Viroporins of Mpox Virus.

Mpox or monkeypox virus (MPXV) belongs to the subclass of Poxviridae and has emerged recently as a global threat. With a limited number of anti-viral drugs available for this new virus species, it is challenging to thwart the illness it begets. Therefore, characterizing new drug targets in the virus may prove advantageous to curbing the disease. Since channels as a family are excellent drug targets, we have sought to identify viral ion channels for this virus, which are instrumental in formulating channel-blocking anti-viral drugs. Bioinformatics analyses yielded eight transmembranous proteins smaller or equal to 100 amino acids in length. Subsequently, three independent bacteria-based assays have pointed to five of the eight proteins that exhibit ion channel activity. Finally, we propose a tentative structure of four ion channels from their primary amino acid sequences, employing AlphaFold2 and molecular dynamic simulation methods. These results may represent the first steps in characterizing MPXV viroporins en route to developing blockers that inhibit their function.

Primitive selection of the fittest emerging through functional synergy in nucleopeptide networks.

Many fundamental cellular and viral functions, including replication and translation, involve complex ensembles hosting synergistic activity between nucleic acids and proteins/peptides. There is ample evidence indicating that the chemical precursors of both nucleic acids and peptides could be efficiently formed in the prebiotic environment. Yet, studies on nonenzymatic replication, a central mechanism driving early chemical evolution, have focused largely on the activity of each class of these molecules separately. We show here that short nucleopeptide chimeras can replicate through autocatalytic and cross-catalytic processes, governed synergistically by the hybridization of the nucleobase motifs and the assembly propensity of the peptide segments. Unequal assembly-dependent replication induces clear selectivity toward the formation of a certain species within small networks of complementary nucleopeptides. The selectivity pattern may be influenced and indeed maximized to the point of almost extinction of the weakest replicator when the system is studied far from equilibrium and manipulated through changes in the physical (flow) and chemical (template and inhibition) conditions. We postulate that similar processes may have led to the emergence of the first functional nucleic-acid-peptide assemblies prior to the origin of life. Furthermore, spontaneous formation of related replicating complexes could potentially mark the initiation point for information transfer and rapid progression in complexity within primitive environments, which would have facilitated the development of a variety of functions found in extant biological assemblies.

Signaling in Systems Chemistry: Programing Gold Nanoparticles Formation and Assembly Using a Dynamic Bistable Network.

Living cells exploit bistable and oscillatory behaviors as memory mechanisms, facilitating the integration of transient stimuli into sustained molecular responses that control downstream functions. Synthetic bistable networks have also been studied as memory entities, but have rarely been utilized to control orthogonal functions in coupled dynamic systems. We herein present a new cascade pathway, for which we have exploited a well-characterized switchable peptide-based replicating network, operating far from equilibrium, that yields two alternative steady-state outputs, which in turn serve as the input signals for consecutive processes that regulate various features of Au nanoparticle shape and assembly. This study further sheds light on how bridging together the fields of systems chemistry and nanotechnology may open up new opportunities for the dynamically controlled design of functional materials.

A Self-Assembled Peptide-Appended Naphthalene Diimide: A Fluorescent Switch for Sensing Acid and Base Vapors.

A histidine-containing bola-amphiphilic molecule (NDIP) containing a peptide-appended naphthalenediimide (NDI) forms fluorescent hydrogels in phosphate buffer and organogels with benzenoid solvents. These gels were characterized by several spectroscopic and microscopic techniques including FT-IR, HR-TEM, powder X-ray diffraction and small-angle X-ray scattering, UV-Vis and fluorescence studies. The gelator molecule exhibits no significant fluorescence in the xerogel state, while it shows a significant fluorescence (bright cyan) in the presence of volatile organic/inorganic acid vapors; this cyan color vanishes in presence of base (ammonia vapors). A reusable paper-strip-based method based on this self-assembled fluorescent material can be used to easily detect hazardous volatile acid and base vapors with the naked eye.

