Improving the physical realism and structural accuracy of protein models by a two-step atomic-level energy minimization

Uncovering the structural stability of Magnaporthe oryzae effectors: a secretome-wide in silico analysis

Rice blast, caused by the ascomycete fungus Magnaporthe oryzae, is a deadly disease and a major threat to global food security. The pathogen secretes small proteinaceous effectors, virulence factors, inside the host to manipulate and perturb the host immune system, allowing the pathogen to colonize and establish a successful infection. While the molecular functions of several effectors are characterized, very little is known about the structural stability of these effectors. We analyzed a total of 554 small secretory proteins (SSPs) from the M. oryzae secretome to decipher key features of intrinsic disorder (ID) and the structural dynamics of the selected putative effectors through thorough and systematic in silico studies. Our results suggest that out of the total SSPs, 66% were predicted as effector proteins, released either into the apoplast or cytoplasm of the host cell. Of these, 68% were found to be intrinsically disordered effector proteins (IDEPs). Among the six distinct classes of disordered effectors, we observed peculiar relationships between the localization of several effectors in the apoplast or cytoplasm and the degree of disorder. We determined the degree of structural disorder and its impact on protein foldability across all the putative small secretory effector proteins from the blast pathogen, further validated by molecular dynamics simulation studies. This study provides definite clues toward unraveling the mystery behind the importance of structural distortions in effectors and their impact on plant-pathogen interactions. The study of these dynamical segments may help identify new effectors as well.Communicated by Ramaswamy H. Sarma.

Exploring chalcone-sulfonyl piperazine hybrids as anti-diabetes candidates: design, synthesis, biological evaluation, and molecular docking study

To address the escalating rates of diabetes mellitus worldwide, there is a growing need for novel compounds. The demand for more affordable and efficient methods of managing diabetes is increasing due to the inevitable side effects associated with existing antidiabetic medications. In this present research, various chalcone-sulfonyl piperazine hybrid compounds (5a-k) were designed and synthesized to develop inhibitors against alpha-glucosidase and alpha-amylase. In addition, several spectroscopic methods, including FT-IR, 1H-NMR, 13C-NMR, and HRMS, were employed to confirm the exact structures of the synthesized derivatives. All synthesized compounds were evaluated for their ability to inhibit alpha-glucosidase and alpha-amylase in vitro using acarbose as the reference standard and they showed excellent to good inhibitory potentials. Compound 5k exhibited excellent inhibitory activity against alpha-glucosidase (IC50 = 0.31 ± 0.01 µM) and alpha-amylase (IC50 = 4.51 ± 1.15 µM), which is 27-fold more active against alpha-glucosidase and 7-fold more active against alpha-amylase compared to acarbose, which had IC50 values of 8.62 ± 1.66 µM for alpha-glucosidase and 30.97 ± 2.91 µM for alpha-amylase. It was discovered from the Lineweaver-Burk plot that 5k exhibited competitive inhibition against alpha-glucosidase. Furthermore, cytotoxicity screening assay results against human fibroblast HT1080 cells showed that all compounds had a good level of safety profile. To explore the binding interactions of the most potent compound (5k) with the active site of enzymes, molecular docking research was conducted, and the results obtained supported the experimental data.

Leishmania donovani adenylosuccinate synthetase requires IMP for dimerization and organization of the active site

Adenylosuccinate synthetase (AdSS), which catalyses the GTP-dependent conversion of inosine monophosphate (IMP) and aspartic acid to succinyl-AMP, plays a major role in purine biosynthesis. In some bacterial AdSS, it is implicated that IMP binding is important to organize the active site, but in certain plant AdSS, GTP performs this role. Here, we report that in Leishmania donovani AdSS, IMP binding favoured dimerization, induced greater conformational change and improved the protein stability more than GTP binding. IMP binding, which resulted in a network of hydrogen bonds, stabilized the conformation of active site loops and brought the switch loop to a closed conformation, which then facilitated GTP binding. Our results provide a basis for designing better inhibitors of leishmanial AdSS.

Amebicidal and Antiadhesion Activities of Knema retusa Extract Against Acanthamoeba triangularis T4 Genotype on Contact Lenses and Modeling Simulation of Its Main Compound, E2N, Against Acanthamoeba Beta-Tubulin

Medicinal plants have been used as alternative agents for the treatment of infections. This study aimed to investigate bioactivities of medicinal plant extracts including Knema retusa extract (Kre) against Acanthamoeba triangularis T4 in vitro and in silico. Anti-Acanthamoeba activities of 44 extracts from 5 plant species were determined. From 44 tested extracts, a chloroform extract of Kre bark showed the strongest anti-Acanthamoeba activities against both trophozoites and cysts, with MIC values of 32.25 and 62.50 μg/mL, respectively. Then, amebicidal and antiadhesion activities of Kre against A. triangularis were investigated. Kre reduced the growth by 3 logs within 8 h at 4 × MIC. Disruption of the cells with abnormal shapes was observed when trophozoites were treated with Kre. Trophozoites had lost their robust acanthopodia and began to shrink after treatment with Kre. Treated cysts exhibited wall disruption and dramatically showed forms of marked retraction. Treatment of Kre at 1/2 × MIC showed about 87% reduction in the trophozoite adhesion, while treatment at 2 × MIC exhibited a 59% reduction in the trophozoite adhesion to the plastic surface, compared with the control. Furthermore, 1 log cells/mL (90%) of the contact lens adhesive trophozoites were reduced and removed after treatment with Kre. Molecular docking indicated that E2N, the main compound in Kre, exhibited strong binding to the ligand binding sites at β-tubulin, with a binding energy of -7.01 kcal/mol and an inhibitory constant of 2.43-7.32 μM. E2N generated multiple connections via hydrogen, hydrophobic, ionic, and water bridge bonding and maintained these connections until the simulation finished, facilitating the creation of stable bindings with the β-tubulin protein as measured by molecular dynamics simulation. These findings suggest that Kre exhibits amebicidal and antiadhesion activities which could be used for the prevention of A. triangularis adhesion to contact lenses.

Computational design, expression, and characterization of a Plasmodium falciparum multi-epitope, multi-stage vaccine candidate (PfCTMAG)

Malaria, a tropical disease, claims the lives of thousands of people annually and the development of resistance to insecticides and antimalarial drugs poses a great challenge to current prevention and control strategies. Current malaria vaccines are limited in efficacy, duration of protection, and safety, due to the high antigenic diversity and complex life cycle of the Plasmodium parasite. This study sought to design and assess a more effective multi-stage, multi-epitope vaccine candidate for the control of malaria. A multi-epitope malaria vaccine candidate was designed in silico using multiple antigens from both the pre-erythrocytic and erythrocytic stages, expressed in bacteria, and its sero-reactivity to antibodies in plasma from malaria-positive (cases) and negative individuals (controls) was assessed using enzyme-linked immunosorbent assay (ELISA). Immunization experiments were equally conducted with BALB/c mice. In-silico analysis revealed that the designed antigen, PfCTMAG (Plasmodium falciparum Circumsporozoite, Thrombospondin-related adhesion protein, Merozoite surface protein 2, Apical asparagine (Asn)-rich protein and Glutamate-Rich Protein), effectively bound to Toll-like receptor 4 (TLR-4) and triggered a strong immune response. In sero-reactivity studies, malaria-positives (cases) had higher anti-PfCTMAG IgG ( p  = 0.024) and IgM ( p < 0.001) levels compared to malaria negatives (controls). The mice immunized with PfCTMAG did not show adverse reactions and had higher levels of IgG antibodies (p = 0.002) compared to controls, thereby validating the safety and immunogenicity of PfCTMAG as a promising vaccine candidate.

PSSKB: A Web Application to Study Protein Structures

The proteins expressed during the cell cycle determine cell function and ensure signaling pathway activation in response to environmental influences. Developments in structural biology, biophysics, and bioinformatics provide information on the structure and function of particular proteins including that on the structural changes in proteins due to post-translational modification (PTM) and amino acid substitutions (AAS), which is essential for understanding protein function and life cycle. These are PTMs and AASs that often modulate the function and alter the stability and localization of a protein in a cell. PSSKB is a platform that integrates all necessary tools for modeling the five common natural modifications and all canonical AASs in proteins. The available tools are not limited to the local database, so the user can select a protein from Uniprot ID or PDB ID. The result will be a three-dimensional (3D) representation of the modified structure, as well as an analysis of the changes in the performance of the intact and modified structures after energy minimization compared with the original structure, which not only makes it possible to evaluate AAS/PTM influence of on a protein's characteristics but also to use the 3D model for further studies. Additionally, PSSKB enables the user to search, align, overlay, and determine the exact coordinates of protein structure fragments. The search results are a set of structural motifs similar to the query and ranked by statistical significance. The platform is fully functional and publicly available at https://psskb.org/. No registration is required to access the platform. A tutorial video can be found at https://psskb.org/page/about. Services provided on the platform are based on previously developed and published software. SCPacker applied for PTM Modeling and AAS services available at GitHub (https://github.com/protdb/SCPacker). SaFoldNet applied for a Similar Search service is also available at GitHub (https://github.com/protdb/ABBNet).

