model produced β-hairpin peptide sequences with sequence identities as low as 31% compared to the current PDB and 50% compared to non-redundant databases. These results highlight the potential of machine learning-based generative models to push the boundaries of peptide design, creating novel sequences and structures that transcend evolutionary constraints and offer exciting new possibilities in the field.

Purpose This study aims to describe the design and synthesis of two novel azo and imine chromophores-based dyes derived from two different aldehydes with intramolecular colour matching that are pH sensitive. Design/methodology/approach The visible absorption wavelength (λ max ) was extended when azo chromophore was included in imine-based systems. The dyed patterns created sophisticated colour-changing paper packaging sensors with pH-sensitive chromophores using alum as a mediator or mordant. Due to the tight adhesive bonding, the dyes on paper’s cellulose fibres could not be removed by ordinary water even at extremely high or low pH, which was confirmed by scanning electron microscopy analysis. The dyed patterns demonstrated an evident, sensitive and fast colour-changing mechanism with varying pH, from pale yellow to red for Dye-I and from pale yellow to brown-violet for Dye-II. Findings The λ max for colour changing was recorded from 400 to 490 nm for Dye-I, whereas from 400 to 520 for Dye-II. The freshness judgement of food was checked using actual experiments with cooked crab spoilage, where the cooked crab was incubated at 37 o C for 6 h to see the noticeable colour change from yellow to brown-violet with Dye-II. The colour-changing mechanism was studied with Fourier transform infrared (FTIR) spectra at different pH, and thin layer chromatography, nuclear magnetic resonance and FTIR spectroscopy studied the desired structure formation of the dyes. Potential uses for smart packaging sensors include quickly detecting food freshness during transportation or right before consumption. Originality/value 1. Two novel azo-imine dyes have been synthesized with a pH-responsive effect. 2. The pH-responsive mechanism was studied. 3. The study was supported by computational chemistry using density functional theory. 4. The obtained dyes were used to make pH-responsive sensors for seafood packaging to judge the freshness.

In patients with von-Hippel Lindau (VHL) disease, hypoxia-independent accumulation of HIF-2α leads to increased transcriptional activity of HIF-2α:ARNT that drives cancers such as renal cell carcinoma. Belzutifan, a recently FDA-approved drug, is designed to prevent the transcriptional activity of HIF-2α:ARNT, thereby overcoming the consequences of its unnatural accumulation in VHL-dependent cancers. Emerging evidence suggests that the naturally occurring variant G323E located in the HIF-2α drug binding pocket prevents inhibitory activity of belzutifan analogs, though the mechanism of inhibition remains unclear. Interestingly, proximal phosphorylation at neighboring T324, previously shown to regulate HIF-2 protein interactions, has also been proposed to affect HIF-2 drug binding. Here, we used molecular dynamics (MD) simulations to understand and compare the molecular-level effects of G323E and phospho-T324 (pT324) on the belzutifan bound-HIF-2α:ARNT complex. We find that both G323E and pT324 increase structural flexibility within the drug binding site and reduce the apparent binding affinity for belzutifan. Whereas the effects of G323E are concentrated in the binding pocket Fα helix within the HIF-2α PAS-B domain, pT324 decreased the belzutifan binding affinity and stabilized the HIF-2 heterodimer through an alternate mechanism involving polar interactions between the HIF-2α PAS-B and PAS-A domains. Further analysis via ensemble machine learning uncovered important and distinct interchain residue interactions modified by G323E and pT324. These findings reveal a molecular mechanism of G323E-induced drug resistance and suggest that pT324 may also affect the efficacy of HIF-2 drug binding interactions via allosteric effects.

De novo peptide design is a new frontier that has broad application potential in the biological and biomedical fields. Most existing models for de novo peptide design are largely based on sequence homology that can be restricted based on evolutionarily derived protein sequences and lack the physicochemical context essential in protein folding. Generative machine learning for de novo peptide design is a promising way to synthesize theoretical data that are based on, but unique from, the observable universe. In this study, we created and tested a custom peptide generative adversarial network intended to design peptide sequences that can fold into the β-hairpin secondary structure. This deep neural network model is designed to establish a preliminary foundation of the generative approach based on physicochemical and conformational properties of 20 canonical amino acids, for example, hydrophobicity and residue volume, using extant structure-specific sequence data from the PDB. The beta generative adversarial network model robustly distinguishes secondary structures of β hairpin from α helix and intrinsically disordered peptides with an accuracy of up to 96% and generates artificial β-hairpin peptide sequences with minimum sequence identities around 31% and 50% when compared against the current NCBI PDB and nonredundant databases, respectively. These results highlight the potential of generative models specifically anchored by physicochemical and conformational property features of amino acids to expand the sequence-to-structure landscape of proteins beyond evolutionary limits.

