Binding Propensity Research Articles

Polycystic Ovary Syndrome (PCOS) Inhibitory Drug Screening from Selective Inositols

Polycystic ovary syndrome (PCOS) is a heterogeneous ailment characterized by a combination of symptoms, including signs of androgen excess (hirsutism and/or hyperandrogenemia), ovarian dysfunction-oligo-ovulation and/or polycystic ovarian morphology (PCOM)), reproductive abnormalities, obesity, menstrual irregularity, type 2 diabetes (T2DM), hypertension, dyslipidemia, and depression. PubChem, enriched with 110 million chemicals, yielded 6327 inositol derivatives. Lipinski rule of five (MW up to 500 g/mol, H-bond donors 1–5, H-bond acceptors up to 10) criteria has been used for filtration of 582 compounds initial stage. Using escalating molecular weight, 101 molecules were selected from 582, to control this and rogen. To explore the possibility of androgen inhibition, various computational approaches, such as PASSprediction,protein-ligand interactions through molecular docking, chemical descriptors by DFT study, ADMET, bioavailability, and molecular dynamic (MD) simulation, were adopted by using the most accepted methods. Out of 101 inositol derivatives, 90 compounds were found to have more testosterone-inhibiting properties than ovulation-inhibiting or insulin-promoting properties in the PASS prediction investigation. Molecular docking analysis reveals a binding propensity for inositols of more than -7.4 kcal/mol between the androgen receptor protein (3RLJ) and inositols. Some of the most frequent bonded sites are shown to be at the MET:745 and ARG:752 amino acid residues, where the ligand (inositols) forms both hydrogen and hydrophobic bonds. In contrast, the Density Functional Theory (DFT) was used to predict the chemical and physical characteristics of promising inositols in this research. Furthermore, ADME, toxicity, and carcinogenicity factors were analyzed to validate the drugs' potential as safe, effective treatments for PCOS.MD simulation was done for the ligands L60, L77, and L88 against the target protein. The result of RMSD and RMSF revealed that the stability of docked complex is very high. As a conclusion, the in silico research suggests that the three inositols (L60, L77, and L88) are the most promising candidates for PCOS-preventative drugs that still need clinical or additional study

Molecular interaction of lysozyme with therapeutic drug azithromycin: Effect of sodium dodecyl sulfate on binding profile

This paper describes an inclusive biophysical study elucidating the interaction of therapeutic drug azithromycin (Azith) with hen egg white lysozyme (HEWL). Spectroscopic and computational tools have been employed to study the interaction of Azith with HEWL at pH 7.4. The fluorescence quenching constant values (Ksv) exhibited a decrease with the increase in temperature which revealed the occurrence of static quenching mechanism between Azith and HEWL. The thermodynamic data demonstrated that hydrophobic interactions were predominantly involved in the Azith-HEWL interaction. The negative value of standard Gibbs free energy (ΔG°) stated that the Azith-HEWL complex formed via spontaneous molecular interactions. The effect of sodium dodecyl sulfate (SDS) surfactant monomers on the binding propensity of Azith with HEWL was insignificant at lower concentrations however the binding significantly decreased at increased concentrations of the former. Far-UV CD data revealed alteration in the secondary structure of HEWL in the presence of Azith and the overall HEWL conformation changed. Molecular docking results revealed that the binding of Azith with HEWL takes place through hydrophobic interactions and hydrogen bonds.

