Binding Propensity Research Articles

Design, Synthesis, QSAR Studies, and Molecular Modeling of Some Novel Bis Methyl 2-[3-(benzo[d]thiazol-2-yl)-2-terephthaloyl-bis-4-oxo-thiazolidin- 5-ylidene]acetates and Screening of their Antioxidant and Enzyme Inhibition Properties.

Benzothiazolamine-based bisthiourea precursors were prepared in good yields. These bisthiourea derivatives were cyclized into symmetrical Bis Methyl 2-[3-(benzothiazol- 2-yl)-2-terephthaloyl-bis-4-oxo-thiazolidin-5-ylidene]acetates, by their condensation with (DMAD) dimethyl but-2-meditate in the presence of dry methanol. All these compounds were evaluated for their biological applications. Antioxidant activities were performed by adopting a DPPH radical assay, and an in vitro enzyme inhibition assay was performed to investigate their enzyme inhibitory potential against butyrylcholinesterase (BChE) and acetylcholinesterase (AChE). Molecular modeling and QSAR studies were performed to monitor the binding propensity of imidathiazolidinone derivatives with enzymes and DNA. Also, electronic and steric descriptors were calculated to determine the effect of structure on the activity of imidathiazolidinone derivatives. The characterization of all the synthesized compounds was done by their physical data, FT-IR, NMR and elemental analysis.

Profiling genetically driven alternative splicing across the Indonesian archipelago

One of the regulatory mechanisms influencing the functional capacity of genes is alternative splicing (AS). Previous studies exploring the splicing landscape of human tissues have shown that AS has contributed to human biology, especially in disease progression and the immune response. Nonetheless, this phenomenon remains poorly characterized across human populations, and it is unclear how genetic and environmental variation contribute to AS. Here, we examine a set of 115 Indonesian samples from three traditional island populations spanning the genetic ancestry cline that characterizes Island Southeast Asia. We conduct a global AS analysis between islands to ascertain the degree of functionally significant AS events and their consequences. Using an event-based statistical model, we detected over 1,500 significant differential AS events across all comparisons. Additionally, we identify over 6,000 genetic variants associated with changes in splicing (splicing quantitative trait loci [sQTLs]), some of which are driven by Papuan-like genetic ancestry, and only show partial overlap with other publicly available sQTL datasets derived from other populations. Computational predictions of RNA binding activity reveal that a fraction of these sQTLs directly modulate the binding propensity of proteins involved in the splicing regulation of immune genes. Overall, these results contribute toward elucidating the role of genetic variation in shaping gene regulation in one of the most diverse regions in the world.

Indole analogs as potential anti-breast cancer agents: Design, synthesis, in-vitro bioevaluation with DFT, molecular docking and ADMET studies

Being a belligerent malignancy, triple-negative breast cancer poses unmet clinical challenges due to lack of targeted therapy, rapid growth rate and metastasis, high heterogeneity, and increased risk of recurrence. Diverse 1-(1H-indol-1-yl)-2-((5-aryl-4H-1,2,4-triazol-3-yl)thio))ethanones have been synthesized in substantial yield (81-87 %) by clubbing 1-(chloroacetyl)indoles with substituted triazoles under refluxing conditions of 4-5 h. The indole integrates demonstrated substantial antitumor efficacy in the MTT assay against the MDA-MB-231 cell line and substituting indole moiety with a halogen (bromo) significantly improves the anti-breast cancer action of the synthesized hybrids compared to the unsubstituted ring. Compound 4i featuring halogen substituent on both the indole and phenyl moieties displayed the highest anticancer action with an IC50 value of 2.121 μM The synthetic variants exhibited a notable binding propensity against the EGFR-TK receptor (PDB ID:1M17). Through in-silico ADMET screening, the pharmacological proclivity of the title compounds has been convicted. The notable bioactivity of the indole hybrids projects them as a potential lead in developing anti-breast cancer medications, especially against TNBC.