Multiscale simulations reveal architecture of NOTCH protein and ligand specific features

NOTCH, a single-pass transmembrane protein, plays a crucial role in cell fate determination through cell-to-cell communication. It interacts with two canonical ligands, Delta-like (DLL) and Jagged (JAG), located on neighboring cells to regulate diverse cellular processes. Despite extensive studies on the functional roles of NOTCH and its ligands in cellular growth, the structural details of full-length NOTCH and its ligands remain poorly understood. In this study, we employed fragment-based modeling and multiscale simulations to study the full-length structure of the human NOTCH ectodomain, comprising 1756 amino acids. We performed coarse-grained dynamics simulations of NOTCH in both glycosylated and nonglycosylated forms to investigate the role of glycosylation in modulating its conformational dynamics. In apo form, coarse-grained simulations revealed that glycosylated NOTCH protein can transition from an elongated structure of ∼86 nm from the membrane surface to a semicompact state (∼23.81 ± 9.98 nm), which aligns with cryo-EM data. To transition from the apo form to ligand-bound forms of NOTCH, we followed an atomistic and integrative modeling approach to model the interactions between NOTCH-DLL4 and NOTCH-JAG1. Atomistic simulations of the smaller bound fragment EGF8-13 patch revealed conformational plasticity critical for NOTCH binding, while integrative modeling of full-length complexes suggested a larger binding surface than reported previously. Simulations of pathogenic mutations revealed that E360K and R448Q disrupted the NOTCH-ligand interaction surfaces, causing dissociation. In contrast, C1133Y in the Abruptex domain compromised protein stability by disrupting the domain's interaction with the ligand-binding domain in the apo form of NOTCH-ECD. These findings provide a detailed molecular understanding of NOTCH and its ligands, offering insights that could enable the development of novel therapeutic approaches to selectively target pathogenic NOTCH signaling.

A claudin5-binding peptide enhances the permeability of the blood-brain barrier in vitro

The blood-brain barrier (BBB) maintains brain homeostasis but also prevents most drugs from entering the brain. No paracellular diffusion of solutes is allowed because of tight junctions that are made impermeable by the expression of claudin5 (CLDN5) by brain endothelial cells. The possibility of regulating the BBB permeability in a transient and reversible fashion is in strong demand for the pharmacological treatment of brain diseases. Here, we designed and tested short BBB-active peptides, derived from the CLDN5 extracellular domains and the CLDN5-binding domain of Clostridium perfringens enterotoxin, using a robust workflow of structural modeling and in vitro validation techniques. Computational analysis at the atom level based on solubility and affinity to CLDN5 identified a CLDN5-derived peptide not reported previously called f1-C5C2, which was soluble in biological media, displayed efficient binding to CLDN5, and transiently increased BBB permeability. The peptidomimetic strategy described here may have potential applications in the pharmacological treatment of brain diseases.

Molecular Evolution of Paralogous Cold Shock Proteins in E. coli: A Study of Asymmetric Divergence and Protein Functional Networks

Nine homologous Cold Shock Proteins (Csps) have been recognized in the E.coli Cold Shock Domain gene family. These Csps function as RNA chaperones. This study aims to establish the evolutionary relationships among these genes by identifying and classifying their paralogous counterparts. It focuses on the physicochemical, structural, and functional analysis of the genes to explore the phylogeny of the Csp gene family. Computational tools were employed for protein molecular modeling, conformational analysis, functional studies, and duplication-divergence assessments. The research also examined amino acid conservation, protein mutations, domain-motif patterns, and evolutionary residue communities to better understand residual interactions, evolutionary coupling, and co-evolution. H33, M5, W11 and F53 residues were highly conserved within the protein family. It was further seen that residues M5, G17, G58, G61, P62, A64, V67 were intolerant to any kind of mutation whereas G3, D40, G41, Y42, S44, T54, T68, S69 were most tolerable towards substitutions. The study of residue communities displayed that the strongest residue coupling was observed in N13, F18, S27, F31, and W11. It was observed that all the gene pairs except CspF/CspH had new motifs generated over time. It was ascertained that all the gene pairs underwent asymmetric expression divergence after duplication. The Ka/ Ks ratio also revealed that all residues undertook neutral and purifying selection pressure. New functions were seen to develop in gene pairs evident from generation of new motifs. The discovery of new motifs and functions in Csps highlights their adaptive versatility, crucial for E. coli's resilience to environmental stressors and valuable for understanding bacterial stress response mechanisms. These findings will pave the way for future investigations into Csp evolution, with potential applications in microbial ecology and antimicrobial strategy development.

Phylogenetic analysis and homology modelling of a new Cry8A crystal protein expressed in a sporulating soil bacterium

Cry proteins, commonly found in Gram-positive soil bacteria, are used worldwide as aerial sprays or in transgenic plants for controlling crop pest populations and insect vectors. Via PCR analysis, a spore producing soil isolate (BV5) was speculated to encode a Cry gene. Partial nucleotide sequence of the amplified PCR fragment showed homology with the Cry8 genes present in GenBank. A full-length Cry gene was cloned, and the predicted protein sequence grouped the newly isolated Cry protein with other Cry8A present in GenBank with a high possibility of it being a new Cry8. SDS-PAGE and MALDI-TOF mass spectrometry confirmed the expression of a single 135 KDa protein matching uniquely to the putative protein sequence of the BV5 Cry gene. However, bioassay against the coleopteran Anthonomus grandis (Coleopterans are a known Cry8A target), showed no activity. Phylogenetic analysis and homology modelling was performed to characterize the protein structure and function. These analyses suggest a series of mutations in one of the variable loops on the surface of the protein.

All1750 of Anabaena PCC 7120 encodes a novel NAD+-dependent amine dehydrogenase having broad substrate range

Native amine dehydrogenases (AmDHs) are rare and typically have narrow substrate specificity and low processivity. Therefore, they are often modified using protein engineering for industrial and pharmaceutical applications. This study presents identification and characterization of a novel native amine dehydrogenase (AmDH) encoding WD40 protein (All1750) from Anabaena PCC 7120. Heterologous expression of all1750 in E. coli enhanced its tolerance to abiotic stressors such as drought, cadmium, and NaCl, as evidenced by increase in gene expression (2-10-fold), spot assay results (3-4-fold) and decreased ROS generation (0.2-1.8-fold). Molecular docking analysis showed that All1750 has broad substrate binding activity, indicating its catalytic potential in amine oxidation. All1750 exhibited the appreciable enzymatic activity with acetophenone (0.8-1.0-fold increase), followed by 4-fluorophenyl acetone and 4-fluoropropiophenone. The Km values for acetophenone and 4-fluorophenyl acetone were 4.2-12.1-fold higher, suggesting a greater affinity of All1750 for these low-cost substrates compared to the expensive 4-fluoropropiophenone. Recombinant All1750 showed optimal enzyme activity at pH 8.0 and maintained thermo-stability at 70 °C with a half-life of approximately 3 h. Our findings provide valuable insights into the industrial application of the All1750 protein. This native AmDH from Anabaena can effectively utilize diverse cost-effective substrates, making it a promising biocatalyst for chiral amine biosynthesis.

Design of a multi-epitope vaccine candidate against carrion disease by immunoinformatics approach

Carrion's disease, caused by the bacterium Bartonella bacilliformis, is a serious public health problem in Peru, Ecuador and Colombia. Currently there is no available vaccine against B. bacilliformis. While antibiotics are the standard treatment, resistant strains have been reported, and there is a potential spread of the vector that transmits the bacteria. This study aimed to design a multi-epitope vaccine candidate against the causative agent of Carrion's disease using immunoinformatics tools. Predictions of B-cell epitopes, as well as CD4+ and CD8+T cell epitopes, were performed from the entire proteome of B. bacilliformis KC583 using the most frequent alleles from Peru, Ecuador, Colombia, and worldwide. B-cell epitopes and T-cell nested epitopes from outer membrane and virulence-associated proteins were selected. Epitopes were filtered out based on promiscuity, non-allergenicity, conservation, non-homology and non-toxicity. Two vaccine constructs were assembled using linkers. The tertiary structure of the constructs was predicted, and their stability was evaluated through molecular dynamics simulations. The most stable construct was selected for molecular docking with the TLR4 receptor. This study proposes a vaccine construct evaluated in silico as a potential vaccine candidate against Bartonella bacilliformis.

Gene silencing of Histidyl-tRNA synthetase in Leishmania donovani promastigotes inhibits parasite growth and reduces virulence: A comprehensive computational and in vitro study

The majority of anti-leishmanial drugs used for treating trypanosomatid parasites help to reduce human morbidity and mortality. However, parasites have developed drug resistance, which has made it challenging to treat leishmaniasis. Therefore, new drugs and drug targets need to be identified. Protein synthesis is a crucial anabolic mechanism necessary for parasite survival. Histidyl-tRNA synthetase (HisRS) is an essential enzyme that is required for histidine incorporation into proteins. Recent studies on HisRS have shown differences between trypanosomatid HisRS and human HisRS, which could lead to the development of trypanosomatid HisRS structure-based inhibitors. This study aims to determine the role of L. donovani HisRS (LdHisRS) in parasite growth and virulence in vitro using RNAi. The silencing effect of LdHisRS expression was determined using qPCR. The results showed that after 24 and 48 h of incubation with 90 ng siRNAs, LdHisRS mRNA expression levels were significantly reduced by ∼3.14-fold and ∼3.90-fold, respectively. SiRNA-treated parasites also exhibited ∼46.6 % delayed growth and ∼47 % reduced virulence. Additionally, homology modeling, virtual screening, and molecular docking studies were performed with potential inhibitors that have significant suppressive activity in bacteria, fungi, and viruses. Halofuginone was found to have the best binding affinity of -9.09 kcal/mol as a potent inhibitor against LdHisRS. The molecular dynamics (MD) results showed that halofuginone could interact with the various active site segments, potentially blocking substrate access. The data on gene silencing through siRNA suggests that LdHisRS is essential for the parasite's growth and survival. The computational findings could lead to the development of a potent ligand (halofuginone) as a future anti-leishmanial drug, paving the way for an effective therapeutic treatment.