Computational analysis of drug resistance of taxanes bound to human β-tubulin mutant (D26E)

The single-point mutation D26E in human β-tubulin is associated with drug resistance seen with two anti-mitotic taxanes (paclitaxel and docetaxel) when used to treat cancers. The molecular mechanism of this resistance remains elusive. However, docetaxel and a third-generation taxane, cabazitaxel, are thought to overcome this resistance. Here, structural models of both the wildtype (WT) and D26E mutant (MT) human β-tubulin were constructed based on the crystal structure of pig β-tubulin in complex with docetaxel (PDB ID: 1TUB). The three taxanes were docked into the WT and MT β-tubulin, and the resulting complexes were submitted to three independent runs of 200 ns molecular dynamic simulations, which were then averaged. MM/GBSA calculations revealed the binding energy of paclitaxel with WT and MT β-Tubulin to be −101.5 ± 8.4 and −90.4 ± 8.9 kcal/mol, respectively. The binding energy of docetaxel was estimated to be −104.7 ± 7.0 kcal/mol with the WT and −103.8 ± 5.5 kcal/mol with the MT β-tubulin. Interestingly, cabazitaxel was found to have a binding energy of −122.8 ± 10.8 kcal/mol against the WT and −106.2 ± 7.0 kcal/mol against the MT β-tubulin. These results show that paclitaxel and docetaxel bound to the MT less strongly than the WT, suggesting possible drug resistance. Similarly, cabazitaxel displayed a greater binding propensity against WT and MT β-tubulin than the other two taxanes. Furthermore, the dynamic cross-correlation matrices (DCCM) analysis suggests that the single-point mutation D26E induces a subtle dynamical difference in the ligand-binding domain. Overall, the present study revealed how the single-point mutation D26E may reduce the binding affinity of the taxanes, however, the effect of the mutation does not significantly affect the binding of cabazitaxel.

Silica-magnetite nanoparticles: Synthesis, characterization and nucleic acid separation potential

Silica-coated magnetic nanoparticles can be utilized for the magnetic separation of nucleic acids, which is an important step in many clinical procedures. A series of silica-functionalized superparamagnetic iron oxide nanoparticles (SiO2@MNPs) was synthesized to efficiently separate nucleic acids for the sensitive detection of viral infections. Magnetite nanoparticles (MNPs) coated with different thicknesses of silica layer resulting from different ratios of tetraethylorthosilicate (TEOS) precursor to magnetite (TEOS/MNPs = 0.4, 1.0, 2.0, 3.0, 4.0, 5.0 ml/g) have been selected for characterization of their physico-chemical properties and biological activities. The SiO2@MNPs' morphology, size, magnetic and surface properties, cytotoxicity and nucleic acid binding propensity were determined to select the ones with the highest RNA separation potential. Our results showed that RNA-binding properties and magnetic separation efficiency are nanoparticle size-dependent. The highest binding and separation efficiencies were detected for the smaller SiO2@MNPs with TEOS/MNPs (v/w) ratios equal to 1.0 and 2.0. These nanoparticles are promising candidates for clinical application relevant to RNA viruses.

Fmoc-phenylalanine-based fluorimetric and colorimetric dual-channel probes for the detection of Fe3+, Cu2+ and F-

Organic fluorophores that can generate readable signals on interaction with various metal ions are extensively used for their detection and quantification. The inherent metal binding affinity of amino acids can be utilized in developing fluorescent metal ion sensors by connecting them with appropriate fluorophores. Such sensors reported thus far mainly used histidine and to a lesser extent, tyrosine, methionine, etc., due to the presence of side chains with metal binding propensity. Herein, we report four Fmoc-phenylalanine (Fmoc-Phe)-based metal ion sensors for the selective detection of Fe3+ and Cu2+. The general design of the probes consisted of Fmoc-Phe connected to naphthalene/pyrene units through amide or triazole linkers. The absorbance of the probes gradually enhanced with the addition of increasing amounts of Fe3+ and Cu2+ ions. The colorless probe solutions turned yellow under visible light with the addition of these metal ions allowing colorimetric detection. A regular decrease in the emission intensity was noticed on adding Fe3+ and Cu2+ ions to probe solutions suggesting a ‘turn-off’ response. The probes were highly selective towards these two metal ions with a response time of less than 60 s. The detection limit for both metal ions was in the lower micromolar levels (0.67 to 3.14 μM). The binding stoichiometry and quenching mechanism were analyzed using Job’s plot method and Stern-Volmer analysis. The probe-Fe3+ complexes were further used as a turn-on sensor to detect fluoride ions. We also demonstrated the real-time detection of Fe3+, Cu2+ and F- using the filter paper strips coated with the probes under UV light of 365 nm.