Whole genome regulatory effect of MoISW2 and consequences for the evolution of the rice plant pathogenic fungus Magnaporthe oryzae.

Isw2 proteins, ubiquitous across eukaryotes, exhibit a propensity for DNA binding and exert dynamic influences on local chromosome condensation in an ATP-dependent fashion, thereby modulating the accessibility of neighboring genes to transcriptional machinery. Here, we report the deletion of a putative MoISW2 gene, yielding substantial ramifications on plant pathogenicity. Subsequent gene complementation and chromatin immunoprecipitation sequencing (ChIP-seq) analyses were conducted to delineate binding sites. RNA sequencing (RNA-seq) assays revealed discernible impacts on global gene regulation along chromosomes in both mutant and wild-type strains, with comparative analyses against 55 external RNA-seq data sets corroborating these findings. Notably, MoIsw2-mediated binding and activities delineate genomic loci characterized by pronounced gene expression variability proximal to MoIsw2 binding sites, juxtaposed with comparatively stable expression in surrounding regions. The contingent genes influenced by MoIsw2 activity predominantly encompass niche-determinant genes, including those encoding secreted proteins, secondary metabolites, and stress-responsive elements, alongside avirulence genes. Furthermore, our investigations unveil a spatial correlation between MoIsw2 binding motifs and known transposable elements (TEs), suggesting a potential interplay wherein TE transposition at these loci could modulate the transcriptional landscape of Magnaporthe oryzae in a strain-specific manner. Collectively, these findings position MoIsw2 as a plausible master regulator orchestrating the delicate equilibrium between genes vital for biomass proliferation, akin to housekeeping genes, and niche-specific determinants crucial for ecological adaptability. Stress-induced TE transposition, in conjunction with MoIsw2 activity, emerges as a putative mechanism fostering enhanced mutagenesis and accelerated evolution of niche-determinant genes relative to housekeeping counterparts.IMPORTANCEIsw2 proteins are conserved in plants, fungi, animals, and other eukaryotes. We show that a fungal Isw2 protein in the rice pathogen Magnaporthe oryzae binds to retrotransposon (RT) DNA motifs and affects the epigenetic gene expression landscape of the fungal genome. Mainly ecological niche determinant genes close to the binding motifs are affected. RT elements occur frequently in DNA between genes in most organisms. They move place and multiply in the genome, especially under physiological stress. We further discuss the Isw2 and RT combined activities as a possible sought-after mechanism that can cause biased mutation rates and faster evolution of genes necessary for reacting to abiotic and biotic challenges. The most important biotic challenges for plant pathogens are the ones from the host plants' innate immunity. The overall result of these combined activities will be an adaptation-directed evolution of niche-determinant genes.

Enzymatic bioremediation of polycyclic aromatic hydrocarbons (PAHs) in contaminated soil: a study on the recombinant laccase TVL

ABSTRACT Polycyclic aromatic hydrocarbons (PAHs) are pervasive and persistent pollutants in contaminated soil, posing a severe health and environmental threat. Enzymatic bioremediation presents a viable solution for the remediation of PAH-contaminated soil. In this study, a recombinant laccase with the encoding gene originating from Trametes villosa and recombinantly expressed in Aspergillus oryzae, designated as TVL, was discovered to possess strong PAH reduction capabilities. The specific enzyme activity of TVL was 73485 and 5102 LAMU/g enzyme protein at pH 5.0/7.0 and 37°C. Furthermore, it exhibited significant benzo[a]pyrene degradation, with 100% and 90.48% degradation at pH 5.0/7.0 after 24 h in the liquid phase. The degradation process of benzo[a]pyrene in soil was thoroughly investigated. Optimal conditions were identified as 15 mg/g NK-BSoil-3 and 1.35 mg/g HBT, resulting in a removal rate of 37.54% within 7 days when 0.01 U/g of TVL was applied. The potential mechanisms were investigated using molecular docking simulation. The binding energy between benzo[a]pyrene and TVL protein is notably robust, suggesting a higher propensity for enzyme binding. The TVL protein pocket contains nine amino acids that can interact most strongly with benzo[a]pyrene. Consequently, the recombinant laccase TVL holds considerable practical significance in bioremediation.