Self-Assembling Peptide-Based Hydrogel: Regulation of Mechanical Stiffness and Thermal Stability and 3D Cell Culture of Fibroblasts.

A histidine-containing peptide-based amphiphile (P1) forms a transparent hydrogel within a pH range of 5.5 to 8.5 in phosphate buffer solution. Interestingly, thermal stability and mechanical stiffness are modulated by incorporating different types of dicarboxylic acids into the hydrogels. Inclusion of succinic acid with the molar ratio 2:1 (peptide:dicarboxylic acid) yields improved properties compared to the other tested dicarboxylic acids such as oxalic, glutaric and octanedioic acids. Transmission electron microscopic (TEM) images show the assembly of nanospheres is responsible for the hydrogel obtained from the assembly of native peptide. However, a morphological transformation takes place from nanosphere to nanofibers, when the peptide gels with succinic acid. XRD and FT-IR studies reveal interactions between peptide amphiphiles and the acids are responsible for the formation of a two-component hydrogel. Gel stiffness is enhanced considerably upon the addition of succinic acid to P1 with a 1:2 molar ratio. The two-component gel consisting of peptide and succinic acid has been successfully used for three-dimensional cell culture using mouse fibroblast cell line (NIH-3T3). This indicates future promise for the application of such peptide-based gels as tunable biomaterials in cell culture and regenerative medicine.

Amino-Acid-Based Metallo-Hydrogel That Acts Like an Esterase.

A histidine-based amphiphile containing a C14 fatty acyl chain, N- histidyl N'-myristry ethyl amine (AM1, 14.7 mM) forms hydrogels in the presence of Fe3+ (within the range 1.47 to 4.41 mM) and Hg2+ (within the range 3.67 to 11.02 mM) ions in aqueous dispersions at pH 6.6 (27 °C). The imidazole ring of the histidine residue plays a vital role to interact with these metal-ions. The thermal and mechanical stability of these metallo-hydrogels can be tuned by changing the proportion of amphiphile to metal ion ratio (1:0.1 to 1:0.3 for Fe3+-containing gel and 1:0.25 to 1:0.75 for Hg2+-containing gel). The metallo-hydrogels were characterized by different spectroscopic and microscopic techniques, low- and wide-angle powder X-ray diffraction, and small-angle X-ray scattering studies. FT-IR and NMR spectroscopic studies indicate the participation of the imidazole ring in metal-ion binding. Low- and wide-angle powder X-ray diffraction and small-angle X-ray scattering data are in favor of a layered structure of the supramolecular assembly of the AM1 in the presence of metal-ions. Both, the amphiphiles and the metal ion induced hydrogels reveal catalytic activity of p-nitrophenyl esters hydrolysis for the acetyl, n-butyl and n-octyl esters . Ferric ion containing metallo-hydrogel exhibits higher catalytic activity than the corresponding AM1 aggregate in the absence of metal ions.

Peptide-based ambidextrous bifunctional gelator: applications in oil spill recovery and removal of toxic organic dyes for waste water management.

A low molecular weight peptide-based ambidextrous gelator molecule has been discovered for efficient control of water pollution. The gelator molecules can gel various organic solvents with diverse polarity, e.g. n-hexane, n-octane, petroleum ether, petrol, diesel, aromatic solvents like chlorobenzene, toluene, benzene, o-xylene and even aqueous phosphate buffer of pH 7.5. These gels have been thoroughly characterized using various techniques including field emission scanning electron microscopy, Fourier transform infrared spectroscopy, X-ray powder diffraction analysis, small angle X-ray scattering and rheological experiments. Interestingly, hydrogel obtained from the gelator molecule has been found to absorb toxic organic dyes (both cationic and anionic dyes) from dye-contaminated water. The gelator molecule can be reused for several cycles, indicating its possible future use in waste water management. Moreover, this gelator can selectively gel petrol, diesel, pump oil from an oil-water mixture in the presence of a carrier solvent, ethyl acetate, suggesting its efficient application for oil spill recovery. These results indicate that the peptide-based ambidextrous gelator produces soft materials (gels) with dual function: (i) removal of toxic organic dyes in waste water treatment and (ii) oil spill recovery.

