Specifically targeting antimicrobial peptides for inhibition of Candidatus Liberibacter asiaticus.

AIMS: Huanglongbing (citrus greening) is a plant disease putatively caused by the unculturable Gram-negative bacterium Candidatus Liberibacter asiaticus (CLas), and it has caused severe damage to citrus plantations worldwide. There are no definitive treatments for this disease, and conventional disease control techniques have shown limited efficacy. This work presents an in silico evaluation of using specifically targeting anti-microbial peptides (STAMPs) consisting of a targeting segment and an antimicrobial segment to inhibit citrus greening by inhibiting the BamA protein of CLas, which is an outer membrane protein crucial for bacterial viability. METHODS AND RESULTS: Initially, a set of peptides with a high affinity toward BamA protein were screened and evaluated via molecular docking and molecular dynamics simulations and were verified in vitro via bio-layer interferometry (BLI). In silico studies and BLI experiments indicated that two peptides, HASP2 and HASP3, showed stable binding to BamA. Protein structures for STAMPs were created by fusing known anti-microbial peptides (AMPs) with the selected short peptides. The binding of STAMPs to BamA was assessed using molecular docking and binding energy calculations. The attachment of high-affinity short peptides significantly reduced the free energy of binding for AMPs, suggesting that it would make it easier for the STAMPs to bind to BamA. Efficacy testing in vitro using a closely related CLas surrogate bacterium showed that STAMPs had greater inhibitory activity than AMP alone. CONCLUSIONS: In silico and in vitro results indicate that the STAMPs can inhibit CLas surrogate Rhizobium grahamii more effectively compared to AMPs, suggesting that STAMPs can achieve better inhibition of CLas, potentially via enhancing the site specificity of AMPs.

Inhibition of a conserved bacterial dual-specificity phosphatase confers plant tolerance to Candidatus Liberibacter spp.

"Candidatus Liberibacter spp." are insect-vectored, fastidious, and vascular-limited phytopathogens. They are the presumptive causal agents of potato zebra chip, tomato vein clearing, and the devastating citrus greening disease worldwide. There is an urgent need to develop new strategies to control them. In this study, we characterized a dual-specificity serine/tyrosine phosphatase (STP) that is well conserved among thirty-three geographically diverse "Candidatus Liberibacter spp." and strains that infect multiple Solanaceaea and citrus spp. The STP is expressed in infected plant tissues, localized at the plant cytosol and plasma membrane, and interferes with plant cell death responses. We employed an in silico target-based molecular modeling and ligand screen to identify two small molecules with high binding affinity to STP. Efficacy studies demonstrated that the two molecules can inhibit "Candidatus Liberibacter spp." but not unrelated pathogens and confer plant disease tolerance. The inhibitors and strategies are promising means to control "Candidatus Liberibacter spp."

Escherichia coli resistance mechanism AcrAB-TolC efflux pump interactions with commonly used antibiotics: a molecular dynamics study.

While antibiotic resistance poses a threat from both Gram-positive bacteria (GPB) and Gram-negative bacteria (GNB), GNB pose a more imminent public health hazard globally. GNB are a threat to growing antibiotic resistance because of the complex makeup of the membrane. The AcrAB-TolC efflux pump is a known resistance mechanism of Escherichia coli (E. coli) cells. This study utilized molecular dynamics modeling to visualize some of the changes occurring at a molecular level when airborne bacteria are exposed to stress and antibiotics. This study was conducted to build upon previous experimental research showing that there is an increase in antibiotic resistance and efflux pump activity when exposed to aerosolization. AcrB and AcrAB-TolC proteins were simulated under standard and increased pressure to compare the effect of aerosolization on the binding to the three different antibiotics (puromycin (PUY), ampicillin (AMP) and sulfamethoxazole-trimethoprim (SXT)) to the AcrB binding site. Analysis such as root-mean-square deviation of atomic positions and root-mean-square fluctuation, the opening of TolC, and the significant molecular mechanics with generalized Born and surface area solvation (MM-GBSA) scores associated with specific ligands were recorded. Resistance in experimental data indicated a relationship between the docking scores and some ligand-protein interactions. Results showed that there was more flexibility in the proteins within simulations conducted under standard pressure for the AcrB protein and the full tripartite complex AcrAB-TolC, showing that increased pressure causes more rigidity. MM-GBSA scores, used to calculate the free energy of ligand-protein binding, did not show a significant change, but interestingly, the strongest MM-GBSA scores were for ligands that moved to another binding pocket and did not result in resistance or opening of the efflux pump. However, the ligand moved from the binding site and did not cause the opening of TolC to increase significantly, whereas PUY and AMP were bound to the binding site for the duration of all simulations. AMP ligands under increased pressure showed the largest change in opening of the TolC efflux pump and aligns with experimental data showing E. coli cells had the most resistance to AMP after aerosolization. These results, in addition to other real-time changes such as OM proteins and mutations of targets within the cell, could be used to delineate and mitigate antibiotic resistance mechanisms.