β-Lactoglobulin Enhances Clay and Activated Carbon Binding and Protection Properties for Cadmium and Lead.

The removal of heavy metals from wastewater remains a challenge due to the limitations of current remediation methods. This study aims to develop multicomponent composites as inexpensive and environmentally friendly sorbents with enhanced capture of cadmium (Cd) and lead (Pb). The composites are based on calcium montmorillonite (CM) and activated carbon (AC) because of their proven effectiveness as sorbents for diverse toxins in environmental settings. In this study, we used a combination of computational and experimental methods to delineate that β-lactoglobulin enhances CM and AC binding and protection properties for Cd and Pb. Modeling and molecular dynamics simulations investigated the formation of material systems formed by CM and AC in complex with β-lactoglobulin and predicted their capacity to bind heavy metal ions at neutral pH conditions. Our simulations suggest that the enhanced binding properties of the material systems are attributed to the presence of several binding pockets formed by β-lactoglobulin for the two heavy metal ions. At neutral pH conditions, divalent Cd and Pb shared comparable binding propensities in all material systems, with the former being consistently higher than the latter. To validate the interactions depicted in simulations, two ecotoxicological models (L. minor and H. vulgaris) were exposed to Cd, Pb, and a mixture of the two. The inclusion of CM-lactoglobulin (β-lactoglobulin amended CM) and AC-lactoglobulin (β-lactoglobulin amended AC) at 0.05-0.2% efficiently and dose-dependently reduced the severe toxicity of metals and increased the growth parameters. This high efficacy of protection shown in the ecotoxicological models may result from the numerous possible interaction pockets of the β-lactoglobulin-amended materials depicted in simulations. The ecotoxicological models support the agreement with computations. This study serves as a proof of concept on how computations in tandem with experiments can be used in the design of multicomponent clay- and carbon-based sorbent amended systems with augmented functionalities for particular toxins.

Thiosemicarbazone-based Dioxomolybdenum (VI) complexes as inorganic nucleases

This study focuses on the design of alkyl-substituted thiosemicarbazones from 5-bromosalicylaldehyde and substituted thiosemicarbazides and the corresponding dioxomolybdenum(VI) complexes, hitherto unreported. In addition to elemental analyses, the synthesized ligands and the corresponding complexes are further analyzed by physico-chemical and spectroscopic techniques. The DNA interaction studies are based on UV absorption titration and gel electrophoretic methods. The binding constants (Kb) for the ligands (L1-L4) are found to be 1.20 ± 0.1 × 104 M−1; 1.32 ± 0.2 × 104 M−1; 1.27 ± 0.3 × 104 M−1 and 1.25 ± 0.3 × 104 M−1 respectively and that of the complexes (C1–C4) are 1.45 ± 0.2 × 104 M−1; 2.10 ± 0.4 × 104 M−1; 1.54 ± 0.2 × 104 M−1 and 2.13 ± 0.2 × 104 M−1, respectively. The complexes have shown relatively higher binding propensity as compared to that of the ligands. Further, as the outcome of gel electrophoresis studies, the ligands show a cleavage pattern of nicked circular (Form I). However, the complexes show cleavage patterns of both nicked circular and supercoiled, Forms I & II respectively. This implies that both the ligands and complexes possess varying binding efficacy with DNA and accordingly the cleavage patterns also differ.

Unraveling DNA Triplex Assembly: Mass Spectrometric Investigation of Modified Triplex Forming Oligonucleotides for Enhanced Gene Targeting.