Structural insights into interactions of new polymeric (μ–oxo) bridged Cu(II) complexes of taurine with yeast tRNA by spectroscopic and computational approaches and its application towards chemoresistant cancer lines

RNA-targeted drugs are considered as safe treatment option for the cure of many chronic diseases preventing off-targeted delivery and acute toxic manifestations. FDA has approved many such RNA therapies in different phases of clinical trials, validating their use for the treatment of various chronic diseases. We report herein, new water-soluble (μ–oxo) bridged polymeric Cu(II) complexes of taurine (2–aminoethane sulfonic acid) complexes 1 and 2. The therapeutic potency of 1 and 2 was ascertained by studying biophysical interactions with tRNA/ct-DNA. The experimental results demonstrated that the complexes interacted avidly to nucleic acids through intercalation mode depicting a specific preference for tRNA in comparison to ct–DNA and, moreover 2 showed higher binding propensity than 1. The electrophoretic behaviour of the complexes with plasmid pBR322 DNA and tRNA were examined by gel mobility assay that revealed a concentration-dependent activity with complex 2 performing more efficient cleavage as compared to complex 1. Cytotoxicity results on cancer cell strains displayed higher cytotoxicity than complex 1 against treated cancer cells. The synthesized copper(II) taurine complexes have met the basic criteria of anticancer drug design as they are structurally well-characterized, exhibiting good solubility in water, lipophilic in nature with superior intercalating propensity towards tRNA and cytotoxic in nature.

Insight into the Binding Mechanisms of Quartz-Selective Peptides: Toward Greener Flotation Processes.

Mining practices, chiefly froth flotation, are being critically reassessed to replace their use of biohazardous chemical reagents in favor of biofriendly alternatives as a path toward green processes. In this regard, this study aimed at evaluating the interactions of peptides, as potential floatation collectors, with quartz using phage display and molecular dynamics (MD) simulations. Quartz-selective peptide sequences were initially identified by phage display at pH = 9 and further modeled by a robust simulation scheme combining classical MD, replica exchange MD, and steered MD calculations. Our residue-specific analyses of the peptides revealed that positively charged arginine and lysine residues were favorably attracted by the quartz surface at basic pH. The negatively charged residues at pH 9 (i.e., aspartic acid and glutamic acid) further showed affinity toward the quartz surface through electrostatic interactions with the positively charged surface-bound Na+ ions. The best-binding heptapeptide combinations, however, contained both positively and negatively charged residues in their composition. The flexibility of peptide chains was also shown to directly affect the adsorption behavior of the peptide. While attractive intrapeptide interactions were dominated by a weak peptide-quartz binding, the repulsive self-interactions in the peptides improved the binding propensity to the quartz surface. Our results showed that MD simulations are fully capable of revealing mechanistic details of peptide adsorption to inorganic surfaces and are an invaluable tool to accelerate the rational design of peptide sequences for mineral processing applications.

DNA Binding and Cleavage, Stopped-Flow Kinetic, Mechanistic, and Molecular Docking Studies of Cationic Ruthenium(II) Nitrosyl Complexes Containing "NS4" Core.