Binding behavior of receptor binding domain of the SARS-CoV-2 virus and ivermectin.

The COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), sparked an international debate on effective ways to prevent and treat the virus. Specifically, there were many varying opinions on the use of ivermectin (IVM) throughout the world, with minimal research to support either side. IVM is an FDA-approved antiparasitic drug that was discovered in the 1970s and was found to show antiviral activity. The objective of this study is to examine the binding behavior and rates of association and dissociation between SARS-CoV-2 receptor binding domain (RBD), IVM, and their combination using aminopropylsilane (APS) biosensors as surrogates for the hydrophobic interaction between the viral protein and human angiotensin-converting enzyme 2 (ACE2) receptors to determine the potential of IVM as a repurposed drug for SARS-CoV-2 prevention and treatment. The IVM, RBD, and combination binding kinetics were analyzed using biolayer interferometry (BLI) and validated with multiple in silico techniques including protein-ligand docking, molecular dynamics simulation, molecular mechanics-generalized Born surface area (MM-GBSA), and principal component analysis (PCA). Our results suggest that with increasing IVM concentrations the association rate with the hydrophobic biosensor increases with a simultaneous decrease in dissociation. Significant kinetic changes to RBD, when combined with IVM, were found only at a concentration a thousand times the approved dosage with minimal changes found over a 35-min time period. Our study suggests that IVM is not an effective preventative or treatment method at the currently approved dosage.

Identification of Fungicide Combinations for Overcoming Plasmopara viticola and Botrytis cinerea Fungicide Resistance.

Fungal diseases, including downy mildew (caused by Plasmopara viticola) and gray mold (caused by Botrytis cinerea), significantly impact the marketable yield of grapes produced worldwide. Cytochrome b of the mitochondrial respiratory chain of these two fungi is a key target for Quinone outside inhibitor (QoI)-based fungicide development. Since the mode of action (MOA) of QoI fungicides is restricted to a single site, the extensive usage of these fungicides has resulted in fungicide resistance. The use of fungicide combinations with multiple targets is an effective way to counter and slow down the development of fungicide resistance. Due to the high cost of in planta trials, in silico techniques can be used for the rapid screening of potential fungicides. In this study, a combination of in silico simulations that include Schrödinger Glide docking, molecular dynamics, and Molecular Mechanism-Generalized Born Surface Area calculation were used to screen the most potent QoI and non-QoI-based fungicide combinations to wild-type, G143A-mutated, F129L-mutated, and double-mutated versions that had both G143A and F129L mutations of fungal cytochrome b. In silico docking studies indicated that mandestrobin, famoxadone, captan, and thiram have a high affinity toward WT cytochrome b of Botrytis cinerea. Although the QoIs mandestrobin and famoxadone were effective for WT based on in vitro results, they were not broadly effective against G143A-mutated isolates. Famoxadone was only effective against one isolate with G143A-mutated cytochrome b. The non-QoI fungicides thiram and captan were effective against both WT and isolates with G143A-mutated cytochrome b. Follow-up in silico docking and molecular dynamics studies suggested that fungicide combinations consisting of famoxadone, mandestrobin, fenamidone, and thiram should be considered in field testing targeting Plasmopara viticola and Botrytis cinerea fungicide resistance.