Novel Dolutegravir and Lenacapavir Resistance Patterns in Human Immunodeficiency Virus Type 2 Infection: A Case Report

Background

The treatment management of human immunodeficiency virus (HIV)-2 infection presents greater challenges compared to HIV-1 infection, primarily because of inherent resistance against non-nucleoside reverse transcriptase inhibitors. Integrase strand transfer inhibitors, particularly dolutegravir, have improved treatment outcomes for people with HIV-2. Lenacapavir, a novel and potent antiretroviral capsid inhibitor, offers additional therapeutic options. However, limited knowledge exists regarding HIV-2 resistance against dolutegravir and lenacapavir.

Methods

We report the case of a treatment-experienced individual who did not achieve virological suppression with regimens containing dolutegravir and lenacapavir. Clinical monitoring, genotypic and phenotypic resistance assays, and in silico structural modeling were performed.

Results

Lenacapavir was added to a failing regimen of boosted darunavir, twice daily dolutegravir, and 2 nucleoside reverse transcriptase inhibitors. Initially, this addition led to a decline in the viral load and increase in CD4+ T-cell count, despite the identification of a previously unreported combination of integrase resistance mutations. However, virological suppression was not achieved and viral load, although reduced, resumed increasing. This rebound was associated with the development of an N73D capsid substitution in HIV-2, which conferred resistance against lenacapavir. Based on cell-based assays predicting hypersusceptibility to bictegravir, the regimen was adjusted to oral lenacapavir plus bictegravir/emtricitabine/tenofovir alafenamide, resulting in a resumption in viral load decline.

Conclusions

Although lenacapavir demonstrated therapeutic potential, our case underscores the critical need to combine it with other fully active antiretroviral agents to prevent the rapid emergence of resistance and achieve long-term virological control in treatment-experienced individuals with HIV-2.

Integrating structure-guided and fragment-based inhibitor design to combat bedaquiline resistant Mycobacterium tuberculosis: a molecular dynamics study

The first FDA approved, MDR-TB inhibitory drug bedaquiline (BDQ), entraps the c-ring of the proton-translocating F0 region of enzyme ATP synthase of Mycobacterium tuberculosis, thus obstructing successive ATP production. Present-day BDQ-resistance has been associated with cardiotoxicity and mutation(s) in the atpE gene encoding the c subunit of ATP synthase (ATPc) generating five distinct ATPc mutants: Ala63→Pro, Ile66→Met, Asp28→Gly, Asp28→Val and Glu61→Asp. We created three discrete libraries, first by repurposing bedaquiline via scaffold hopping approach, second one having natural plant compounds and the third being experimentally derived analogues of BDQ to identify one drug candidate that can inhibit ATPc activity more efficiently with less toxic properties. For this purpose, we adopted techniques like molecular dynamics simulation, virtual screening, PCA, DCCM, binding affinity analysis to gauge structure-function relationship of the L136-ATPc complexes. L136 was found to induce a distinguishable conformational change in the bound ATPc which captivated the c9 rotor ring. L136 displays a binding free energy of -57.294, -59.027, -57.273, -58.726, -55.889 and -58.651 kcal/mol for ATPc_WT and the five respective mutants. The pIC50 value for the L136 ligand for the same proteins was unveiled to be 6.760, 7.285, 6.898, 7.222, 6.987 and 7.687. Moreover, L136 exhibited a strong ADMET profile. Furthermore, we discovered that the change in the hydrophobic platform in ATPc mutants hinders BDQ binding, which is overcome by L136, ensuring efficient binding and providing an assessment of L136's mechanism of ATPc inhibition. L136 provides a scope for in vivo test for future clinical drug trials.

Comprehensive In Vitro Evaluation of Antibacterial, Antioxidant, and Computational Insights into Blepharis ciliaris (L.) B. L. Burtt from Hail Mountains, Saudi Arabia

The arid mountainous region of Hail in Saudi Arabia has a variety of desert vegetation, some of which are conventionally used in Bedouin traditional medicine. These plants need scientific examination. This research seeks to examine Blepharis ciliaris using a thorough multi-analytical methodology that includes antibacterial and antioxidant assessments as well as computational modeling. GC-MS analysis of the methanolic extract revealed 17 organic compounds, including pentadecanoic acid, ethyl methyl ester (2.63%); hexadecanoic acid, methyl ester (1.00%); 9,12-octadecadienoic acid (Z,Z)-, methyl ester (2.74%); 9-octadecenoic acid, methyl ester (E) (2.78%); octadecanoic acid (5.88%); 9-tetradecenoic acid (Z) (3.22%); and undec-10-enoic acid, undec-2-n-1-yl ester (5.67%). The DPPH test evaluated antioxidant activity, revealing a notable increase with higher concentrations of the methanolic extract, achieving maximum inhibition of 81.54% at 1000 µg/mL. The methanolic extract exhibited moderate antibacterial activity, with average inhibition zones of 10.33 ± 1.53 mm, 13.33 ± 1.53 mm, 10.67 ± 1.53 mm, and 10.00 ± 2.00 mm against Staphylococcus aureus, Bacillus subtilis, Escherichia coli, and Serratia marcescens, respectively, as determined by the disk diffusion method. The minimum inhibitory concentration (MIC) values were 500 µg/mL for S. aureus and B. subtilis, whereas E. coli and S. marcescens showed susceptibility at 1000 µg/mL. Computational simulations were employed to assess the toxicity, drug-likeness, and ADMET profiles of compounds derived from Blepharis ciliaris. Thirteen bioactive compounds were assessed in silico against Staphylococcus aureus sortase A (PDB: 1T2O), Bacillus subtilis BsFabHb (PDB: 8VDB), Escherichia coli LPS assembly protein (LptD) (PDB: 4RHB), and a modeled Serratia marcescens outer-membrane protein TolC, focusing on cell wall and membrane structures. Compound 3, (+)-Ascorbic acid 2,6-dihexadecanoate, shown significant binding affinities to B. subtilis BsFabHb, E. coli LPS assembly protein, and S. marcescens TolC.

Immunoinformatics design of a multi-epitope vaccine for Chlamydia trachomatis major outer membrane proteins

Chlamydia trachomatis (CT) remains a significant infectious cause of blindness and sexually transmitted infections worldwide. The objective and novelty of this study lie in using different serovars of CT to design a broad-spectrum multi-epitope vaccine that might confer immunity against different CT infections. As the major outer membrane protein in CT has good immunodominance properties and high conservation and also determines the several serotypes of CT, it is selected as an antibody target in this study. T-cell and B-cell epitopes from serovars A, B, D, E, L1, and L2 were predicted and combined into a single construct by incorporating adjuvants and linkers to enhance immunogenicity and stability. Physicochemical characterization confirmed the constructed vaccine's anti-allergic, immunogenicity, and thermostable characteristics, followed by structural modeling to refine its 3D configuration. The 3D model structure of the vaccine was validated through the Ramachandran plot and ProSA z-score. Molecular docking studies of the vaccine demonstrated stable binding with toll-like receptor 3, along with molecular dynamics simulations and binding free energy calculations supporting the complex's stability. In silico cloning has indicated a high potential for expression in Escherichia coli. Lastly, immune simulations revealed robust activation of B cells, cytotoxic T cells, and antigen-presenting cells, alongside significant production of IgM, IgG antibodies, and balanced Th1/Th2 cytokine response, which is crucial for effective immunity. These results suggest the multi-epitope vaccine could effectively induce comprehensive immune responses against CT, highlighting the need for further in vivo validation to advance this promising candidate toward clinical use.

Anti-adherent effects of Rhizophora apiculata bark and leaf extracts and computational prediction of the effects of its compound on β-tubulin interaction in Acanthamoeba triangularis genotype 4

Background and Aim

Acanthamoeba, an opportunistic protozoan, exists widely in natural sources and can cause infections in humans and animals. The absence of effective monotherapy after the initial infection leads to chronic disease and recurrence. Tubulin protein is a vital target for design-targeted drug discovery. Anti-tubulin drugs are also used to treat Acanthamoeba infections, although resistance to these drugs has been observed. Therefore, it is necessary to identify a new targeted drug for Acanthamoeba infections. Therefore, this study aimed to assess the in vitro activity of ethanol extracts of Rhizophora apiculata extracts (RAE) against Acanthamoeba spp. and to predict its chemical compound on β-tubulin interaction.

Materials and Methods

In this study, anti-Acanthamoeba activity with minimal inhibitory concentration (MIC) and minimal parasiticidal concentration (MPC) determination of ethanolic RAE from leaves, blossoms, buds, branches, and barks was tested on four Acanthamoeba trophozoites and cysts: Acanthamoeba triangularis WU 19001, Acanthamoeba polyphaga American Type Culture Collection (ATCC) 30461, Acanthamoeba castellanii ATCC 50739, and A. castellanii ATCC 30010. The inhibitory effect on adherence was determined by the ability of Acanthamoeba adherence on 96-well plates, and its adhesive acanthopodia structure was evaluated using scanning electron microscopy analysis. In addition, the minimum cytotoxic concentrations (MCC) of R. apiculata leaf extract (RALE) and bark extract (RABE) were evaluated on Vero and HaCaT cell lines using the MTT assay. Phytochemical compounds from RALE and RABE were also analyzed by gas chromatography-mass spectrometry (GC-MS). Molecular docking and molecular dynamic analysis predicted the binding sites of chemicals in extracts and β-tubulin protein.

Results

The results revealed that A. triangularis and A. polyphaga trophozoites had the highest inhibition at 90% at a MIC of 8 mg/mL after treatment with RALE and RABE, respectively, at 24 h. Those MPC values were exhibited at 16 mg/mL against A. triangularis trophozoites. In addition, both extracts inhibited the adhesive properties of all Acanthamoeba approximately 80%-90% at 4 mg/mL, as well as adherent structural acanthopodia loss. MCC was 0.25 mg/mL, provided to be harmless to mammalian cells. GC-MS analysis supported that 8 and 11 major phytochemicals were from RABE and RALE, respectively. Molecular docking and molecular dynamics demonstrated that Acanthamoeba-β-tubulin exhibited potent root-mean-square deviation, root mean square fluctuation, and binding free energy values with clionasterol (from RABE and RALE) and stigmasterol (from RALE). Based on our results, ethanolic RABE and RALE exhibited anti-Acanthamoeba activity in reducing adhesion. In silico showed that promising clionasterol and stigmasterol interacted with a targeting β-tubulin.