Deoxyribonucleic acid triplexes have potential roles in a range of biological processes involving gene and transcriptional regulation. A major challenge in exploiting the formation of these higher-order structures to target genes in vivo is their low stability, which is dependent on many factors including the length and composition of bases in the sequence. Here, different DNA base modifications have been explored, primarily using native mass spectrometry, in efforts to enable stronger binding between the triplex forming oligonucleotide (TFO) and duplex target sites. These modifications can also be used to overcome pyrimidine interruptions in the duplex sequence in promoter regions of genomes, to expand triplex target sequences for antigene therapies. Using model sequences with a single pyrimidine interruption, triplex forming oligonucleotides containing locked nucleic acid base modifications were shown to have a higher triplex binding propensity than DNA-only and dSpacer-containing TFOs. However, the triplex forming ability of these systems was limited by the competitive formation of multiple higher order assemblies. Triplex forming sequences that correspond to specific gene targets from the Pseudomonas aeruginosa genome were also investigated, with LNA-containing TFOs the only variant able to form triplex using these sequences. This work indicates the advantages of utilizing synthetically modified TFOs to form triplex assemblies in vivo for potential therapeutic applications and highlights the advantages of native mass spectrometry for the study of their formation.

Capturing the Effects of Single Atom Substitutions on the Inhibition Efficiency of Glycogen Synthase Kinase-3β Inhibitors via Markov State Modeling and Experiments.

Small modifications in the chemical structure of ligands are known to dramatically change their ability to inhibit the activity of a protein. Unraveling the mechanisms that govern these dramatic changes requires scrutinizing the dynamics of protein-ligand binding and unbinding at the atomic level. As an exemplary case, we have studied Glycogen Synthase Kinase-3β (GSK-3β), a multifunctional kinase that has been implicated in a host of pathological processes. As such, there is a keen interest in identifying ligands that inhibit GSK-3β activity. One family of compounds that are highly selective and potent inhibitors of GSK-3β is exemplified by a molecule termed COB-187. COB-187 consists of a five-member heterocyclic ring with a thione at C2, a pyridine substituted methyl at N3, and a hydroxyl and phenyl at C4. We have studied the inhibition of GSK-3β by COB-187-related ligands that differ in a single heavy atom from each other (either in the location of nitrogen in their pyridine ring, or with the pyridine ring replaced by a phenyl ring), or in the length of the alkyl group joining the pyridine and the N3. The inhibition experiments show a large range of half-maximal inhibitory concentration (IC50) values from 10 nM to 10 μM, implying that these ligands exhibit vastly different propensities to inhibit GSK-3β. To explain these differences, we perform Markov State Modeling (MSM) using fully atomistic simulations. Our MSM results are in excellent agreement with the experiments in that they accurately capture differences in the binding propensities of the ligands. The simulations show that the binding propensities are related to the ligands' ability to attain a compact conformation where their two aromatic rings are spatially close. We rationalize this result by sampling numerous binding and unbinding events via funnel metadynamics simulations, which show that indeed while approaching the bound state, the ligands prefer to be in their compact conformation. We find that the presence of nitrogen in the aromatic ring increases the probability of attaining the compact conformation. Protein-ligand binding is understood to be dictated by the energetics of interactions and entropic factors, like the release of bound water from the binding pockets. This work shows that changes in the conformational distribution of ligands due to atom-level modifications in the structure play an important role in protein-ligand binding.

Nanoparticle-based targeted therapy through EGFR tyrosine kinase inhibitors and their recent advances in lung cancer therapy

The emergence and subsequent advancement of nanotechnology in recent years have greatly benefited the healthcare sector, particularly in the treatment of cancer. As per study, major fatalities are related to the lung cancer. For many years, oral tyrosine kinase inhibitors (TKIs) against the epidermal growth factor receptor (EGFR) family of receptors have been used in the clinic to treat human malignancies, although they observed some very serious adverse effects in the treatment of lung cancer, especially in non-small cell lung cancer (NSCLC). Despite EGFR-TKIs’ exceptional qualities as small-molecule targeted medications, their applicability is nevertheless limited by their poor solubility, inconsistent oral bioavailability, high daily dose needs, high plasma albumin binding propensity, and initial/acquired drug resistance. Article’s purpose is to investigate EGFR-TKI’s effects on lung cancer and get around some of its drawbacks, nanotechnology will be an innovative strategy. An effective tool to increase the effectiveness of these pharmaceuticals is nanotechnology by methods other than oral. This article signifies that a range of nanomedicine delivery systems have been developed to effectively distribute EGFR-TKIs with improved drug release kinetics and tissue-targeting capacity. This review article intends to present information regarding lung cancer and EGFR relation, mechanism of recently approved EGFR-TKI’s targeted therapy, an updated landscape of EGFR-TKIs and their clinical status over lung cancer, advantages and disadvantages of nanotechnology, and new breakthroughs in nano-delivery which mentioned as a significantly better over traditional drug chemotherapy and delivery.