Montelukast and Telmisartan as Inhibitors of SARS-CoV-2 Omicron Variant.

Earlier studies with montelukast (M) and telmisartan (T) have revealed their potential antiviral properties against SARS-CoV-2 wild-type (WT) but have not assessed their efficacy against emerging Variants of Concern (VOCs) such as Omicron. Our research fills this gap by investigating these drugs' impact on VOCs, a topic that current scientific literature has largely overlooked. We employed computational methodologies, including molecular mechanics and machine learning tools, to identify drugs that could potentially disrupt the SARS-CoV-2 spike RBD-ACE2 protein interaction. This led to the identification of two FDA-approved small molecule drugs, M and T, conventionally used for treating asthma and hypertension, respectively. Our study presents an additional potential use for these drugs as antivirals. Our results show that both M and T can inhibit not only the WT SARS-CoV-2 but also, in the case of M, the Omicron variant, without reaching cytotoxic concentrations. This novel finding fills an existing gap in the literature and introduces the possibility of repurposing these drugs for SARS-CoV-2 VOCs, an essential step in responding to the evolving global pandemic.

Identification of Fungicide Combinations Targeting Plasmopara viticola and Botrytis cinerea Fungicide Resistance Using Machine Learning.

Downy mildew (caused by Plasmopara viticola) and gray mold (caused by Botrytis cinerea) are fungal diseases that significantly impact grape production globally. Cytochrome b plays a significant role in the mitochondrial respiratory chain of the two fungi that cause these diseases and is a key target for quinone outside inhibitor (QoI)-based fungicide development. Since the mode of action (MOA) of QoI fungicides is restricted to a single active site, the risk of developing resistance to these fungicides is deemed high. Consequently, using a combination of fungicides is considered an effective way to reduce the development of QoI resistance. Currently, there is little information available to help in the selection of appropriate fungicides. This study used a combination of in silico simulations and quantitative structure-activity relationship (QSAR) machine learning algorithms to screen the most potent QoI-based fungicide combinations for wild-type (WT) and the G143A mutation of fungal cytochrome b. Based on in silico studies, mandestrobin emerged as the top binder for both WT Plasmopara viticola and WT Botrytis cinerea cytochrome b. Famoxadone appeared to be a versatile binder for G143A-mutated cytochrome b of both Plasmopara viticola and Botrytis cinerea. Thiram emerged as a reasonable, low-risk non-QoI fungicide that works on WT and G143A-mutated versions of both fungi. QSAR analysis revealed fenpropidin, fenoxanil, and ethaboxam non-QoIs to have a high affinity for G143A-mutated cytochrome b of Plasmopara viticola and Botrytis cinerea. Above-QoI and non-QoI fungicides can be considered for field studies in a fungicide management program against Plasmopara viticola- and Botrytis cinerea-based fungal infections.

In silico and in vitro evaluation of imatinib as an inhibitor for SARS-CoV-2.

The rapid geographic expansion of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the infectious agent of Coronavirus Disease 2019 (COVID-19) pandemic, poses an immediate need for potent drugs. Enveloped viruses infect the host cell by cellular membrane fusion, a crucial mechanism required for virus replication. The SARS-CoV-2 spike glycoprotein, due to its primary interaction with the human angiotensin-converting enzyme 2 (ACE2) cell-surface receptor, is considered a potential target for drug development. In this study, around 5,800 molecules were virtually screened using molecular docking. Five molecules were selected for in vitro experiments from those that reported docking scores lower than -6 kcal/mol. Imatinib, a Bcr-Abl tyrosine kinase inhibitor, showed maximum antiviral activity in Vero cells. We further investigated the interaction of imatinib, a compound under clinical trials for the treatment of COVID-19, with SARS-CoV-2 RBD, using in silico methods. Molecular dynamics simulations verified that imatinib interacts with RBD residues that are critical for ACE2 binding. This study also provides significant molecular insights on potential repurposable small-molecule drugs and chemical scaffolds for the development of novel drugs targeting the SARS-CoV-2 spike RBD.Communicated by Ramaswamy H. Sarma.