Conclusion

The RABE and RALE exhibited a potential anti-adherent effect on A. triangularis, low toxicity, and the clionasterol and stigmasterol in RABE and RALE predicted to interact the targeted β-tubulin. These agents may be used as alternative therapeutic agents in the management of disease using a sustainable one-heath approach.

Tracing the intraspecies expansion of glyoxalase genes and their expanding roles across the genus Oryza

The genus Oryza is of utmost importance to human civilization as two of its species became agronomically productive and widely cultivated, and also because wild rice is a treasure trove of beneficial alleles that can be used for crop improvement. Most of the wild rice genotypes are known for their stress tolerance several times more than the domesticated rice varieties. In this study, we aimed to carry out an exhaustive genomic survey to identify glyoxalase I (GLYI) and glyoxalase II (GLYII) genes across the 11 rice genomes sequenced so far. Notably, we found the putatively functional metal-dependent GLYI and GLYII enzymes to be conserved throughout domestication and a few homologous pairs to have undergone beneficial mutations to drive positive selection, and thus, acquire newer functions. Interestingly, we also report four newly identified GLYII members in O. sativa subsp. japonica in addition to the three previously reported GLYII genes. The presence of different types of cis-elements in the promoter region of the glyoxalase genes gives insights into their role and regulation under various developmental processes besides stress adaptation. Publicly available data suggests the role of glyoxalase genes particularly in salinity stress in both wild and cultivated rice as is also confirmed through qRT-PCR. Interestingly, we found less accumulation of MG and concurrently higher enzymatic activity of GLYI and GLYII proteins in stressed seedlings of selected wild rice genotypes indicating that glyoxalases indeed contribute to the intrinsic stress tolerance of wild rice.

Vaccination with OprB porin, and its epitopes offers protection against A. baumannii infections in mice

A. baumannii is a deadly antimicrobial resistance pathogen that acquires drug resistance through different mechanisms. Therefore, it is necessary to investigate all its virulence factors and design effective vaccines against it. For this purpose, OprB, an outer membrane porin, was investigated in this study, and its secondary and tertiary structures, physicochemical properties, and B-T epitopes were determined. The vaccine potential of this protein and its linear, non-continuous, and chimeric epitopes were also in-vivo analyzed. Based on the results, two surface epitopes and one non-continuous epitope were identified. Surface contiguous epitopes were produced recombinantly and non-continuous epitope sequences were synthesized and then produced. The chimeric epitope was also produced via the SOE-PCR technique. Active and passive immunization of mice with the whole OprB protein, non-continuous epitope, contiguous epitopes, two epitopes in chimeric form, as well as the mixture of two purified epitopes showed that the survival level and total IgG titer of the mice compared to non-vaccinated mice or mice that were vaccinated with an internal fragment increased significantly. The bacterial load in the immunized mice's lung, liver, kidney, and spleen was much lower than in the control groups, and the TNF-α, IFN-γ, and IL-6 cytokines levels were also lower in these groups and were similar to the naive mice. On the other hand, subunit vaccines showed acceptable safety and due to their minimal cross-activity, their use is much safer.

Molecular hybridization assisted multi-technique approach for designing USP21 inhibitors to halt catalytic triad-mediated nucleophilic attack and suppress pancreatic ductal adenocarcinoma progression: A molecular dynamics study

AIMS

Pancreatic cancer, the 12th-most common cancer, globally, is highly challenging to treat due to its complex epigenetic, metabolic, and genomic characteristics. In pancreatic ductal adenocarcinoma, USP21 acts as an oncogene by stabilizing the long isoform of Transcription Factor 7, thereby activating the Wnt signaling pathway. This study aims to inhibit activation of this pathway through computer-aided drug discovery. Accordingly, four libraries of compounds were designed to target the USP21's catalytic domain (Cys221, His518, Asp534), responsible for its deubiquitinating activity.

MAIN METHODS

Utilizing an array of computer-aided drug design methodologies, such as molecular docking, virtual screening, principal component analysis, molecular dynamics simulation, and dynamic cross-correlation matrix, the structural and functional characteristics of the USP21-inhibitor complex were examined. Following the evaluation of the binding affinities, 20 potential ligands were selected, and the best ligand was subjected to additional molecular dynamics simulation study.

KEY FINDINGS

The results indicated that the ligand-bound USP21 exhibited reduced structural fluctuations compared to the unbound form, as evident from RMSD, RMSF, Rg, and SASA graphs. ADMET analysis of the top ligand showed promising pharmacokinetic and pharmacodynamic profiles, good bioavailability, and low toxicity. The stable conformations of the proposed drug when bound to their target cavities indicate a robust binding affinity of -9.3 kcal/mol. The drug exhibits an elevated pKi value of 6.82, a noteworthy pIC50 value of 5.972, and a pKd value of 6.023 proving its high affinity and inhibitory potential towards the target.

SIGNIFICANCE

In-vitro testing of the top compound (MOLHYB-0436) could lead to its use as a potential treatment for pancreatic cancer.

Development of a carbohydrate-binding protein prediction algorithm using structural features of stacking aromatic rings

Carbohydrate-protein interactions play fundamental roles in numerous aspects of biological activities, and the search for new carbohydrate (CHO)-binding proteins (CBPs) has long been a research focus. In this study, through the analysis of CBP structures, we identified significant enrichment of aromatic residues in CHO-binding regions. We further summarized the structural features of these aromatic rings within the CHO-stacking region, namely "exposing" and "proximity" features, and developed a screening algorithm that can identify CHO-stacking Trp (tryptophan) residues based on these two features. Our Trp screening algorithm can achieve high accuracy in both CBP (specificity score 0.93) and CBS (Carbohydrate binding site, precision score 0.77) prediction using experimentally determined protein structures. We also applied our screening algorithm on AlphaGO pan-species predicted models and observed significant enrichment of carbohydrate-related functions in predicted CBP candidates across different species. Moreover, through carbohydrate arrays, we experimentally verified the CHO-binding ability of four candidate proteins, which further confirms the robustness of the algorithm. This study provides another perspective on proteome-wide CBP and CBS prediction. Our results not only help to reveal the structural mechanism of CHO-binding, but also provide a pan-species CBP dataset for future CHO-protein interaction exploration.

Structural and functional characterization of haemoglobin genes in Labeo catla: Insights into hypoxic adaptation and survival

Haemoglobin (HB) protein comprises four subunits: two identical α-subunits (HBA) and two identical β-subunits (HBB), encoded by the HBA and HBB genes. In this investigation, 5'/3' RACE PCR (Rapid Amplification of cDNA Ends) was used to obtain complete coding sequences (CDSs) of both the genes from farmed Labeo catla. The resulting CDSs were 432 base pairs and 447 base pairs for HBA and HBB, respectively, corresponding to 143 and 148 amino acids. Phylogenetic analysis revealed close relationships with other cyprinids, with Labeo rohita being the closest relative. Functional analysis and protein structure prediction were conducted using bioinformatics tools. Expression profiling of both genes was checked in various tissues under control (C) and hypoxic (H) conditions. Notably, under hypoxia, HBA and HBB genes were significantly upregulated (P < 0.05) initially, followed by a return to normal expression levels. Similar trends were observed for Hif1α (Hypoxia-inducible factor one alpha) and EPO (Erythropoietin) genes. Additionally, haematological indices also significantly increased corresponding to the gene expressions. However, with the decrease in the expression of these genes an onset of mortality was observed in the hypoxia (H) treated groups. The results of the current study explored the role of haemoglobin genes in adaptation to the hypoxic condition.

Predictive immunoinformatics reveal promising safety and anti-onchocerciasis protective immune response profiles to vaccine candidates (Ov-RAL-2 and Ov-103) in anticipation of phase I clinical trials

Onchocerciasis (river blindness) is a debilitating tropical disease that causes significant eye and skin damage, afflicting millions worldwide. As global efforts shift from disease management to elimination, vaccines have become crucial supplementary tools. The Onchocerciasis Vaccine for Africa (TOVA) Initiative was established in 2015, to advance at least one vaccine candidate initially targeting onchocerciasis in infants and children below 5 years of age, through Phase I human trials by 2025. Notably, Ov-RAL-2 and Ov-103 antigens have shown great promise during pre-clinical development, however, the overall success rate of vaccine candidates during clinical development remains relatively low due to certain adverse effects and immunogenic limitations. This study, thus, aimed at predicting the safety and immunogenicity of Ov-RAL-2 and Ov-103 potential onchocerciasis vaccine candidates prior to clinical trials. Advanced molecular simulation models and analytical immunoinformatics algorithms were applied to predict potential adverse side effects and efficacy of these antigens in humans. The analyses revealed that both Ov-RAL-2 and Ov-103 demonstrate favourable safety profiles as toxicogenic and allergenic epitopes were found to be absent within each antigen. Also, both antigens were predicted to harbour substantial numbers of a wide range of distinct epitopes (antibodies, cytokines, and T- Cell epitopes) associated with protective immunity against onchocerciasis. In agreement, virtual vaccination simulation forecasted heightened, but sustained levels of primary and secondary protective immune responses to both vaccine candidates over time. Ov-103 was predicted to be non-camouflageable, as it lacked epitopes identical to protein sequences in the human proteome. Indeed, both antigens were able to bind with high affinity and activate the innate immune TLR4 receptor, implying efficient immune recognition. These findings suggest that Ov-RAL-2 and Ov-103 can induce sufficient protective responses through diverse humoral and cellular mechanisms. Overall, our study provides additional layer of evidence for advancing the clinical development of both vaccine candidates against onchocerciasis.