This work aimed to evaluate in vitro DNA binding mechanistically of cationic nitrosyl ruthenium complex [RuNOTSP]+ and its ligand (TSPH2) in detail, correlate the findings with cleavage activity, and draw conclusions about the impact of the metal center. Theoretical studies were performed for [RuNOTSP]+, TSPH2, and its anion TSP-2 using DFT/B3LYP theory to calculate optimized energy, binding energy, and chemical reactivity. Since nearly all medications function by attaching to a particular protein or DNA, the in vitro calf thymus DNA (ctDNA) binding studies of [RuNOTSP]+ and TSPH2 with ctDNA were examined mechanistically using a variety of biophysical techniques. Fluorescence experiments showed that both compounds effectively bind to ctDNA through intercalative/electrostatic interactions via the DNA helix's phosphate backbone. The intrinsic binding constants (Kb), (2.4 ± 0.2) × 105 M-1 ([RuNOTSP]+) and (1.9 ± 0.3) × 105 M-1 (TSPH2), as well as the enhancement dynamic constants (KD), (3.3 ± 0.3) × 104 M-1 ([RuNOTSP]+) and (2.6 ± 0.2) × 104 M-1 (TSPH2), reveal that [RuNOTSP]+ has a greater binding propensity for DNA compared to TSPH2. Stopped-flow investigations showed that both [RuNOTSP]+ and TSPH2 bind through two reversible steps: a fast second-order binding, followed by a slow first-order isomerization reaction via a static quenching mechanism. For the first and second steps of [RuNOTSP]+ and TSPH2, the detailed binding parameters were established. The total binding constants for [RuNOTSP]+ (Ka = 43.7 M-1, Kd = 2.3 × 10-2 M-1, ΔG0 = -36.6 kJ mol-1) and TSPH2 (Ka = 15.1 M-1, Kd = 66 × 10-2 M, ΔG0 = -19 kJ mol-1) revealed that the relative reactivity is approximately ([RuNOTSP]+)/(TSPH2) = 3/1. The significantly negative ΔG0 values are consistent with a spontaneous binding reaction to both [RuNOTSP]+ and TSPH2, with the former being very favorable. The findings showed that the Ru(II) center had an effect on the reaction rate but not on the mechanism and that the cationic [RuNOTSP]+ was a more highly effective DNA binder than the ligand TSPH2 via strong electrostatic interaction with the phosphate end of DNA. Because of its higher DNA binding affinity, cationic [RuNOTSP]+ demonstrated higher cleavage efficiency towards the minor groove of pBR322 DNA via the hydrolytic pathway than TSPH2, revealing the synergy effect of TSPH2 in the form of the complex. Furthermore, the mode of interaction of both compounds with ctDNA has also been supported by molecular docking.

Differential Binding and Conformational Dynamics of Tau Microtubule-Binding Repeats with a Preformed Amyloid-β Fibril Seed.

Both senile plaques formed by amyloid-β (Aβ) and neurofibrillary tangles (NFTs) comprised of tau are pathological hallmarks of Alzheimer's disease (AD). The accumulation of NFTs better correlates with the loss of cognitive function than senile plaques, but NFTs are rarely observed without the presence of senile plaques. Hence, cross-seeding of tau by preformed Aβ amyloid fibril seeds has been proposed to drive the aggregation of tau and exacerbate AD progression, but the molecular mechanism remains unknown. Here, we first identified cross-interaction hotspots between Aβ and tau using atomistic discrete molecular dynamics simulations (DMD) and confirmed the critical role of the four microtubule-binding repeats of tau (R1-R4) in the cross-interaction with Aβ. We further investigated the binding structure and dynamics of each tau repeat with a preformed Aβ fibril seed. Specifically, R1 and R3 preferred to bind the Aβ fibril lateral surface instead of the elongation end. In contrast, R2 and R4 had higher binding propensities to the fibril elongation end than the lateral surface, enhancing β-sheet content by forming hydrogen bonds with the exposed hydrogen bond donors and acceptors. Together, our results suggest that the four repeats play distinct roles in driving the binding of tau to different surfaces of an Aβ fibril seed. Binding of tau to the lateral surface of Aβ fibril can increase the local concentration, while the binding to the elongation surface promotes β-sheet formation, both of which reduce the free energy barrier for tau aggregation nucleation and subsequent fibrillization.

A hybrid approach to assess the structural impact of longnoncodingRNA mutations uncovers key NEAT1 interactions in colorectal cancer.