Evaluation of Candidatus Liberibacter Asiaticus Efflux Pump Inhibition by Antimicrobial Peptides.

Citrus greening, also known as Huanglongbing (HLB), is caused by the unculturable bacterium Candidatus Liberibacter spp. (e.g., CLas), and has caused a devastating decline in citrus production in many areas of the world. As of yet, there are no definitive treatments for controlling the disease. Antimicrobial peptides (AMPs) that have the potential to block secretion-dependent effector proteins at the outer-membrane domains were screened in silico. Predictions of drug-receptor interactions were built using multiple in silico techniques, including molecular docking analysis, molecular dynamics, molecular mechanics generalized Born surface area analysis, and principal component analysis. The efflux pump TolC of the Type 1 secretion system interacted with natural bacteriocin plantaricin JLA-9, blocking the ß barrel. The trajectory-based principal component analysis revealed the possible binding mechanism of the peptides. Furthermore, in vitro assays using two closely related culturable surrogates of CLas (Liberibacter crescens and Rhizobium spp.) showed that Plantaricin JLA-9 and two other screened AMPs inhibited bacterial growth and caused mortality. The findings contribute to designing effective therapies to manage plant diseases associated with Candidatus Liberibacter spp.

ELIXIR-A: An Interactive Visualization Tool for Multi-Target Pharmacophore Refinement.

Pharmacophore modeling is an important step in computer-aided drug design for identifying interaction points between the receptor and ligand complex. Pharmacophore-based models can be used for de novo drug design, lead identification, and optimization in virtual screening as well as for multi-target drug design. There is a need to develop a user-friendly interface to filter the pharmacophore points resulting from multiple ligand conformations. Here, we present ELIXIR-A, a Python-based pharmacophore refinement tool, to help refine the pharmacophores between multiple ligands from multiple receptors. Furthermore, the output can be easily used in virtual pharmacophore-based screening platforms, thereby contributing to the development of drug discovery.

Binding behavior of spike protein and receptor binding domain of the SARS-CoV-2 virus at different environmental conditions.

A novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was identified as the cause of the COVID-19 pandemic that originated in China in December 2019. Although extensive research has been performed on SARS-CoV-2, the binding behavior of spike (S) protein and receptor binding domain (RBD) of SARS-CoV-2 at different environmental conditions have yet to be studied. The objective of this study is to investigate the effect of temperature, fatty acids, ions, and protein concentration on the binding behavior and rates of association and dissociation between the S protein and RBD of SARS-CoV-2 and the hydrophobic aminopropylsilane (APS) biosensors using biolayer interferometry (BLI) validated with molecular dynamics simulation. Our results suggest three conditions-high ionic concentration, presence of hydrophobic fatty acids, and low temperature-favor the attachment of S protein and RBD to hydrophobic surfaces. Increasing the temperature within an hour from 0 to 25 °C results in S protein detachment, suggesting that freezing can cause structural changes in the S protein, affecting its binding kinetics at higher temperature. At all the conditions, RBD exhibits lower dissociation capabilities than the full-length S trimer protein, indicating that the separated RBD formed stronger attachment to hydrophobic surfaces compared to when it was included in the S protein.

Druggability assessment of precursor membrane protein as a target for inhibiting the Zika virus.