α-Glucosidase isoform G contributes to heme detoxification in Rhodnius prolixus and its knockdown affects Trypanosoma cruzi metacyclogenesis

The triatomine bug Rhodnius prolixus is a hematophagous hemipteran and a primary vector of Trypanosoma cruzi, the causative agent of Chagas' disease (CD), in Central America and Northern South America. Blood-feeding poses significant challenges for hematophagous organisms, particularly due to the release of high doses of pro-oxidant free heme during hemoglobin digestion. In this arthropod, most of the free heme in the gut is aggregated into hemozoin (Hz), an inert and non-oxidative biocrystal. Two major components present in the perimicrovillar membranes (PMM) of triatomine insects have been previously implicated in heme crystallization: lipids and the biochemical marker of the PMM, the enzyme α-glucosidase. In this study, we investigated the role of R. prolixus α-glucosidase isoform G (Rp-αGluG) in heme detoxification and the effects of its knockdown on the insect physiology. The effect of α-glucosidase isoform G (αGluG) knockdown on T. cruzi proliferation and metacyclogenesis was also investigated. Initially, a 3D structure of Rp-αGluG was predicted by comparative modeling and then subjected to molecular docking with the heme molecule, providing in silico support for understanding the process of Hz biocrystallization. Next, adult females of R. prolixus were challenged with RNAi against Rp-αGluG (dsαGluG) to assess physiological and phenotypic changes caused by its knockdown. Our data show that the group challenged with dsαGluG produced less Hz, resulting in more intact hemoglobin available in the digestive tract. These animals also laid fewer eggs, which had a lower hatching rate. In addition, T. cruzi metacyclogenesis was significantly lower in the dsαGluG group. The present work demonstrates the importance of Rp-αGluG in heme detoxification, the digestive and reproductive physiology of R. prolixus, as well as its influence on the life cycle of T. cruzi. Since heme neutralization is a vital process for hematophagous bugs, our study provides useful information for the development of new strategies targeting the Hz formation and potentially affecting the vectorial transmission of Chagas disease.

Development of a bioluminescent homogenous nanobody-based immunoassay for the detection of prostate-specific antigen (PSA)

Prostate cancer is the most prevalent cancer in men. At present, the diagnosis and screening of prostate cancer rely on the essential biomarker known as prostate-specific antigen (PSA). The main purpose of this study was to develop a novel immunoassay for the detection of PSA based on a tri-part split-nanoluciferase system and a nanobody targeting PSA. In our approach, two small components of the split-nanoluciferase, referred to as β9 and β10, were individually fused to two anti-PSA nanobodies, N7 and N23. When these proteins bind to PSA and in the presence of the third nanoluciferase component, called Δ11S, the split-nanoluciferase components are brought into close proximity, facilitating the reassembly of the active nanoluciferase and activation of luminescence. These proteins were expressed in a bacterial expression system, purified, and employed for the intended immunoassay. The developed immunoassay demonstrated the capability to sensitively detect PSA within a linear range from 1.0 to 20.0 ng/mL with LOD of 0.4 ng/mL, and the results obtained through this immunoassay agreed with those derived from the ELISA. Our study indicates that the homogeneous immunoassay developed with nanobodies exhibits remarkable specificity for PSA and can serve as a reliable, fast, and user-friendly test for detecting PSA.

The Phylogenomic Characterization of Planotetraspora Species and Their Cellulases for Biotechnological Applications

This study aims to evaluate the in silico genomic characteristics of five species of the genus Planotetraspora: P. kaengkrachanensis, P. mira, P. phitsanulokensis, P. silvatica, and P. thailandica, with a view to their application in therapeutic research. The 16S rRNA comparison indicated that these species were phylogenetically distinct. Pairwise comparisons of digital DNA-DNA hybridization (dDDH) and OrthoANI values between these studied type strains indicated that dDDH values were below 62.5%, while OrthoANI values were lower than 95.3%, suggesting that the five species represent distinct genomospecies. These results were consistent with the phylogenomic study based on core genes and the pangenome analysis of these five species within the genus Planotetraspora. However, the genome annotation showed some differences between these species, such as variations in the number of subsystem category distributions across whole genomes (ranging between 1979 and 2024). Additionally, the number of CAZYme (Carbohydrate-Active enZYme) genes ranged between 298 and 325, highlighting the potential of these bacteria for therapeutic research applications. The in silico physico-chemical characteristics of cellulases from Planotetraspora species were analyzed. Their 3D structure was modeled, refined, and validated. A molecular docking analysis of this cellulase protein structural model was conducted with cellobiose, cellotetraose, laminaribiose, carboxymethyl cellulose, glucose, and xylose ligand. Our study revealed significant interaction between the Planotetraspora cellulase and cellotetraose substrate, evidenced by stable binding energies. This suggests that this bacterial enzyme holds great potential for utilizing cellotetraose as a substrate in various applications. This study enriches our understanding of the potential applications of Planotetraspora species in therapeutic research.

Identification and functional characterization of the npc-2-like domain containing rust effector protein that suppresses cell death in plants

The MD-2-related lipid-recognition (ML/Md-2) domain is a lipid/sterol-binding domain that are involved in sterol transfer and innate immunity in eukaryotes. Here we report a genome-wide survey of this family, identifying 84 genes in 30 fungi including plant pathogens. All the studied species were found to have varied ML numbers, and expansion of the family was observed in Rhizophagus irregularis (RI) with 33 genes. The molecular docking studies of these proteins with cholesterol derivatives indicate lipid-binding functional conservation across the animal and fungi kingdom. The phylogenetic studies among eukaryotic ML proteins showed that Puccinia ML members are more closely associated with animal (insect) npc2 proteins than other fungal ML members. One of the candidates from leaf rust fungus Puccinia triticina, Pt5643 was PCR amplified and further characterized using various studies such as qRT-PCR, subcellular localization studies, yeast functional complementation, signal peptide validation, and expression studies. The Pt5643 exhibits the highest expression on the 5th day post-infection (dpi). The confocal microscopy of Pt5643 in onion epidermal cells and N. benthamiana shows its location in the cytoplasm and nucleus. The functional complementation studies of Pt5643 in npc2 mutant yeast showed its functional similarity to the eukaryotic/yeast npc2 gene. Furthermore, the overexpression of Pt5643 also suppressed the BAX, NEP1, and H₂O₂-induced program cell death in Nicotiana species and yeast. Altogether the present study reports the novel function of ML domain proteins in plant fungal pathogens and their possible role as effector molecules in host defense manipulation.

Computational exploration of protein structure dynamics and RNA structural consequences of PKD1 missense variants: implications in ADPKD pathogenesis

We analyzed the impact of nine previously identified missense PKD1 variants from our studies, including c.6928G > A p.G2310R, c.8809G > A p.E2937K, c.2899 T > C p.W967R, c.6284A > G p.D2095G, c.6644G > A p.R2215Q, c.7810G > A p.D2604N, c.11249G > C p.R3750P, c.1001C > T p.T334M, and c.3101A > G p.N1034S on RNA structures and PC1 protein structure dynamics utilizing computational tools. RNA structure analysis was done using short RNA snippets of 41 nucleotides with the variant position at the 21st nucleotide, ensuring 20 bases on both sides. The secondary structures of these RNA snippets were predicted using RNAstructure. Structural changes of the mutants compared to the wild type were analyzed using the MutaRNA webserver. Molecular dynamics (MD) simulation of PC1 wild-type and mutant protein regions were performed using GROMACS 2018 (GROMOS96 54a7 force field). Findings revealed that five variants including c.8809G > A (p.E2937K), c.11249G > C (p.R3750P), c.3101A > G (p.N1034S), c.6928G > A (p.G2310R), c.6644G > A (p.R2215Q) exhibited major alterations in RNA structures and thereby their interactions with other proteins or RNAs affecting protein structure dynamics. While certain variants have minimal impact on RNA conformations, their observed alterations in MD simulations indicate impact on protein structure dynamics highlighting the importance of evaluating the functional consequences of genetic variants by considering both RNA and protein levels. The study also emphasizes that each missense variant exerts a unique impact on RNA stability, and protein structure dynamics, potentially contributing to the heterogeneous clinical manifestations and progression observed in Autosomal Dominant Polycystic Kidney Disease (ADPKD) patients offering a novel perspective in this direction. Thus, the utility of studying the structure dynamics through computational tools can help in prioritizing the variants for their functional implications, understanding the molecular mechanisms underlying variability in ADPKD presentation and developing targeted therapeutic interventions.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-024-04057-9.

In Vivo Exposure of Deltamethrin Dysregulates the NFAT Signalling Pathway and Induces Lung Damage

Deltamethrin is an insecticide used to control harmful agricultural insects that otherwise damage crops and to control vector-borne diseases. Long-term exposure to deltamethrin results in the inflammation of the lungs. The present study elucidates the molecular mechanism underlying the deltamethrin-induced lung damage. The lung samples were extracted from the Swiss albino mice following the treatment of low (2.5 mg/kg) and high (5 mg/kg) doses of deltamethrin. The mRNA expression of TCR, IL-4, and IL-13 showed upregulation, while the expression of NFAT and FOS was downregulated following a low dose of deltamethrin. Moreover, the expression of TCR was downregulated with the exposure of a high dose of deltamethrin. Furthermore, the immunohistochemistry data confirmed the pattern of protein expression for TCR, FOS, IL-4, and IL-13 following a low dose of deltamethrin exposure. However, no change was seen in the TCR, NFAT, FOS, JUN, IL-4, and IL-13 immunopositive cells of the high-dose treatment group. Also, ELISA results showed increased expression of IL-13 in the BAL fluid of animals exposed to low doses of deltamethrin. Overall, the present study showed that deltamethrin exposure induces lung damage and immune dysregulation via dysregulating the NFAT signalling pathway.