Size specific emission in peptide capped gold quantum clusters with tunable photoswitching behavior.

Three different types of fluorescent gold clusters (namely blue, green and red emitting) have been prepared from a gold precursor (chloroauric acid) under moderate conditions in aqueous medium. A cysteine containing dipeptide has been used for the formation of these quantum clusters as this peptide molecule contains a thiol group in the side chain to cap these nascently formed clusters and the free amino and carboxylic moieties assist in water solubility. Thus, the clusters are also environmentally friendly as the capped peptide is made up of only naturally occurring protein amino acids. These clusters have been well characterized by using UV-visible, fluorescence, X-ray photoelectron spectroscopy (XPS)spectroscopy, matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) and ultrahigh resolution field emission gun-transmission electron microscopy (UHR-FEG-TEM). Arrangements of gold atoms and their interaction with the corresponding ligands in three different fluorescent clusters have been predicted computationally. The excited state behavior of three different clusters has also been studied using time dependent density functional theory (TD-DFT). Time correlated single photon counting (TCSPC) and computational studies suggest intersystem crossing (S1 → T1) in the case of red-emitting Au23 clusters. Interestingly, these gold clusters exhibit semiconducting and photoswitching properties (Ion/Ioff), which are shown to be controlled by varying the size of these clusters. This holds future promise of using these gold cluster based nanomaterials for optoelectronic applications.

A dipeptide-based superhydrogel: Removal of toxic dyes and heavy metal ions from waste water.

A short peptide-based molecule has been found to form a strong hydrogel at phosphate buffer solution of pH 7.46. The hydrogel has been characterized thoroughly using various techniques including field emission scanning electron microscopy (FE-SEM), wide angle powder X-ray diffraction (PXRD), and rheological analysis. It has been observed from FE-SEM images that entangled nanofiber network is responsible for gelation. Rheological investigation demonstrates that the self-assembly of this synthetic dipeptide results in the formation of mechanically strong hydrogel with storage modulus (G') around 104 Pa. This gel has been used for removing both cationic and anionic toxic organic dyes (Brilliant Blue, Congo red, Malachite Green, Rhodamine B) and metal ions (Co2+ and Ni2+ ) from waste water. Moreover, only a small amount of the gelator is required (less than 1 mg/mL) for preparation of this superhydrogel and even this hydrogel can be reused three times for dye/metal ion absorption. This signifies the importance of the hydrogel towards waste water management.

Peptide based hydrogels for cancer drug release: modulation of stiffness, drug release and proteolytic stability of hydrogels by incorporating d-amino acid residue(s).

Synthetic tripeptide based noncytotoxic hydrogelators have been discovered for releasing an anticancer drug at physiological pH and temparature. Interestingly, gel stiffness, drug release capacity and proteolytic stability of these hydrogels have been successfully modulated by incorporating d-amino acid residues, indicating their potential use for drug delivery in the future.

Time-dependent gel to gel transformation of a peptide based supramolecular gelator.

A dipeptide with a long fatty acid chain at its N-terminus gives hydrogels in phosphate buffer in the pH range 7.0-8.5. The hydrogel with a gelator concentration of 0.45% (w/v) at pH 7.46 (physiological pH) provides a very good platform to study dynamic changes within a supramolecular framework as it exhibits remarkable change in its appearance with time. Interestingly, the first formed transparent hydrogel gradually transforms into a turbid gel within 2 days. These two forms of the hydrogel have been thoroughly investigated by using small angle X-ray scattering (SAXS), powder X-ray diffraction (PXRD), field emission scanning electron microscopic (FE-SEM) and high-resolution transmission electron microscopic (HR-TEM) imaging, FT-IR and rheometric analyses. The SAXS and low angle PXRD studies substantiate different packing arrangements for the gelator molecules for these two different gel states (the freshly prepared and the aged hydrogel). Moreover, rheological studies of these two gels reveal that the aged gel is stiffer than the freshly prepared gel.