The Zika virus (ZIKV), a significant zoonotic flavivirus, was neglected as a human pathogen until the recent epidemic. The rapid geographic spread of the virus and association with neurological disorders has created a global public health concern pressing the need for anti-ZIKV drugs. Previous ZIKV drug discovery research has focused on three primary targets, RNA-dependent RNA polymerase, envelope protein, and viral proteases, and none has yet resulted in a commercially viable inhibitor. In the quest for finding effective inhibitors, it is important to expand the number of targets available for drug discovery research. To this end, the ZIKV precursor membrane protein (prM) comes to the forefront as a potential target due to its critical role in virus infectivity and pathogenicity. prM acts as a chaperone for envelope protein folding and prevents premature fusion of virions to the host membrane and has not been attempted as a drug target before. One critical requirement for a protein to be an effective target is the ability of the protein to be druggable, i.e. having active sites that can bind to specific ligands. In this work, the druggability of prM was assessed via molecular docking combined molecular dynamics simulations followed binding affinity kinetics studies. Compounds that had a high affinity to the prM protein were screened in silico and ligand-binding free energies were computed using molecular mechanics with generalized Born and surface area continuum solvation (MM-GBSA) method. In vitro binding kinetics via biolayer interferometry (BLI) and interaction analysis confirmed that prM could be targeted for drug discovery to combat ZIKV infection.Communicated by Ramaswamy H. Sarma.

An RNA-dependent RNA polymerase inhibitor for tick-borne encephalitis virus.

Tick-borne encephalitis virus (TBEV) is a medically important representative of the Flaviviridae family. The TBEV genome encodes a single polyprotein, which is co/post-translationally cleaved into three structural and seven non-structural proteins. Of the non-structural proteins, NS5, contains an RNA-dependent RNA polymerase (RdRp) domain that is highly conserved and is responsible for the genome replication. Screening for potential antivirals was done using a hybrid receptor and ligand-based pharmacophore search likely targeting the RdRp domain. For the identification of pharmacophores, a mixture of small probe molecules and nucleotide triphosphates were used. The ligand/receptor interaction screenings of structures from the ZINC database resulted in five compounds. Zinc 3677 and 7151 exhibited lower cytotoxicity and were tested for their antiviral effect against TBEV in vitro. Zinc 3677 inhibited TBEV at micromolar concentrations. The results indicate that Zinc 3677 represents a good target for structure-activity optimizations leading potentially to a discovery of effective TBEV antivirals.

Complexes Formed by Hydrophobic Interaction between Ag-Nanospheres and Adsorbents for the Detection of Methyl Salicylate VOC.

Surface-enhanced Raman spectroscopy (SERS) has been widely investigated in many applications. However, only little work has been done on using SERS for the detection of volatile organic compounds (VOCs), primarily due to the challenges associated with fabricating SERS substrates with sufficient hotspots for signal enhancement and with the surface interfacially compatible for the VOCs. This study investigated the phase transfer of Ag-nanospheres (AgNSs) from the aqueous phase to the non-aqueous phase by electrostatic interaction induced by cationic surfactants, and the feasibility of the transferred AgNSs as SERS substrates for the determination of methyl salicylate VOC. Results indicated that one of three cationic surfactants, tetraoctylammonium bromide (TOAB) dissolved in organic solvent showed successful phase transfer of the AgNSs confirmed by several characterization analyses. The complex formed by hydrophobic interaction between the transferred AgNSs and Tenax-TA adsorbent polymer was able to be utilized as a SERS substrate, and the volatile of methyl salicylate could be easily determined from SERS measurements at 4 h static volatile collection. Therefore, the proposed new techniques can be effectively employed to areas where many VOCs relevant to food and agriculture need to be analyzed.

A non-beta-lactam antibiotic inhibitor for enterohemorrhagic Escherichia coli O104:H4.

The overuse of antibiotics has caused an increased prevalence of drug-resistant bacteria. Bacterial resistance in E. coli is regulated via production of ß-lactam-hydrolyzing ß-lactamases enzymes. Escherichia coli O104: H4 is a multi-drug resistant strain known to resist ß-lactam as well as several other antibiotics. Here, we report a molecular dynamic simulation-combined docking approach to identify, screen, and verify active pharmacophores against enterohemorrhagic Escherichia coli (EHEC). Experimental studies revealed a boronic acid cyclic monomer (BACM), a non-ß-lactam compound, to inhibit the growth of E. coli O104: H4. In vitro Kirby Bauer disk diffusion susceptibility testing coupled interaction analysis suggests BACM inhibits E. coli O104:H4 growth by not only inhibiting the ß-lactamase pathway but also via direct inhibition of the penicillin-binding protein. These results suggest that BACM could be used as a lead compound to develop potent drugs targeting beta-lactam resistant Gram-negative bacterial strains. KEY MESSAGES: • An in silico approach was reported to identify pharmacophores against E. coli O104: H4. • In vitro studies revealed a non-ß-lactam compound to inhibit the growth of E. coli O104: H4. • This non-ß-lactam compound could be used as a lead compound for targeting beta-lactam strains.

