Molecular dynamics simulations show how antibodies may rescue HIV-1 mutants incapable of infecting host cells.

High mutation and replication rates of HIV-1 result in the continuous generation of variants, allowing it to adapt to changing host environments. Mutations often have deleterious effects, but variants carrying them are rapidly purged. Surprisingly, a particular variant incapable of entering host cells was found to be rescued by host antibodies targeting HIV-1. Understanding the molecular mechanism of this rescue is important to develop and improve antibody-based therapies. To unravel the underlying mechanisms, we performed fully atomistic molecular dynamics simulations of the HIV-1 gp41 trimer responsible for viral entry into host cells, its entry-deficient variant, and its complex with the rescuing antibody. We find that the Q563R mutation, which the entry-deficient variant carries, prevents the native conformation of the gp41 6-helix bundle required for entry and stabilizes an alternative conformation instead. This is the consequence of substantial changes in the secondary structure and interactions between the domains of gp41. Binding of the antibody F240 to gp41 reverses these changes and re-establishes the native conformation, resulting in rescue. To test the generality of this mechanism, we performed simulations with the entry-deficient L565A variant and antibody 3D6. We find that 3D6 binding was able to reverse structural and interaction changes introduced by the mutation and restore the native gp41 conformation. Viral variants may not only escape antibodies but be aided by them in their survival, potentially compromising antibody-based therapies, including vaccination and passive immunization. Our simulation framework could serve as a tool to assess the likelihood of such resistance against specific antibodies.Communicated by Ramaswamy H. SarmaCommunicated by Ramaswamy H. Sarma.

Riding the Wave: Unveiling the Conformational Waves from RBD of SARS-CoV-2 Spike Protein to ACE2.

The binding affinity between angiotensin-converting enzyme 2 (ACE2) and the receptor-binding domain (RBD) plays a crucial role in the transmission and reinfection of SARS-CoV2. Here, microsecond molecular dynamics simulations revealed that point mutations in the RBD domain induced conformational transitions that determined the binding affinity between ACE2 and RBD. These structural changes propagated through the RBD domain, altering the orientation of both ACE2 and RBD residues at the binding site. ACE2 receptor shows significant structural heterogeneity, whereas its binding to the RBD domain indicates a much greater degree of structural homogeneity. The receptor was more flexible in its unbound state with the binding of RBD domains inducing structural transitions. The structural heterogeneity observed in the ACE2 unbound form plays a role in the promiscuity of viral entry, as it may allow the receptor to interact with various related and unrelated ligands. Furthermore, rigidity may be important for stabilizing the complex and ensuring the proper orientation of the RBD-binding interface with ACE2. The greater structural homogeneity observed in the ACE2-RBD complex revealed the effectiveness of neutralizing antibodies and vaccines that are primarily directed toward the RBD-binding interface. The binding of the B38 monoclonal antibody revealed restricted conformational transitions in the RBD and ACE2 receptors, attributed to its potent binding interaction.

Aquaporin-4 Mediated Aggregation of Alzheimer's Amyloid ß-Peptide.

Clearance of Alzheimer's amyloid oligomers from the brain is crucial for preventing cell toxicity. Dementia complications arise as a result of apoptosis, which is caused by peptide plaques on the lipid surface of cells. Here, we employed all-atom and coarse-grained molecular dynamics simulations to investigate the aggregation of amyloid peptides at the lipid surface and the role of aquaporin-4 (AQP4) in facilitating peptide clearance from astrocytes. The network of protein-protein interactions through text mining revealed that the expression of AQP4 and amyloid aggregation were strongly correlated. It has also been revealed that the role of aquaporins in the etiology of Alzheimer's disease involves several interconnected proteins and pathways. The nature of aggregation at the surface of the 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipid bilayer was revealed by the interaction of amyloid oligomers. The membrane-bound pore region of AQP4 interacts with the peptide and slows its aggregation. This interaction maintains the helical content of the peptide while lowering its toxicity at the lipid surface. The hydrophobicity of the peptide also decreased because of these interactions, which may help in the removal of the peptide from astrocytes. Long-term coarse-grained MD simulations demonstrated different features of oligomer aggregation at the surface and strong oligomer attraction to AQP4, which inhibited aggregation. Additionally, the water dynamics of aquaporins demonstrate how the selectivity filter is broken to disrupt water flow. Our findings also provide insight into the physiological alterations in brain tissue associated with Alzheimer's disease, including water retention and increased water flow in the CSF. Furthermore, in vitro thioflavin fluorescence spectroscopy revealed a slower aggregation of the peptide in the presence of AQP4.

Hinged Bipodal Furoylthiourea-Based Ru(II)-Arene Complexes: Effect of (ortho, meta, or para)-Substitution on Coordination and Anticancer Activity.