Infection by a multidrug-resistant Corynebacterium diphtheriae strain: prediction of virulence factors, CRISPR-Cas system analysis, and structural implications of mutations conferring rifampin resistance

Cases of diphtheria, even in immunized individuals, are still reported in several parts of the world, including in Brazil. New outbreaks occur in Europe and other continents. In this context, studies on Corynebacterium diphtheriae infections are highly relevant, both for a better understanding of the pathogenesis of the disease and for controlling the circulation of clones and antimicrobial resistance genes. Here we present a case of cutaneous infection by multidrug-resistant Corynebacterium diphtheriae and provide its whole-genome sequencing. Genomic analysis revealed resistance genes, including tet(W), sul1, cmx, rpoB2, rbpA and mutation in rpoB. We performed phylogenetic analyzes and used the BRIG to compare the predicted resistance genes with those found in genomes from other significant isolates, including those associated with some outbreaks. Virulence factors such as spaD, srtBC, spaH, srtDE, surface-anchored pilus proteins (sapD), nonfimbrial adhesins (DIP0733, DIP1281, and DIP1621), embC and mptC (putatively involved in CdiLAM), sigA, dtxR and MdbA (putatively involved) in post-translational modification, were detected. We identified the CRISPR-Cas system in our isolate, which was classified as Type II-U based on the database and contains 15 spacers. This system functions as an adaptive immune mechanism. The strain was attributed to a new sequence type ST-928, and phylogenetic analysis confirmed that it was related to ST-634 of C. diphtheriae strains isolated in French Guiana and Brazil. In addition, since infections are not always reported, studies with the sequence data might be a way to complement and inform C. diphtheriae surveillance.

Efficacy of a stable broadly protective subunit vaccine platform against SARS-CoV-2 variants of concern

The emergence and ongoing evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has highlighted the need for rapid vaccine development platforms that can be updated to counteract emerging variants of currently circulating and future emerging coronaviruses. Here we report the development of a "train model" subunit vaccine platform that contains a SARS-CoV-2 Wuhan S1 protein (the "engine") linked to a series of flexible receptor binding domains (RBDs; the "cars") derived from SARS-CoV-2 variants of concern (VOCs). We demonstrate that these linked subunit vaccines when combined with Sepivac SWE™, a squalene in water emulsion (SWE) adjuvant, are immunogenic in Syrian hamsters and subsequently provide protection from infection with SARS-CoV-2 VOCs Omicron (BA.1), Delta, and Beta. Importantly, the bivalent and trivalent vaccine candidates offered protection against some heterologous SARS-CoV-2 VOCs that were not included in the vaccine design, demonstrating the potential for broad protection against a range of different VOCs. Furthermore, these formulated vaccine candidates were stable at 2-8 °C for up to 13 months post-formulation, highlighting their utility in low-resource settings. Indeed, our vaccine platform will enable the development of safe and broadly protective vaccines against emerging betacoronaviruses that pose a significant health risk for humans and agricultural animals.

Structural Characterization of Heat Shock Protein 90β and Molecular Interactions with Geldanamycin and Ritonavir: A Computational Study

Drug repositioning is an important therapeutic strategy for treating breast cancer. Hsp90β chaperone is an attractive target for inhibiting cell progression. Its structure has a disordered and flexible linker region between the N-terminal and central domains. Geldanamycin was the first Hsp90β inhibitor to interact specifically at the N-terminal site. Owing to the toxicity of geldanamycin, we investigated the repositioning of ritonavir as an Hsp90β inhibitor, taking advantage of its proven efficacy against cancer. In this study, we used molecular modeling techniques to analyze the contribution of the Hsp90β linker region to the flexibility and interaction between the ligands geldanamycin, ritonavir, and Hsp90β. Our findings indicate that the linker region is responsible for the fluctuation and overall protein motion without disturbing the interaction between the inhibitors and the N-terminus. We also found that ritonavir established similar interactions with the substrate ATP triphosphate, filling the same pharmacophore zone.

Comparative structural studies on Bovine papillomavirus E6 oncoproteins: Novel insights into viral infection and cell transformation from homology modeling and molecular dynamics simulations

Bovine papillomavirus (BPV) infects cattle cells worldwide, leading to hyperproliferative lesions and the potential development of cancer, driven by E5, E6, and E7 oncoproteins along with other cofactors. E6 oncoprotein binds experimentally to various proteins, primarily paxillin and MAML1, as well as hMCM7 and CBP/p300. However, the molecular and structural mechanisms underlying BPV-induced malignant transformation remain unclear. Therefore, we have modeled the E6 oncoprotein structure from non-oncogenic BPV-5 and compared them with oncogenic BPV-1 to assess the relationship between structural features and oncogenic potential. Our analysis elucidated crucial structural aspects of E6, highlighting both conserved elements across genotypes and genotype-specific variations potentially implicated in the oncogenic process, particularly concerning primary target interactions. Additionally, we predicted the location of the hMCM7 binding site on the N-terminal of BPV-5 E6. This study enhances our understanding of the structural characteristics of BPV E6 oncoproteins and their interactions with host proteins, clarifying structural differences and similarities between high and low-risk BPVs. This is important to understand better the mechanisms involved in cell transformation in BPV infection, which could be used as a possible target for therapy.

Prefoldins are novel regulators of the unfolded protein response in artemisinin resistant Plasmodium falciparum malaria

Emerging Artemisinin (ART) resistance in Plasmodium falciparum (Pf) poses challenges for the discovery of novel drugs to tackle ART-resistant parasites. Concentrated efforts toward the ART resistance mechanism indicated a strong molecular link of ART resistance with upregulated expression of unfolded protein response pathways involving Prefoldins (PFDs). However, a complete characterization of PFDs as molecular players taking part in ART resistance mechanism, and discovery of small molecule inhibitors to block this process have not been identified to date. Here, we functionally characterized all Pf Prefoldin subunits (PFD1-6) and established a causative role played by PFDs in ART resistance by demonstrating their expression in intra-erythrocytic parasites along with their interactions with Kelch13 protein through immunoprecipitation coupled MS/MS analysis. Systematic biophysical interaction analysis between all subunits of PFDs revealed their potential to form a complex. The role of PFDs in ART resistance was confirmed in orthologous yeast PFD6 mutants, where PfPFD6 expression in yeast mutants reverted phenotype to ART resistance. We identified an FDA-approved drug "Biperiden" that restricts the formation of Prefoldin complex and inhibits its interaction with its key parasite protein substrates, MSP-1 and α-tubulin-I. Moreover, Biperiden treatment inhibits the parasite growth in ART-sensitive Pf3D7 and resistant Pf3D7k13R539T strains. Ring survival assays that are clinically relevant to analyze ART resistance in Pf3D7k13R539T parasites demonstrate the potency of BPD to inhibit the growth of survivor parasites. Overall, our study provides the first evidence of the role of PfPFDs in ART resistance mechanisms and opens new avenues for the management of resistant parasites.

In silico structural features of the CgNR5A: CgDAX complex and its role in regulating gene expression of CYP target genes in Crassostrea gigas

Contamination of aquatic environments has been steadily increasing due to human activities. The Pacific oyster Crassostrea gigas has been used as a key species in studies assessing the impacts of contaminants on human health and the aquatic biome. In this context, cytochrome P450 (CYPs) play a crucial role in xenobiotic metabolism. In vertebrates many of these CYPs are regulated by nuclear receptors (NRs) and little is known about the NRs role in C. gigas. Particularly, the CgNR5A represents a homologue of SF1 and LRH-1 found in vertebrates. Members of this group can regulate genes of CYPs involved in lipid/steroid metabolism, with their activity regulated by other NR, called as DAX-1, generating a NR complex on DNA response elements (REs). As C. gigas does not exhibit steroid biosynthesis pathways, CgNR5A may play other physiological roles. To clarify this issue, we conducted an in silico investigation of the interaction between CgNR5A and DNA to identify potential C. gigas CYP target genes. Using molecular docking and dynamics simulations of the CgNR5A on DNA molecules, we identified a monomeric interaction with extended REs. This RE was found in the promoter region of 30 CYP genes and also the NR CgDAX. When the upstream regulatory region was analyzed, CYP2C39, CYP3A11, CYP4C21, CYP7A1, CYP17A1, and CYP27C1 were mapped as the main genes regulated by CgNR5A. These identified CYPs belong to families known for their involvement in xenobiotic and lipid/steroid metabolism. Furthermore, we reconstructed a trimeric complex, previously proposed for vertebrates, with CgNR5A:CgDAX and subjected it to molecular dynamics simulations analysis. Heterotrimeric complex remained stable during the simulations, suggesting that CgDAX may modulate CgNR5A transcriptional activity. This study provides insights into the potential physiological processes involving these NRs in the regulation of CYPs associated with xenobiotic and steroid/lipid metabolism.

Genetic and in silico analysis of Indian sporadic young onset patient with amyotrophic lateral sclerosis

BACKGROUND

Amyotrophic lateral sclerosis (ALS) is an old onset devastating neurodegenerative disorder. Young-onset ALS cases especially sporadic ones who are between 25 and 45 years are rarely affected by the disease. Despite the identification of numerous candidate genes associated with ALS, the etiology of the disease remains elusive due to extreme genetic and phenotypic variability. The advent of affordable whole exome sequencing (WES) has opened new avenues for unraveling the disease's pathophysiology better.

METHODS AND RESULTS

We aimed to determine the genetic basis of an Indian-origin, young onset sporadic ALS patient with very rapid deterioration of the disease course without any cognitive decline who was screened for mutations in major ALS candidate genes by WES. Variants detected were reconfirmed by Sanger sequencing. The clinicopathological features were investigated and two heterozygous missense variants were identified: R452W, not previously associated with ALS, present in one of the four conserved C terminal domains in ANXA11 and R208W in SIGMAR1, respectively. Both of these variants were predicted to be damaging by pathogenicity prediction tools and various in silico methods.