Mechanics of controlled release of insulin entrapped in polyacrylic acid gels via variable electrical stimuli.

Controlled release insulin delivery systems possess multiple advantages over conventional ones, including maintaining desired blood glucose levels for prolonged periods and minimizing complications due to insulin overdose. Compared to other controlled-release mechanisms, electro-responsive polymers present the advantages of high controllability and ability to be coupled with microelectronics. This paper reports the possibility of using electro-responsive polyacrylic acid (PAA) and polymethacrylic acid (PMA) hydrogels for controlled delivery of insulin using intermittent electrical signals via matrix deformation. PAA hydrogels showed very good electrical responsivity under both constant and step current inputs, releasing up to 80% of protein at 10 V stimulus, compared to 20% release in the absence of stimulus. Analysis of spatial variation under electrical stimuli suggested that release of protein is a combined effect of deformation of the hydrogel and electrophoresis of protein molecules. Binding interaction analysis revealed that insulin entrapment is largely due to hydrogen bonding between the polymer matrix and insulin, and flooding the matrix with electrical charge likely disrupts the attractive forces that kept protein in place helping the release of the proteins. Understanding the molecular interactions affecting insulin retention and release mechanisms of PAA hydrogels is useful for developing and optimizing hydrogel-based controlled drug release systems.

Electrical Field Reversibly Modulates Enzyme Kinetics of Hexokinase Entrapped in an Electro-Responsive Hydrogel.

In this paper, the potential use of electro-responsive poly(acrylic acid) (PAA) gels as reversible enzyme activity regulators is analyzed. This was evaluated by measuring the glucose conversion by hexokinase embedded PAA hydrogels under external electrical stimuli. Hexokinase physically entrapped within PAA gels showed a significant increase in activity under an electrical stimulus as compared to in the absence of a stimulus. Kinetic studies revealed that the change in reaction rate could be attributed to the change of Vmax under a stimulus, while Km was unaffected by the stimulus, which suggested that the increase in reaction rate under an electrical stimulus was due to increased accessibility of the active site. Optimum stimuli-responsive behavior that resulted in maximum conversion under a stimulus and minimum conversion in the absence of a stimulus was obtained at 5.5 pH and 30 °C. The significant difference between the pH optima for the entrapped enzyme and the pure enzyme can be attributed to the acidic nature of the polymeric matrix. Higher cross-linker concentrations resulted in a reduction of both enzyme release and glucose conversion, and a reasonable trade-off between conversion and release could be obtained at 5% cross-linker concentration. Application of a stepwise electrical stimulus revealed that the entrapped enzymes could sustain responsive properties over multiple cycles of electrical switching. Entrapped hexokinase also showed much better reusability compared to pure hexokinase, a combined result of higher enzyme retention and increased stability. No significant impact of the polymer on the interaction between enzyme and glucose was observed. Thus, this system enables electro-responsive modulation of enzyme activity without any reduction in enzyme activity. The studies revealed that conjugation of electro-responsive polymers to enzymes has the potential to reversibly modulate enzymatic reactions via the application of external electrical stimuli, which is promising for bioprocessing and enzymatic separation applications.

Evaluating apoenzyme-coenzyme-substrate interactions of methane monooxygenase with an engineered active site for electron harvesting: a computational study.