Long noncoding RNAs (lncRNAs) are emerging players in cancer and they entail potential as prognostic biomarkers or therapeutic targets. Earlier studies have identified somatic mutations in lncRNAs that are associated with tumor relapse after therapy, but the underlying mechanisms behind these associations remain unknown. Given the relevance of secondary structure for the function of some lncRNAs, some of these mutations may have a functional impact through structural disturbance. Here, we examined the potential structural and functional impact of a novel A > G point mutation in NEAT1 that has been recurrently observed in tumors of colorectal cancer patients experiencing relapse after treatment. Here, we used the nextPARS structural probing approach to provide first empirical evidence that this mutation alters NEAT1 structure. We further evaluated the potential effects of this structural alteration using computational tools and found that this mutation likely alters the binding propensities of several NEAT1-interacting miRNAs. Differential expression analysis on these miRNA networks shows upregulation of Vimentin, consistent with previous findings. We propose a hybrid pipeline that can be used to explore the potential functional effects of lncRNA somatic mutations.

In silico investigation of binding propensity of hematoxylin derivative and damnacanthal for their potential inhibitory effect on HIV-1 Vpr from different subtypes

HIV-1, the causative agent of AIDS leads to many deaths worldwide though few options are available as therapeutics. To deal with the continuous mutation in the virus genome, requirement of new drugs is always there. Subtype variation plays a crucial role in case of HIV-1 therapeutics development. In this study, we want to investigate some pre examined molecules that can be effective for HIV-1 VPR. Inhibition of several protein–protein interactions with the small molecules will lead to identify some molecules as therapeutics other than the conventional drugs. We retrieved the sequences of different subtypes from the database and representative sequences were identified. Representative structures were modelled and validated using MD simulations. Forty molecules, showing anti Vpr activity in vitro were identified from literature survey and those were docked with each subtype representative structures. Two molecules a stable Hematoxylin Derivative (SHD) and Damnacanthal (D3), these were shown to be bind more effectively for all the subtypes. The stability of the protein and those two small molecule complexes were identified again with MD simulation followed by the binding energy calculation. Thus, these molecules can be thought as any option other than the conventional drug targeting HIV-1 Vpr. Communicated by Ramaswamy H. Sarma

Interaction of barley β-glucan with food dye molecules – An insight from pulse dipolar EPR spectroscopy

The interactions between dietary fibers (DFs) and small molecules are of great interest to food chemistry and nutrition science. However, the corresponding interaction mechanisms and structural rearrangements of DFs at the molecular level are still opaque due to the usually weak binding and the lack of appropriate techniques to determine details of conformational distributions in such weakly organized systems. By combining our previously established methodology on stochastic spin-labelling of DFs with the appropriately revised set of pulse electron paramagnetic resonance techniques, we present here a toolkit to determine the interactions between DFs and small molecules, using barley β-glucan as an example for neutral DF and a selection of food dye molecules as examples for small molecules. The proposed here methodology allowed us to observe subtle conformational changes of β-glucan by detecting multiple details of the local environment of the spin labels. Substantial variations of binding propensities were detected for different food dyes.

Phenolic compounds as histone deacetylase inhibitors: binding propensity and interaction insights from molecular docking and dynamics simulations.

Histone deacetylases are well-established target enzymes involved in the pathology of different diseases including cancer and neurodegenerative disorders. The approved HDAC inhibitor drugs are associated with cellular toxicities. Different phenolic compounds have been shown to possess inhibitory activities against HDACs and are, therefore, considered safer alternatives to synthetic compounds. Here, we elucidated the binding mode and calculated the binding propensity of some of the top phenolic compounds against different isoforms representing different classes of Zn2+ ion-containing HDACs using the molecular docking approach. Our data reaffirmed the activity of the studied phenolic compounds against HDACs. Binding interaction analysis suggested that these compounds can block the activity of HDACs with or without binding to the active site zinc metal ion. Furthermore, molecular dynamics (MD) simulations were carried out on the selected crystal and docking complexes of each selected HDAC isoform. Analysis of root-mean-square displacement (RMSD) showed that the phenolic compounds demonstrated a stable binding mode over 50ns in a way that is comparable to the cocrystal ligands. Together, these findings can aid future efforts in the search for natural inhibitors of HDACs.