We set out to design and synthesize bipodal ligands with the phenyl group as the spacer and varied the substitution on the spacer between ortho (L1), meta (L2), and para (L3). The respective ligands and complexes containing either p-cymene (PL1-PL3) or benzene (BL1-BL3) as the arene unit were synthesized and characterized successfully. The influence of the ligands due to substitution change on their coordination behavior was quite minimal; however, the differences were seen in the anticancer activity of the complexes. DFT studies revealed the structural variations between the three different substitutions, which was further confirmed by single-crystal X-ray diffraction studies. The anticancer activity of the complexes could be correlated with their rate of hydrolysis and their lipophilicity index as determined by UV-visible spectroscopy. The cell death mechanism of the active complexes was deduced to be apoptotic via staining assays, flow cytometry, and Western blot analysis.

Graphene oxide as a dual template for induced helicity of peptides.

Artificial template-mediated fabrication of secondary structures within peptides always attracts great interest in biological systems due to several biomimetic interactions. In all earlier studies, a uniform template containing molecules/nanomaterials was used to target only one type of peptide at a time, which extensively limits the diversity in the generation of artificial protein surface/binding sites. This limitation can be overcome by the incorporation of more than one binding template (heterogeneity) in a single system, for example, Janus nanomaterials, which are challenging and difficult to synthesize. In this context, graphene oxide (GO) is considered an artificial binding site (template). It contains two distinctive binding zones, i.e., surface and edge, which can induce the secondary structure of peptides based on complementary interactions. To establish our concept, we have implemented a hybrid sequence i.e., i, i + 4, i + 7 and i + 11 pattern peptides, which defines a more linear surface, suitable for recognition by the two-dimensional GO. Depending on the amino acid residue at the specific locations, we observed substantial enhancement of peptide helicity either at the surface or at the edges of GO from the random coil. However, non-interacting peptides remain as a random coil. We have established this by circular dichroism study at various conditions, as well as atomic force microscopy and optical imaging study. Furthermore, we have also established our observations using molecular dynamics (MD) simulations. This study reveals that the synthesized GO-peptides composite with different secondary structures and recognition residues can mimic biological systems.

The potential role of procyanidin as a therapeutic agent against SARS-CoV-2: a text mining, molecular docking and molecular dynamics simulation approach.

A novel coronavirus (SARS-CoV-2) has caused a major outbreak in human all over the world. There are several proteins interplay during the entry and replication of this virus in human. Here, we have used text mining and named entity recognition method to identify co-occurrence of the important COVID 19 genes/proteins in the interaction network based on the frequency of the interaction. Network analysis revealed a set of genes/proteins, highly dense genes/protein clusters and sub-networks of Angiotensin-converting enzyme 2 (ACE2), Helicase, spike (S) protein (trimeric), membrane (M) protein, envelop (E) protein, and the nucleocapsid (N) protein. The isolated proteins are screened against procyanidin-a flavonoid from plants using molecular docking. Further, molecular dynamics simulation of critical proteins such as ACE2, Mpro and spike proteins are performed to elucidate the inhibition mechanism. The strong network of hydrogen bonds and hydrophobic interactions along with van der Waals interactions inhibit receptors, which are essential to the entry and replication of the SARS-CoV-2. The binding energy which largely arises from van der Waals interactions is calculated (ACE2=-50.21 ± 6.3, Mpro=-89.50 ± 6.32 and spike=-23.06 ± 4.39) through molecular mechanics Poisson-Boltzmann surface area also confirm the affinity of procyanidin towards the critical receptors. Communicated by Ramaswamy H. Sarma.

Mechanistic insights into the effects of key mutations on SARS-CoV-2 RBD-ACE2 binding.

Some recent SARS-CoV-2 variants appear to have increased transmissibility compared to the original strain. An underlying mechanism could be the improved ability of the variants to bind receptors on the target cells and infect them. In this study, we provide atomic-level insights into the binding of the receptor binding domain (RBD) of the wild-type SARS-CoV-2 spike protein and its single (N501Y), double (E484Q, L452R) and triple (N501Y, E484Q, L452R) mutated variants to the human ACE2 receptor. Using extensive all-atom molecular dynamics simulations and advanced free energy calculations, we estimate the associated binding affinities and binding hotspots. We observe significant secondary structural changes in the RBD of the mutants, which lead to different binding affinities. We find higher binding affinities for the double (E484Q, L452R) and triple (N501Y, E484Q, L452R) mutated variants than for the wild type and the N501Y variant, which could contribute to the higher transmissibility of recent variants containing these mutations.

Construction of a simple dual-channel fluorescence chemosensor for Cu2+ ion and GSSG detection and its mitochondria-targeting bioimaging applications.

Numerous chemosensors have been developed for next-generation detection systems because of their ease of use and promising characteristics to distinguish signals between various analytes binding. However, given their typically poor emission response and arduous preparation methods, very few chemosensing probes have been commercialized to date. In this work, a simple, naphthoquinone-based mitochondria-targeting chemosensor (CIA) has been fabricated for the simultaneous detection of Cu2+ and GSSG (glutathione oxidized) through an "on-off" mode in a buffered semi-aqueous solution. Significantly, the CIA chemosensor showed a sensitive detection response towards Cu2+ and GSSG with low detection limits (0.309 µM, and 0.226 µM, respectively). In addition, the detection mechanism of CIA was thoroughly verified and confirmed using numerous analytical techniques. Furthermore, CIA was utilized as a sequential fluorescence biomarker to detect Cu2+ in human cervical cancer cell lines. These findings indicate that the chemosensor CIA can discriminate human cancer cells from normal cells. The CIA was also confirmed to possess the ability to target mitochondria. More importantly, the present CIA chemosensor detected Cu2+ in zebrafish larvae, indicating the probe has tissue penetration ability.