Low-temperature methane oxidation is one of the greatest challenges in energy research. Although methane monooxygenase (MMO) does this catalysis naturally, how to use this biocatalyst in a fuel cell environment where the electrons generated during the oxidation process is harvested and used for energy generation has not yet been investigated. A key requirement to use this enzyme in a fuel cell is wiring of the active site of the enzyme directly to the supporting electrode. In soluble MMO (sMMO), two cofactors, i.e., nicotinamide adenine di-nucleotide (NAD+) and flavin adenine dinucleotide (FAD) provide opportunities for direct attachment of the enzyme system to a supporting electrode. However, once modified to be compatible with a supporting metal electrode via FeS functionalization, how the two cofactors respond to complex binding phenomena is not yet understood. Using docking and molecular dynamic simulations, modified cofactors interactions with sMMO-reductase (sMMOR) were studied. Studies revealed that FAD modification with FeS did not interfere with binding phenomena. In fact, FeS introduction significantly improved the binding affinity of FAD and NAD+ on sMMOR. The simulations revealed a clear thermodynamically more favorable electron transport path for the enzyme system. This system can be used as a fuel cell and we can use FeS-modified-FAD as the anchoring molecule as opposed to using NAD+. The overall analysis suggests the strong possibility of building a fuel cell that could catalyze methane oxidation using sMMO as the anode biocatalyst.

Inorganic iron-sulfur clusters enhance electron transport when used for wiring the NAD-glucose dehydrogenase based redox system.

Wiring the active site of an enzyme directly to an electrode is the key to ensuring efficient electron transfer for the proper performance of enzyme-based bioelectronic systems. Iron-sulfur complexes, the first link between proteins and mediating molecules in the biological electron transport chain(s), possess an intrinsic electron transport capability. The authors demonstrate the application of inorganic iron-sulfur clusters (Fe-S) viz. FeS, FeS2, Fe2S3, and Fe3S4, as molecular wires to mediate electron transport between a glucose-selective redox enzyme and the gold electrode. It is shown that Fe-S can emulate the functionality of the natural electron transport chain. Voltammetric studies indicate a significant improvement in electron transport, surface coverage, and resilience achieved by the Fe-S-based glucose anodes when compared to a conventional pyrroloquinoline quinone (PQQ)-based electrode. The Fe-S-based glucose anodes showed glucose oxidation at a potential of +0.5 V vs. Ag/AgCl with Tris-HCl buffer (pH 8) acting as a carrier. The current densities positively correlated with the concentrations of glucose in the range 0.1-100 mM displaying detection limits of 0.77 mM (FeS), 1.22 mM (FeS2), 2.95 mM (Fe2S3), and 14.57 mM (Fe3S4). The metal-anchorable sulfur atom, the strong π-coordinating iron atom, the favorable redox properties, low cost, and natural abundance make Fe-S an excellent electron-mediating relay capable of wiring redox active sites to electrode surfaces. Graphical abstract Schematic representation of inorganic iron-sulfur clusters used as molecular wires to facilitate direct electron transfer between NAD-glucose dehydrogenase and the gold electrode. The iron-sulfur based glucose anodes improve current response to selectively sense glucose concentrations in the range 0.1-100 mM.

Antivirals for allosteric inhibition of Zika virus using a homology model and experimentally determined structure of envelope protein.

OBJECTIVE: An approach to inhibiting enveloped flaviviruses is to deter the ability of the envelope protein(s) binding onto glycoproteins. In previous work, using a small ~100-amino acid homology model of Zika virus envelope protein (ZVEP), we proved the susceptibility of Zika virus to inhibition. In this work, we verify the efficacy of the homology model based antiviral search method using a larger protein (>400 amino acids) and comparing the results with the experimentally determined one (PDB ID:5IRE). RESULTS: By examining how glycan molecules, small-molecule probes and screened ligands that have a high affinity to ZVEP, we report the mechanics of ZVEP to inhibition via allosteric blockage of the glycan-binding domain while proposing even more possibly potent inhibitors. The small molecular probes based study using the homology model and subsequently verified using actual experimental structure, 5IRE, revealed that ZVEP is druggable. A pharmacophore analysis followed by screening showed at least four ligands that allosterically binds to the glycan binding domain constituted by residues VAL 153 and ASN 154 in 5IRE. Based on further selection criteria ZINC40621658 was identified to have high potential to be a strong antiviral candidate for Zika virus inhibition.