CONCLUSION

Our study revealed two potentially pathogenic variants in two ALS candidate genes. The genetic makeup of ALS patients from India has been the subject of a few prior studies, but none of them examined ANXA11 and SIGMAR1 genes so far. These results establish the framework for additional research into the pathogenic processes behind these variations that result in sporadic ALS disease and further our understanding of the genetic makeup of Indian ALS patients.

Copper resistance in the cold: Genome analysis and characterisation of a PIB-1 ATPase in Bizionia argentinensis

Copper homeostasis is a fundamental process in organisms, characterised by unique pathways that have evolved to meet specific needs while preserving core resistance mechanisms. While these systems are well-documented in model bacteria, information on copper resistance in species adapted to cold environments is scarce. This study investigates the potential genes related to copper homeostasis in the genome of Bizionia argentinensis (JUB59-T), a psychrotolerant bacterium isolated from Antarctic seawater. We identified several genes encoding proteins analogous to those crucial for copper homeostasis, including three sequences of copper-transport P1B-type ATPases. One of these, referred to as BaCopA1, was chosen for cloning and expression in Saccharomyces cerevisiae. BaCopA1 was successfully integrated into yeast membranes and subsequently extracted with detergent. The purified BaCopA1 demonstrated the ability to catalyse ATP hydrolysis at low temperatures. Structural models of various BaCopA1 conformations were generated and compared with mesophilic and thermophilic homologous structures. The significant conservation of critical residues and structural similarity among these proteins suggest a shared reaction mechanism for copper transport. This study is the first to report a psychrotolerant P1B-ATPase that has been expressed and purified in a functional form.

Humanization of the antigen-recognition domain does not impinge on the antigen-binding, cytokine secretion, and antitumor reactivity of humanized nanobody-based CD19-redirected CAR-T cells

BACKGROUND

The immunogenicity of the antigen-recognition domains of chimeric antigen receptor (CAR)-T cells leads to immune responses that may compromise the antitumor effects of the adoptively transferred T cells. Herein, we attempt to humanize a CD19-specific VHH (named H85) using in silico techniques and investigate the impact of antigen-recognition domain humanization on CAR expression and density, cytokine secretion, and cytolytic reactivity of CAR-T cells based on the humanized VHH.

METHODS

H85 was humanized (named HuH85), and then HuH85 was compared with H85 in terms of conformational structure, physicochemical properties, antigenicity and immunogenicity, solubility, flexibility, stability, and CD19-binding capacity using in silico techniques. Next, H85CAR-T cells and HuH85CAR-T cells were developed and CAR expression and surface density were assessed via flow cytometry. Ultimately, the antitumor reactivity and secreted levels of IFN-γ, IL-2, and TNF-α were assessed following the co-cultivation of the CAR-T cells with Ramos, Namalwa, and K562 cells.

RESULTS

In silico findings demonstrated no negative impacts on HuH85 as a result of humanization. Ultimately, H85CAR and HuH85CAR could be surface-expressed on transduced T cells at comparable levels as assessed via mean fluorescence intensity. Moreover, H85CAR-T cells and HuH85CAR-T cells mediated comparable antitumor effects against Ramos and Namalwa cells and secreted comparable levels of IFN-γ, IL-2, and TNF-α following co-cultivation.

CONCLUSION

HuH85 can be used to develop immunotherapeutics against CD19-associated hematologic malignancies. Moreover, HuH85CAR-T cells must be further investigated in vitro and in preclinical xenograft models of CD19+ leukemias and lymphomas before advancing into clinical trials.

Chimeric lipoproteins for leptospirosis vaccine: immunogenicity and protective potential

Leptospirosis, a neglected zoonotic disease, is caused by pathogenic spirochetes belonging to the genus Leptospira and has one of the highest morbidity and mortality rates worldwide. Vaccination stands out as one of the most effective preventive measures for susceptible populations. Within the outer membrane of Leptospira spp., we find the LIC12287, LIC11711, and LIC13259 lipoproteins. These are of interest due to their surface location and potential immunogenicity. Thorough examination revealed the conservation of these proteins among pathogenic Leptospira spp.; we mapped the distribution of T- and B-cell epitopes along their sequences and assessed the 3D structures of each protein. This information aided in selecting immunodominant regions for the development of a chimeric protein. Through gene synthesis, we successfully constructed a chimeric protein, which was subsequently expressed, purified, and characterized. Hamsters were immunized with the chimeric lipoprotein, formulated with adjuvants aluminum hydroxide, EMULSIGEN®-D, Sigma Adjuvant System®, and Montanide™ ISA206VG. Another group was vaccinated with an inactivated Escherichia coli bacterin expressing the chimeric protein. Following vaccination, hamsters were challenged with a virulent L. interrogans strain. Our evaluation of the humoral immune response revealed the production of IgG antibodies, detectable 28 days after the second dose, in contrast to pre-immune samples and control groups. This demonstrates the potential of the chimeric protein to elicit a robust humoral immune response; however, no protection against challenge was achieved. While this study provides valuable insights into the subject, further research is warranted to identify protective antigens that could be utilized in the development of a leptospirosis vaccine. KEY POINTS: • Several T- and B-cell epitopes were identified in all the three proteins. • Four different adjuvants were used in vaccine formulations. • Immunization stimulated significant levels of IgG2/3 in vaccinated animals.

Copper transporter protein (MctB) as a therapeutic target to elicit antimycobacterial activity against tuberculosis

Tuberculosis (TB) is a prehistoric infection and major etiologic agent of TB, Mycobacterium tuberculosis, which is considered to have advanced from an early progenitor species found in Eastern Africa. By the 1800s, there were approximately 800 to 1000 fatality case reports per 100,000 people in Europe and North America. This research suggests an In-silico study to identify potential inhibitory compounds for the target Mycobacterial copper transport protein (Mctb). ADME-based virtual screening, molecular docking, and molecular dynamics simulations were conducted to find promising compounds to modulate the function of the target protein. Four chemical compounds, namely Anti-MCT1, Anti-MCT2, Anti-MCT3 and Anti-MCT4 out of 1500 small molecules from the Diverse-lib of MTiOpenScreen were observed to completely satisfy Lipinski rule of five and Veber's rule. Further, significantly steady interactions with the MctB target protein were observed. Docking experiments have presented 9 compounds with less than -9.0 kcal/mol free binding energies and further MD simulation eventually gave 4 compounds having potential interactions and affinity with target protein and favorable binding energy ranging from -9.2 to -9.3 kcal/mol. We may propose these compounds as an effective candidate to reduce the growth of M. tuberculosis and may also assist present a novel therapeutic approach for Tuberculosis. In vivo and In vitro validation would be needed to proceed further in this direction.Communicated by Ramaswamy H. Sarma.

Insights into structural vaccinology harnessed for universal coronavirus vaccine development

Structural vaccinology is pivotal in expediting vaccine design through high-throughput screening of immunogenic antigens. Leveraging the structural and functional characteristics of antigens and immune cell receptors, this approach employs protein structural comparison to identify conserved patterns in key pathogenic components. Molecular modeling techniques, including homology modeling and molecular docking, analyze specific three-dimensional (3D) structures and protein interactions and offer valuable insights into the 3D interactions and binding affinity between vaccine candidates and target proteins. In this review, we delve into the utilization of various immunoinformatics and molecular modeling tools to streamline the development of broad-protective vaccines against coronavirus disease 2019 variants. Structural vaccinology significantly enhances our understanding of molecular interactions between hosts and pathogens. By accelerating the pace of developing effective and targeted vaccines, particularly against the rapidly mutating severe acute respiratory syndrome coronavirus 2 and other prevalent infectious diseases, this approach stands at the forefront of advancing immunization strategies. The combination of computational techniques and structural insights not only facilitates the identification of potential vaccine candidates but also contributes to the rational design of vaccines, fostering a more efficient and targeted approach to combatting infectious diseases.

Terbinafine-resistant T. indotineae due to F397L/L393S or F397L/L393F mutation among corticoid-related tinea incognita patients

Tinea incognita (TI) can mimic other dermatoses, presenting a diagnostic challenge for dermatologists. In some uncertain cases, it is crucial to accurately identify the causative agent using internal transcribed spacer (ITS) sequencing. The global issue of drug-resistant dermatophytosis is increasing, with Trichophyton (T.) indotineae being the main cause. This study presents four cases of TI (diagnosed as eczema) by terbinafine-resistant T. indotineae strains and reviews the current global TI epidemiology based on geographical continent and related conditions. Furthermore, squalene epoxidase (SQLE)-associated resistance mechanisms are evaluated. Lesions caused by terbinafine-resistant T. indotineae strains do not respond to allylamine antifungals, thus allowing the infection to spread. Among T. indotineae isolates, the SQLE F397L substitution is the most prevalent mutation contributing to azole resistance. F397L and L393F replacements in SQLE were detected in all isolates that exhibited high-level resistance. L393S was seen in isolates with low-resistant strains. Interestingly, and for the first time, an L393F amino acid substitution in the SQLE gene product was detected in the Iranian clinical T. indotineae strain. Also, a genomics-based update on terbinafine resistance that focuses on T. indotineae is discussed in this study.