Synthesis and Characterization of Metal Complexes [M(L)(Im)]NO3, In Vitro DNA/BSA Binding Behavior and Cytotoxicity on HepG2 Cancer Cells

AbstractA new ligand (HL) was prepared from heterocyclic 8‐Hydroxy‐2‐quinolinecarboxaldehyde and 2‐Aminobenzophenone in one pot synthesis. The metal complexes of the types [Zn(L)(Im)]NO3 (1), [Cu(L)(Im)]NO3 (2) and [Co(L)(Im)]NO3 (3) were prepared by adopting HL and Imidazole under refluxing conditions. The HL and complexes 1–3, were characterized by CHN elemental analysis and spectroscopic methods 1H NMR, 13C NMR, FT‐IR, ToF Mass. The spectroscopic studies suggest square pyramidal geometry in all complexes. The interaction of ligand and complexes with DNA and BSA was conducted by UV‐vis absorption and fluorescence spectroscopy. The Kb value of 2.17×104 M−1 for complex 2 is the highest depicting its greater binding propensity with DNA. Similarly, in BSA binding studies, complex 2 shows greater binding potential in the hydrophobic core probably near the Trp 212 in the subdomain IIA. Furthermore, the complex 2 shows excellent cytotoxicity on HepG2 cancer cells with IC50=74.05±0.69 μM. In the cell cycle analysis of HepG2 cells, it has been observed that complex 2 arrests the cell proliferation in the G1/S phase. Annexin V‐based flow cytometry analysis further indicated 6‐fold apoptotic cell death by complex 2 in the experiment along with non‐specific necrosis cell death.

De novo design and preparation, structural details, and cytotoxic response of a new water soluble (2,2′–bipy)–(phenylalaninato)–μ–chlorido–copper(II) drug candidate against resistant cancer cells

A new water soluble (2,2′–bipyridine)–(phenylalaninato)–μ–chlorido–copper(II) complex was synthesized using ancillary ligands, l-phenylalanine, and 2,2-bipyridine as a chemotherapeutic anticancer agent. The complex was characterized by employing various spectroscopic (UV–visible, FT-IR, EPR, elemental analysis) and single crystal X-ray diffraction technique which revealed the structure of crystal as monoclinic with P21 space group. The interaction studies of the complex with therapeutic drug target, ct-DNA were caried out using various complimentary biophysical techniques, and the corroborative results of these experiments revealed that complex binds avidly through non-covalent electrostatic binding mode in the groove region of DNA. The binding propensity was quantified by calculating the intrinsic binding constant values (Kb and Ksv) which were found to be 3.1 (±0.95) × 105M−1 and 0.4 (±0.05) × 103M−1, respectively. The cleavage studies of copper(II) based drug candidate 1 with pBR322 plasmid DNA were performed in concentration dependent manner and it was demonstrated that complex was capable of conversion of supercoiled form SC (Form I) into nicked form NC (Form II) upon incubation of 3 μM concentration, implicating efficient single strand cleavage of DNA helix. The mechanistic cleavage studies were also performed in the presence various activators viz., DMSO, NaN3, SOD, and H2O2 and the strong inhibition of cleavage process was observed in presence of NaN3 and SOD that suggested an oxidative pathway (Fenton's mechanism) for the Cu(II) complex. The cytotoxicity of the complex was evaluated by SRB assay against the resistant cancer cell lines, viz., Hop-62, MCF-7, AW13516, MDA-MB-231, and SiHa. The cytotoxicity activity demonstrated good therapeutic potency against all the tested cell lines with GI50 value of <10 μM.