Progress of Metal-Based Anticancer Chemotherapeutic Agents in Last two Decades and their Comprehensive Biological (DNA/RNA Binding, Cleavage and Cytotoxicity Activity) Studies.

During last two decades, there has been an enormous growth in the discovery of innovative active inorganic anticancer complexes (exerting remarkable cytotoxicity at sub micro-molar levels) derived from myriad ligand scaffolds, mainly acting on cancerous vs healthy cells by either halting or inhibiting their uncontrolled growth. The phenomenal success of cisplatin to treat numerous forms of solid malignancies has placed metal-based drugs to the forefront of treatment strategies against cancers. More than 10,000 platinum anticancer complexes have been developed during the past 40 years, but only five drugs have been approved for usage in humans while ten more complexes are currently undergoing clinical trials. Most of the compounds have failed either at R&D stages or in preclinical trails. This has led to extensive investigations by researchers of medicinal chemistry, including our group to design and prepare tailored 3d-metallo-drugs and organotin(IV) compounds from some naturally occurring bioactive compounds, such as amino-acids, peptides, chromone derivatives and NSAID's etc. that were used either alone or in cocktail combination, capable of specifically targeting DNA, lnc RNAs and proteins. Furthermore, 3d-metal ions such as copper, cobalt and zinc etc. incorporated in these ligand framework are biocompatible and induce a unique multi-modal mechanism of cytotoxic action involving angiogenesis, ROS-induced DNA damage, apoptosis by p53 mitochondrial genes and caspases etc. The results observed a positive correlation between the binding affinity of complexes with DNA (as quantified by intrinsic binding constant values) and their cytotoxic behavior. Complexes with high DNA binding propensity were typically lethal against a diverse panel of malignant cell types compared to normal cells.

DNA-Binding and Photocleavage Studies of N,N'-Dibenzylidene-9H-Carbazole-3,6-Diamine

The DNA-binding mode of N,N'-Dibenzylidene-9H-Carbazole-3,6-Diamine with CT-DNA was investigated by absorption spectroscopy, EB-DNA displacement, circular dichroism, thermal denaturation and viscosity measurements. Results indicated that these compounds intercalate into the base pairs of CT-DNA. The effect of ionic strength on the fluorescence property of the system indicated the presence of electrostatic interaction via phosphate backbone of DNA helix. The intrinsic binding constant values suggested that compound has DNA binding propensity. This compound promote the cleavage of plasmid pBR322. These results may be useful for the design of N,N'-Dibenzylidene-9H-Carbazole-3,6-Diamine with desired binding characteristics and useful to better understand the DNA binding mode of heterocyclic compound.

Structural Analogs of the GABAkine KRM-II-81 Are Orally Bioavailable Anticonvulsants without Sedation.