Insights into the ATP / GTP selectivity of a GTPase, adenylosuccinate synthetase from Leishmania donovani

Many GTPases have been shown to utilize ATP too as the phosphoryl donor. Both GTP and ATP are important molecules in the cellular environments and play multiple and discrete functional role within the cells. In our present study, we showed that one of the purine metabolic enzymes Adenylosuccinate synthetase from Leishmania donovani (LdAdSS) which belongs to the BioD-superfamily of GTPases can also carry out the catalysis by hydrolysing ATP instead of its cognate substrate GTP albeit with less efficiency. Biochemical and biophysical studies indicated its ability to bind to ATP too but at a higher concentration of ATP compared to that of GTP. Sequence analysis and molecular dynamic simulations suggested that residues of the switch loop and the G4-G5 (593SAXD596) connected motif of LdAdSS plays a role in determining the nucleotide specificity. Though the crucial interaction between Asp596 and the nucleotide is broken when ATP is bound, interactions between the Ala594 and the adenine ring of ATP could still hold ATP in the GTP binding site. The results of the present study suggested that though LdAdSS is GTP specific, it still shows ATP hydrolysing activity.

Identification and Functional Implications of the E5 Oncogene Polymorphisms of Human Papillomavirus Type 16

The persistence of the human papillomavirus type 16 (HPV16) infection on the cervical epithelium contributes to the progression of cervical cancer. Studies have demonstrated that HPV16 genetic variants may be associated with different risks of developing cervical cancer. However, the E5 oncoprotein of HPV16, which is related to several cellular mechanisms in the initial phases of the infection and thus contributes to carcinogenesis, is still little studied. Here we investigate the HPV16 E5 oncogene variants to assess the effects of different mutations on the biological function of the E5 protein. We detected and analyzed the HPV16 E5 oncogene polymorphisms and their phylogenetic relationships. After that, we proposed a tertiary structure analysis of the protein variants, preferential codon usage, and functional activity of the HPV16 E5 protein. Intra-type variants were grouped in the lineages A and D using in silico analysis. The mutations in E5 were located in the T-cell epitopes region. We therefore analyzed the interference of the HPV16 E5 protein in the NF-kB pathway. Our results showed that the variants HPV16E5_49PE and HPV16E5_85PE did not increase the potential of the pathway activation capacity. This study provides additional knowledge about the mechanisms of dispersion of the HPV16 E5 variants, providing evidence that these variants may be relevant to the modulation of the NF-κB signaling pathway.

Polymorphism in the leucine-rich repeats of TLR7 in different breeds of chicken and in silico analysis of its effect on TLR7 structure and function

Chicken toll-like receptor 7 (chTLR7) is a viral sensing pattern recognition receptor and detects ssRNA. The ligand binding site comprises leucine-rich repeats (LRRs) located in the ectodomain of chTLR7. Hence, any polymorphism in the binding site would modify its functional interaction with the ligand, resulting in varied strength of immune response. This study first aimed to compare the single nucleotide polymorphisms (SNPs) associated with the ligand binding site of TLR7 in three indigenous chicken breeds namely Aseel, Kadaknath, Nicobari along with an exotic breed White Leghorn. Four synonymous SNPs (P123P, I171I, N339N and L421L) and four non-synonymous SNPs (I121V, S135T, F356S and S447G) were identified among various breeds. We employed in silico tools to screen the pathogenic nsSNPs and one nsSNP was identified as having potential impact on chTLR7 protein. Moreover, sequence and structure-based methods were used to determine the effect of nsSNPs on protein stability. It revealed I121V, F356S, and S447G as decreasing the stability while S135T increasing the stability of chTLR7. Additionally, docking analysis confirmed that I121V and F356S reduced the binding affinity of ligands (R-848 and polyU) to chTLR7 protein. The results suggest that the nsSNPs found in this study could alter the ligand binding of chTLR7 and modify the immune response between different breeds further contributing to disease susceptibility or resistance. Further, in vitro and in vivo studies are needed to analyze the effect of these SNPs on susceptibility or resistance against various viral diseases in poultry.

Screening of bioactive compounds from selected mushroom species against putative drug targets in Mycobacterium tuberculosis: a multi-target approach

Mycobacterium tuberculosis (Mtb) is a notorious pathogen that causes one of the highest mortalities globally. Due to a pressing demand to identify novel therapeutic alternatives, the present study aims to focus on screening the putative drug targets and prioritizing their role in antibacterial drug development. The most vital proteins involved in the Biotin biosynthesis pathway and the Lipoarabinomannan (LAM) pathway such as biotin synthase (bioB) and alpha-(1->6)-mannopyranosyltransferase A (mptA) respectively, along with other essential virulence proteins of Mtb were selected as drug targets. Among these, the ones without native structures were modelled and validated using standard bioinformatics tools. Further, the interactions were performed with naturally available lead molecules present in selected mushroom species such as Agaricus bisporus, Pleurotus djamor, Hypsizygus ulmarius. Through Gas Chromatography-Mass Spectrometry (GC-MS), 15 bioactive compounds from the methanolic extract of mushrooms were identified. Further, 4 were selected based on drug-likeness and pharmacokinetic screening for molecular docking analysis against our prioritized targets wherein Benz[e]azulene from Pleurotus djamor illustrated a good binding affinity with a LF rank score of -9.036 kcal mol -1 against nuoM (NADH quinone oxidoreductase subunit M) and could be used as a prospective candidate in order to combat Tuberculosis (TB). Furthermore, the stability of the complex are validated using MD Simulations and subsequently, the binding free energy was calculated using MM-GBSA analysis. Thus, the current in silico analysis suggests a promising role of compounds extracted from mushrooms in tackling the TB burden.Communicated by Ramaswamy H. Sarma.

The Impact of Terminal Peptide Extensions of Retinal Inosine 5´Monophosphate Dehydrogenase 1 Isoforms on their DNA-binding Activities

The main structural difference between the mutation-susceptible retinal isoforms of inosine 5´-monophosphate dehydrogenase-1 (IMPDH-1) with the canonical form resides in the C- and N-terminal peptide extensions with unknown structural/functional impacts. In this report, we aimed to experimentally evaluate the functional impact of these extensions on the specific/non-specific single-stranded DNA (ssDNA)-binding activities relative to those of the canonical form. Our in silico findings indicated the possible contribution of the C-terminal segment to the reduced flexibility of the Bateman domain of the enzyme. In addition, the in silico data indicated that the N-terminal tail acts by altering the distance between the tetramers in the concave octamer complex (the native form) of the enzyme. The overall impact of these predicted structural variations became evident, first, through higher Km values with respect to either of the substrates relative to the canonical isoform, as reported previously (Andashti et al. in Mol Cell Biochem 465(1):155-164, 2020). Secondary, the binding of the recombinant mouse retinal isoform IMPDH1 (603) to its specific Rhodopsin target gene was significantly augmented while its binding to non-specific ssDNA was lower than that of the canonical isoform. The DNA-binding activity of the other mouse retinal isoform, IMPDH1(546), to specific and non-specific ssDNA was lower than that of the canonical form most probably due to the in silico predicted rigidity created in the Bateman domain by the C-terminal peptide extension. Furthermore, the DNA binding to the Rhodopsin target gene by each of the IMPDH isoforms influenced in the presence of GTP (Guanosine triphosphate) and ATP (Adenosine triphosphate).

Identification of FDA-approved drugs with triple targeting mode of action for the treatment of monkeypox: a high throughput virtual screening study

According to the Center for Disease Control and Prevention, as of August 23, 94 countries had confirmed 42,954 Monkeypox Virus cases. As specific monkeypox drugs are not yet developed, the treatment depends on repurposed FDA-approved drugs. According to a recent study, the Monkeypox outbreak is caused by a strain with a unique mutation, raising the likelihood that the virus will develop resistance to current drugs by acquiring mutations in the targets of currently used drugs. The probability of multiple mutations in two or more drug targets at a time is always low than mutation in a single drug target. Therefore, we identified 15 triple-targeting FDA-approved drugs that can inhibit three viral targets, including topoisomerase1, p37, and thymidylate kinase, using high throughput virtual screening approach. Further, the molecular dynamics simulation analysis of the top hits such as Naldemedine and Saquinavir with their respective targets reveals the formation of stable conformational changes of the ligand-protein complexes inside the dynamic biological environment. We suggest further research on these triple-targeting molecules to develop an effective therapy for the currently spreading Monkeypox.

Genome-wide characterization and expression profiling of E2F/DP gene family members in response to abiotic stress in tomato (Solanum lycopersicum L.)

BACKGROUND

E2F/DP (Eukaryotic 2 transcription factor/dimerization partner) family proteins play an essential function in the cell cycle development of higher organisms. E2F/DP family genes have been reported only in a few plant species. However, comprehensive genome-wide characterization analysis of the E2F/DP gene family of Solanum lycopersicum has not been reported so far.

RESULTS

This study identified eight nonredundant SlE2F/DP genes that were classified into seven groups in the phylogenetic analysis. All eight genes had a single E2F-TDP domain and few genes had additional domains. Two segmental duplication gene pairs were observed within tomato, in addition to cis-regulatory elements, miRNA target sites and phosphorylation sites which play an important role in plant development and stress response in tomato. To explore the three-dimensional (3D) models and gene ontology (GO) annotations of SlE2F/DP proteins, we pointed to their putative transporter activity and their interaction with several putative ligands. The localization of SlE2F/DP-GFP fused proteins in the nucleus and endoplasmic reticulum suggested that they may act in other biological functions. Expression studies revealed the differential expression pattern of most of the SlE2F/DP genes in various organs. Moreover, the expression of E2F/DP genes against abiotic stress, particularly SlE2F/DP2 and/or SlE2F/DP7, was upregulated in response to heat, salt, cold and ABA treatment. Furthermore, the co-expression analysis of SlE2F/DP genes with multiple metabolic pathways was co-expressed with defence genes, transcription factors and so on, suggested their crucial role in various biological processes.

CONCLUSIONS

Overall, our findings provide a way to understand the structure and function of SlE2F/DP genes; it might be helpful to improve fruit development and tolerance against abiotic stress through marker-assisted selection or transgenic approaches.