X‐ray crystallographic of a novel pyrimidine ligand (LPH) and its metal chelates Cr3+, Ni2+, and Ru3+: A comprehensive study on synthesis, characterization, computational investigations, and biological evaluation toward anticancer and antioxidant

2,4,6‐Triamino‐N‐phenylpyrimidine‐5‐carbothioamide (LPH) was synthesized and extensively characterized. Single crystal X‐ray confirms a monoclinic P21/c space group for LPH. The novel ligand and its chelates of Cr3+, Ni2+, and Ru3+ were studied by elemental analyses, spectral (13C‐,1H‐NMR, UV–visible, IR), magnetic, and thermal measurements. IR spectra indicated that LPH behaves in a bidentate mode through the two NH2 groups of the pyrimidine ring and/or a tetradentate coordination involving the nitrogen atoms of the two NH2 of the pyrimidine ring, NH, and the thioketo (C=S) groups, respectively. By utilizing the Gaussian 09 W program in DFT/B3LYP, we are able to conduct computational estimates of LPH and its metal chelates, yielding insightful data regarding their electronic structure and stability. Biological studies were conducted to assess the isolated compounds' activities against anticancer (MCF‐7), antioxidant (DPPH and ABTS), DNA, and antimicrobial proteins. Molecular docking was employed to investigate the chelates' inhibitory properties, specifically their binding propensity with MCF‐7 cells, revealing possible anticancer action. All the data help to understand LPH and its complexes' production, biological characteristics, and possible therapeutic uses.

De novo design and preparation of Copper(II)–based chemotherapeutic anticancer drug candidates with Boc–glycine and N,N–donor ligands: DNA binding, cleavage profile, and cytotoxic therapeutic response against MCF–7, PC–3, and HCT–116 cells

Two new copper(II) complexes [Cu(Boc–glycine)(2,2–bipyridyl)2]NO31 and [Cu(Boc–glycine)(1,10–phenanthroline)2]NO32 were prepared, and thoroughly characterized by multiple spectroscopic methods. The SC X–ray diffraction studies revealed that the complexes crystallized in triclinic (P 1¯) system with distorted square pyramidal and octahedral geometry in 1 and 2, respectively. To predict the anticancer potential of the drug candidates 1 and 2, binding studies with the ct–DNA were performed by using various complimentary biophysical methods. The drug candidates 1 and 2 interact strongly with DNA exhibiting ‘hypochromic’ effect in the absorbance bands at 300 nm implicating non–covalent intercalation binding mode that could be induced by the presence of strong recognition domain ligand (phen) which is known to ‘wedge–in’ in-between the bases of DNA helix. The intrinsic binding constant, Kb values were quantified by employing Wolfe–Shimer equation, and were found to be 0.10(±0.14) × 105 M−1 and 1.53 × 106(±0.1) M−1, respectively, showing higher binding propensity of 2 as compared to 1. pBR322 plasmid DNA cleavage studies of the complexes 1 and 2 showed that the complexes induced single–strand cleavage of DNA at a low concentration of 20 µM and 15 µM which mediated via an oxidative mechanism. The cytotoxicity activity of complexes was evaluated against MCF–7, PC–3, and HCT–116 cancer cells and the complexes displayed exceptionally good cytotoxicity against the tested cell lines (1, HCT–116:IC50 = 0.6 ± 0.02 μM and 2, MCF–7:IC50 = 1.91 ± 0.1 μM).