Oxyluciferin, which is the light emitter for firefly bioluminescence, has been subjected to extensive chemical modifications to tune its emission wavelength and quantum yield. However, the exact mechanisms for various electron-donating and withdrawing groups to perturb the photophysical properties of oxyluciferin analogs are still not fully understood. To elucidate the substituent effects on the fluorescence wavelength of oxyluciferin analogs, we applied the absolutely localized molecular orbitals (ALMO)-based frontier orbital analysis to assess various types of interactions (i.e. permanent electrostatics/exchange repulsion, polarization, occupied-occupied orbital mixing, virtual-virtual orbital mixing, and charge-transfer) between the oxyluciferin and substituent orbitals. We suggested two distinct mechanisms that can lead to red-shifted oxyluciferin emission wavelength, a design objective that can help increase the tissue penetration of bioluminescence emission. Within the first mechanism, an electron-donating group (such as an amino or dimethylamino group) can contribute its highest occupied molecular orbital (HOMO) to an out-of-phase combination with oxyluciferin's HOMO, thus raising the HOMO energy of the substituted analog and narrowing its HOMO-LUMO gap. Alternatively, an electron-withdrawing group (such as a nitro or cyano group) can participate in an in-phase virtual-virtual orbital mixing of fragment LUMOs, thus lowering the LUMO energy of the substituted analog. Such an ALMO-based frontier orbital analysis is expected to lead to intuitive principles for designing analogs of not only the oxyluciferin molecule, but also many other functional dyes.

We propose a simple procedure for visualizing the electron density changes (EDC) during a chemical reaction, which is based on a mapping of rectangular grid points for a stationary structure into (distorted) positions around atoms of another stationary structure. Specifically, during a small step along the minimum energy pathway (MEP), the displacement of each grid point is obtained as a linear combination of the motion of all atoms, with the contribution from each atom scaled by the corresponding Hirshfeld weight. For several reactions (identity SN2, Claisen rearrangement, Diels-Alder reaction, [3+2] cycloaddition, and phenylethyl mercaptan attack on pericosine A), our EDC plots showed an expected reduction of electron densities around severed bonds (or those with the bond-order lowered), with the opposite observed for newly-formed or enhanced chemical bonds. The EDC plots were also shown for copper triflate catalyzed N2O fragmentation, where the N–O bond weakening initially occurred on a singlet surface, but continued on a triplet surface after reaching the minimum-energy crossing point (MECP) between the two potential energy surfaces.

Design of novel luciferin substrates as near-infrared bioluminescence probes to improve deep-tissue imaging is an active field of research. Several effective analogs of oxyluciferin, such as AkaLumine (bioluminescence wavelength = 677nm), cyclic alkylamino luciferin (CycLuc1) (bioluminescence wavelength = 604 nm) have indeed resulted in longer bioluminescence wavelengths as compared to standard D-luciferin (bioluminescence wavelength = 562nm). Additionally, lower substrate concentration, bioavailability of substrate in the protein binding pocket and higher quantum yield of bioluminescence are also important criterions for the design of ideal luciferin substrate. In order to investigate the effect of substitutions on the oxyluciferin, we have designed a series of luciferin substrates with various functional groups on both 6-hydroxy-benzothiazole and 4(5H)-thiazolone heterocyclic rings. Through performing TDDFT calculations in both gas phase and condensed-phase (using implicit solvent model), we identified several promising combinations of electron donating groups and electron withdrawing groups, as emitted light from these analogs is predicted to be significantly red-shifted compared to standard oxyluciferin. In order to explain shifts in the computed emission wavelengths of oxyluciferin analogs, energy decomposition analysis was performed to study the interaction between molecular orbitals from both oxyluciferin and substituents. In order to design effective bioluminescent probes, effect of microenvironment will be considered along with substrate modifications. QM/MM calculations on luciferin analogs and various mutant luciferase systems can provide useful insights to explain substrate-protein interactions responsible for modulation of bioluminescence wavelength. Herein, we also report relative binding free energies of newly designed luciferin analogs with native firefly luciferase.

In recent years, a series of curcumin analogs have been designed as fluorescent probes for detecting and imaging $${\text {A}}\beta$$ peptide aggregates and reactive oxygen species (ROS) in Alzheimer's disease (AD) brains. In order to gain a better understanding of the photophysical properties of these probe molecules, a systematical computational investigation was performed using the time-dependent density functional theory (TDDFT) calculations. Computed absorption and emission wavelengths well reproduced the spectral shifts among the curcumin analogs. In particular, for a recently proposed pair of probe molecules, CRANAD-5 and CRANAD-61, for sensing ROS in preclinical studies of AD brains, their emission wavelength difference was found to arise from a delocalization of the lowest unoccupied molecular orbital of CRANAD-61 from the curcuminoid backbone to the oxalate moiety. Overall, this study reaffirms the value of employing TDDFT calculations to assist the design of new curcumin-based fluorescence probes for AD research.

•Solvent free, efficient, rapid and environmentally benign Kabachnik-Fields reaction.•High yields, short reaction time and simple work-up procedure.•Recyclable catalyst with no significant loss in activity.•Method tolerates a variety of functional groups with wide substrate scope.