To provide back-up compounds to support the development of the GABAA receptor (GABAAR) potentiator KRM-II-81, three novel analogs were designed: replacing the pyridinyl with 2'-Cl-phenyl (FR-II-60), changing the positions of the N and O atoms in the oxazole ring with addition of an ethyl group (KPP-III-34 and KPP-III-51), or substituting a Br atom for the ethynyl of KRM-II-81 (KPP-III-34). The compounds bound to brain GABAARs. Intraperitoneal administration of FR-II-60 and KPP-III-34 produced anticonvulsant activity in mice [maximal electroshock (MES)-induced seizures or 6 Hz-induced seizures], whereas KPP-III-51 did not. Although all compounds were orally bioavailable, structural changes reduced the plasma and brain (FR-II-60 and KPP-III-51) exposures relative to KRM-II-81. Oral administration of each compound produced dose-dependent increases in the latency for both clonic and tonic seizures and the lethality induced by pentylenetetrazol (PTZ) in mice. Since KPP-III-34 produced the highest brain area under the curve (AUC) exposures, it was selected for further profiling. Oral administration of KPP-III-34 suppressed seizures in corneal-kindled mice, hippocampal paroxysmal discharges in mesial temporal lobe epileptic mice, and PTZ-induced convulsions in rats. Only transient sensorimotor impairment was observed in mice, and doses of KPP-III-34 up to 500 mg/kg did not produce impairment in rats. Molecular docking studies demonstrated that all compounds displayed a reduced propensity for binding to α1His102 compared with the sedating compound alprazolam; the bromine-substituted KPP-III-34 achieved the least interaction. Overall, these findings document the oral bioavailability and anticonvulsant efficacy of three novel analogs of KRM-II-81 with reduced sedative effects. SIGNIFICANCE STATEMENT: A new non-sedating compound, KRM-II-81, with reduced propensity for tolerance is moving into clinical development. Three new analogs were orally bioavailable, produced anticonvulsant effects in rodents, and displayed low sensorimotor impairment. KPP-III-34 demonstrated efficacy in models of pharmacoresistant epilepsy. Docking studies demonstrated a low propensity for compound binding to the α1His102 residue implicated in sedation. Thus, three additional structures have been added to the list of non-sedating imidazodiazepine anticonvulsants that could serve as backups in the clinical development of KRM-II-81.

In silico analysis of TUBA4A mutations in Amyotrophic Lateral Sclerosis to define mechanisms of microtubule disintegration

Amyotrophic lateral sclerosis (ALS) is an inexorably progressive and degenerative disorder of motor neurons with no currently-known cure. Studies to determine the mechanism of neurotoxicity and the impact of ALS-linked mutations (SOD1, FUS, TARDP, C9ORF72, PFN1, TUBA4A and others) have greatly expanded our knowledge of ALS disease mechanisms and have helped to identify potential targets for ALS therapy. Cellular pathologies (e.g., aggregation of mutant forms of SOD1, TDP43, FUS, Ubiqulin2, PFN1, and C9ORF72), mitochondrial dysfunction, neuroinflammation, and oxidative damage are major pathways implicated in ALS. Nevertheless, the selective vulnerability of motor neurons remains unexplained. The importance of tubulins for long-axon infrastructure, and the special morphology and function of motor neurons, underscore the central role of the cytoskeleton. The recent linkage of mutations to the tubulin α chain, TUBA4A, to familial and sporadic cases of ALS provides a new investigative opportunity to shed light on both mechanisms of ALS and the vulnerability of motor neurons. In the current study we investigate TUBA4A, a structural microtubule protein with mutations causal to familial ALS, using molecular-dynamic (MD) modeling of protein structure to predict the effects of each mutation and its overall impact on GTP binding, chain stability, tubulin assembly, and aggregation propensity. These studies predict that each of the reported mutations will cause notable structural changes to the TUBA4A (α chain) tertiary protein structure, adversely affecting its physical properties and functions. Molecular docking and MD simulations indicate certain α chain mutations (e.g. K430N, R215C, and W407X) may cause structural deviations that impair GTP binding, and plausibly prevent or destabilize tubulin polymerization. Furthermore, several mutations (including R320C and K430N) confer a significant increase in predicted aggregation propensity of TUBA4A mutants relative to wild-type. Taken together, these in silico modeling studies predict structural perturbations and disruption of GTP binding, culminating in failure to form a stable tubulin heterocomplex, which may furnish an important pathogenic mechanism to trigger motor neuron degeneration in ALS.

SARS-CoV-2 Omicron Subvariants Balance Host Cell Membrane, Receptor, and Antibody Docking via an Overlapping Target Site.

Variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are emerging rapidly and offer surfaces that are optimized for recognition of host cell membranes while also evading antibodies arising from vaccinations and previous infections. Host cell infection is a multi-step process in which spike heads engage lipid bilayers and one or more angiotensin-converting enzyme 2 (ACE-2) receptors. Here, the membrane binding surfaces of Omicron subvariants are compared using cryo-electron microscopy (cEM) structures of spike trimers from BA.2, BA.2.12.1, BA.2.13, BA.2.75, BA.3, BA.4, and BA.5 viruses. Despite significant differences around mutated sites, they all maintain strong membrane binding propensities that first appeared in BA.1. Both their closed and open states retain elevated membrane docking capacities, although the presence of more closed than open states diminishes opportunities to bind receptors while enhancing membrane engagement. The electrostatic dipoles are generally conserved. However, the BA.2.75 spike dipole is compromised, and its ACE-2 affinity is increased, and BA.3 exhibits the opposite pattern. We propose that balancing the functional imperatives of a stable, readily cleavable spike that engages both lipid bilayers and receptors while avoiding host defenses underlies betacoronavirus evolution. This provides predictive criteria for rationalizing future pandemic waves and COVID-19 transmissibility while illuminating critical sites and strategies for simultaneously combating multiple variants.

Differential binding dynamics of four microtubule-binding repeats of tau with an amyloid-β fibril seed.

Both senile plaques formed by amyloid-beta (Aβ) and neurofibrillary tangles comprised of tau are hallmarks of Alzheimer's disease (AD). The accumulation of neurofibrillary tangles better correlates with the loss of cognitive function than senile plaques, but neurofibrillary tangles are rarely observed without the presence of senile plaques. Hence, cross-seeding of tau by preformed Aβ amyloid fibril seeds has been proposed to drive the aggregation of tau and exacerbate AD progression, but the molecular mechanism remains poorly understood. Herein, we identified cross-interaction hotspots between Aβ and tau using atomistic discrete molecular dynamics simulations (DMD) and confirmed the critical role of the four microtubule-binding repeats of tau (R1-R4) in the cross-interaction with Aβ. We further investigated the binding structure and dynamics of each tau repeat with a preformed Aβ fibril seed. Specifically, R1 and R3 preferred to bind the lateral instead of elongation surfaces of the fibril, preserving similar secondary structures as in the solution. In contrast, R2 and R4 had higher binding propensities to the elongation than lateral surfaces, adopting β-sheet structures by forming hydrogen bonds with the exposed hydrogen bond donors and acceptors. Together, our results suggest that four MTBD repeats play distinct roles in driving the binding of tau to two different surfaces of an Aβ fibril seed. The binding of tau to the lateral surface of Aβ fibril can increase the local concentration, while the binding in the elongation surface promotes β-sheet formation, both of which reduce the free energy barrier for tau aggregation nucleation and subsequent fibrillization. Our computational study offers molecular insight into the experimentally observed cross-seeding of Tau aggregation by pre-formed Aβ fibril seeds and helps better understand the pathological synergy of Aβ and tau aggregation in the etiology of AD.

A Data-Driven Approach to Construct a Molecular Map of Trypanosoma cruzi to Identify Drugs and Vaccine Targets.

Chagas disease (CD) is endemic in large parts of Central and South America, as well as in Texas and the southern regions of the United States. Successful parasites, such as the causative agent of CD, Trypanosoma cruzi have adapted to specific hosts during their phylogenesis. In this work, we have assembled an interactive network of the complex relations that occur between molecules within T. cruzi. An expert curation strategy was combined with a text-mining approach to screen 10,234 full-length research articles and over 200,000 abstracts relevant to T. cruzi. We obtained a scale-free network consisting of 1055 nodes and 874 edges, and composed of 838 proteins, 43 genes, 20 complexes, 9 RNAs, 36 simple molecules, 81 phenotypes, and 37 known pharmaceuticals. Further, we deployed an automated docking pipeline to conduct large-scale docking studies involving several thousand drugs and potential targets to identify network-based binding propensities. These experiments have revealed that the existing FDA-approved drugs benznidazole (Bz) and nifurtimox (Nf) show comparatively high binding energies to the T. cruzi network proteins (e.g., PIF1 helicase-like protein, trans-sialidase), when compared with control datasets consisting of proteins from other pathogens. We envisage this work to be of value to those interested in finding new vaccines for CD, as well as drugs against the T. cruzi parasite.