HSA and DNA binding analysis of antiviral drug cidofovir: Spectroscopic and molecular docking techniques

This article discusses the interaction of antiviral drug cidofovir (CDV) with biomolecules (HSA and DNA) under simulated physiological conditions (pH 7.4). The binding propensity of CDV with DNA was assessed through UV–visible absorption spectroscopy, fluorescence spectroscopy, and molecular docking. The results of fluorescence spectroscopy indicated that the binding of CDV to DNA induced fluorescence quenching through a static quenching mechanism, with a binding constant of 1.03 × 103 M−1 at 293 K. The groove mode of CDV binding to calf thymus DNA (ct-DNA) was validated using dye displacement assays. The results from molecular docking confirmed the binding mode and supported the findings obtained through spectroscopic techniques. Furthermore, the binding propensity of CDV with HSA was assessed through fluorescence spectroscopy, UV–visible absorption spectroscopy, and docking simulation. The fluorescence data indicated that CDV quenches the intrinsic fluorescence of the protein through a static quenching process, with a binding constant of 5.60 × 103 M−1 at 293 K. Meanwhile, the results of docking simulation confirmed our spectroscopic findings.

In silico energetic and molecular dynamic simulations studies demonstrate potential effect of the point mutations with implications for protein engineering in BDNF

Protein engineering by directed evolution is time-consuming. Hence, in silico techniques like FoldX-Yasara for ∆∆G calculation, and SNPeffect for predicting propensity for aggregation, amyloid formation, and chaperone binding are employed to design proteins. Here, we used in silico techniques to engineer BDNF-NTF3 interaction and validated it using mutations with known functional implications for NGF dimer. The structures of three mutants representing a positive, negative, or neutral ∆∆G involving two interface residues in BDNF and two mutations representing a neutral and positive ∆∆G in NGF, which is aligned with BDNF, were selected for molecular dynamics (MD) simulation. Our MD results conclude that the secondary structure of individual protomers of the positive and negative mutants displayed a similar or different conformation from the NTF3 monomer, respectively. The positive mutants showed fewer hydrophobic interactions and higher hydrogen bonds compared to the wild-type, negative, and neutral mutants with similar SASA, suggesting solvent-mediated disruption of hydrogen-bonded interactions. Similar results were obtained for mutations with known functional implications for NGF and BDNF. The results suggest that mutations with known effects in homologous proteins could help in validation, and in silico directed evolution experiments could be a viable alternative to the experimental technique used for protein engineering.

New mono and dinuclear half-sandwiched organoruthenium(II) complexes: Effect of dinuclearity on the biomolecular interaction and cytotoxicity

The present work describes the syntheses and structural characterization of new half sandwiched mono (complex 1) and dinuclear (complex 2) organoruthenium complexes derived from thiosemicarbazone ligand (L1). The molecular structures of compounds were characterized by analytical and multispectroscopic methods which corroborate well with single crystal XRD studies. DFT and TD-DFT studies of compounds revealed that HOMO electron density in L1 is localised on the thiosemicarbazide moiety while the LUMO electron density is evenly distributed over the ligand. However, in complex 1, the HOMO and LUMO is localised on the arene moiety and partially distributed over metal ion while HOMO and LUMO in complex 2 is equally delocalised throughout the complex. The collaborative preliminary DNA binding studies revealed that complexes 1 and 2 exhibited intercalative mode of interaction. The magnitude of DNA binding strength was determined by calculating Kb, K and Ksv values which demonstrated higher DNA binding propensity of complex 2. Furthermore, HSA binding studies of complexes also revealed better binding efficiency of dinuclear complex in contrast to mononuclear complex. The cytotoxic potential of dinuclear complex 2 was examined against triple negative breast cancer cell lines (MDA-MB-468 and MDA-MB-231) via MTT assay.

DNA and bovine serum albumin protein (BSA) interaction of antitumor supramolecular nickel(II) complex: Inference for drug design

To explore the therapeutic potential of supramolecular nickel(II) Schiff base self-assemble complexes, the Schiff base ligand (N, N′-bis(salicylidene)-1,3-diamino-2-propanol) and its Ni(II) complex [Ni2(H2L)2(NCS)2(CH3OH)2](CH3OH)2 were synthesized. Characterization by X-ray crystallography (for the complex), FT-IR, UV–Vis spectroscopy, 1HNMR and elemental analysis (CHN) were performed. Single-crystal X-ray structure of the complex exhibited a distorted octahedral geometry in which each nickel(II) center, in the asymmetric unit, was six coordinated with three N atoms and three O atoms (from Schiff base ligand, methanol and NCS). In vitro Fish Sperm DNA (FS-DNA) and Bovine Serum Albumin (BSA) binding studies of the complex employed UV–Vis and fluorescence spectroscopy, cyclic voltammetry, viscosity measurement and molecular docking. The complex indicated a good binding propensity to BSA and was also bound to FS-DNA, preferably via intercalation. The outputs of the molecular docking study confirmed the experimental results. The complex was found to exert high anticancer activity against the gastric and prostate cancerous cells with putative selective anticancer properties. The death-induced mechanism underlying the complex is mainly related to the intercalator interactions, which may result in apoptosis-programmed cell death.

Fast, accurate ranking of engineered proteins by target-binding propensity using structure modeling

Deep learning-based methods for protein structure prediction have achieved unprecedented accuracy. Yet, their utility in the engineering of protein-based binders remains constrained due to a gap between the ability to predict the structures of candidate proteins and the ability to assess which of those proteins are more probable to bind to a target. To bridge this gap, we introduce Automated Pairwise Peptide-Receptor AnalysIs for Screening Engineered proteins (APPRAISE), a method for predicting the target binding propensity of engineered proteins. After generating models of engineered proteins competing for binding to a target using an established structure-prediction tool such as AlphaFold-Multimer or ESMFold, APPRAISE performs a rapid (under 1 CPU second per model) scoring analysis that takes into account biophysical and geometrical constraints. As proof-of-concept cases, we demonstrate that APPRAISE can accurately classify receptor-dependent vs. receptor-independent adeno-associated viral vectors and diverse classes of engineered proteins such as miniproteins targeting the SARS-CoV-2 spike, nanobodies targeting a G-protein-coupled receptor, and peptides that specifically bind to transferrin receptor or PD-L1. APPRAISE is accessible through a web-based notebook interface using Google Colaboratory (https://tiny.cc/APPRAISE). With its accuracy, interpretability, and generalizability, APPRAISE promises to expand the utility of protein structure prediction and accelerate protein engineering for biomedical applications.

Assessment of virulence potential of &lt;i&gt;Escherichia coli&lt;/i&gt; isolated from clinical and non-clinical sources in port Harcourt, Nigeria.

Escherichia coli commonly occurs as a normal flora found in a variety of gastrointestinal tracts. However, certain strains acquire virulence characteristics. Potentially pathogenic species have also been isolated in non-clinical environments.This often raises concerns on the role these environments play in transmission. This study aimed to assess the occurrence of virulence traits in Escherichia coli isolated from non-clinical and clinical sources in Port Harcourt, Nigeria. Two hundred samples from clinical (urine and stool) and non-clinical (soil and poultry) sources were analyzed. 8 isolation, purification and identification of E. coli isolates were performed using standard bacteriological and biochemical tests. Out of the 200 samples collected, 98 isolates (49%) were confirmed as E. coli. Confirmed E. coli isolates were then tested for virulence using standard phenotypic tests (protease, colicin, congo red, hemolysin, haemagglutination, adhesin and mannose resistant/sensitive haemagglutination). E. coli strains from clinical samples displayed a number of virulence traits ranging frombiofilm producing capabilities (53%), congo red binding propensity (24%), colicin (34%), protease (15%) and hemolysin production (4%) compared to their non-clinical counterpart. All samples were negative for haemagglutination. The total virulence prevalence of E. coli was 81%. Clinical samples possessed more virulence traits (71%) than samples from non-clinical sources (29%), with urine having a higher occurrence among the clinical samples (36%). There is need for an in-depth study on virulence attributes of E. coli and ways to control these factors to minimize the rate of spread and the degree of infections.