Mitochondria-targeted acridine-based dual-channel fluorescence chemosensor for detection of Sn4+ and Cr2O72- ions in water and its application in discriminative detection of cancer cells.

The goal of the present work was to fabricate a new low-cost, easy-to-prepare, dual-channel fluorescence chemosensor comprised of acridine-diphenylacetyl moieties (NDA) to enable remarkable Sn4+ detection in water and biological medium. The resulting NDA-Sn4+ complex was utilized for the distinguished identification of Cr2O72- ions from other anions and biomolecules. These investigations involve the absorption, fluorescence, and electrochemical methods for the detection of Sn4+ and Cr2O72- ions in pure water. The mechanism for NDA-mediated Sn4+ detection was experimentally determined by FT-IR, NMR titrations, mass (ESI) analyses, and DFT calculations. The obtained results indicate that the NDA chemosensor possessed excellent performance characteristics including good water solubility and compatibility, quick response time (less than 10 s), high sensitivity (Sn4+ = 0.268 µM and Cr2O72- = 0.160 µM), and selectivity against coexisting metals, anions, amino acids, and peptides. The chemosensor NDA induced negligible toxicity in live cells and was successfully utilized as a biomarker for the tracking of Sn4+ in human normal and cancer cells. More importantly, NDA demonstrates distinguished recognition of Sn4+ in human cancer cells rather than in normal live cells. Additionally, NDA was shown to act as a mitochondria-targeted probe in FaDu cells.

A dual-channel colorimetric and ratiometric fluorescence chemosensor for detection of Hg2+ ion and its bioimaging applications.

A new colorimetric and ratiometric fluorescence chemosensor 4-((3-(octadecylthio)-1,4-dioxo-1,4-dihydronaphthalen-2-yl)amino)benzenesulfonamide (4DBS) was synthesized and investigated for the selective detection of Hg2+ in DMSO-H2O (9:1, v/v) solution. The chemosensor was efficiently synthesized in two steps via Michael-like addition and nucleophilic substitution reactions. The ratiometric fluorescence turn-on response was obtained towards Hg2+, and its fluorescence emission peak was red-shifted by 140 nm with an associated color change from light maroon to pale yellow due to the intramolecular charge transfer effect. The formed coordination metal complex was further evaluated by FT-IR, 1H NMR, and quantum chemical analyses to confirm the binding mechanism. The detection process was sensitive/reversible, and the calculated limit of detection for Hg2+ was 0.451 µM. Furthermore, 4DBS was effectively utilized as a bioimaging agent for detection of Hg2+ in live cells and zebrafish larvae. Additionally, 4DBS showed distinguishing detection of Hg2+ in cancer cells in comparison with normal cells. Thus, 4DBS could be employed as an efficient bioimaging probe for discriminative identification of human cancer cells.

Mitochondria-targeted dual-channel colorimetric and fluorescence chemosensor for detection of Sn2+ ions in aqueous solution based on aggregation-induced emission and its bioimaging applications.

Several fluorescence and colorimetric chemosensory for Sn2+ detection in an aqueous media have been reported, but applications remain limited for discriminative Sn2+ detection in live human cells and zebrafish larvae. Herein, a mitochondria-targeted Sn2+ "turn-on" colorimetric and fluorescence chemosensor, 2CTA, with an aggregation-induced emission (AIE) response was developed. The sensing of Sn2+ was enabled by a reduction-enabled binding pathway, with the conversion of -CË­O groups to -C-OH groups at the naphthoquinone moiety. The color changed from light maroon to milky white in a buffered aqueous solution. The chemosensor 2CTA possessed the excellent characteristics of good water solubility, fast response (less than 10 s), and high sensitivity (79 nM) and selectivity for Sn2+ over other metal ions, amino acids, and peptides. The proposed binding mechanism was experimentally verified by means of FT-IR and NMR studies. The chemosensor 2CTA was successfully employed to recognize Sn2+ in live human cells and in zebrafish larvae. In addition, a colocalization study proved that the chemosensor had the ability to target mitochondria and overlapped almost completely with MitoTracker Red. Furthermore, a bioimaging study of live cells demonstrated the discriminative detection of Sn2+ in human cancer cells and the practical applications of 2CTA in biological systems.

Highly adaptable and sensitive FRET-based aptamer assay for the detection of Salmonella paratyphi A.

Here we demonstrate a facile and versatile fluorescence resonance energy transfer (FRET) based aptasensor for rapid detection of Salmonella paratyphi A. The assay shows a detection limit up to 10 cfu·mL-1 with no cross-reactivity with other bacterial species. Less than 8% of inter-assay coefficient variance and recovery rate between 85 and 102% attests the assay reliability. The advantages of FRET-based aptamer assay over the conventional immunoassay formats such as ELISA are the specificity, speed, reliability, and simplicity of the assay. The ssDNA aptamers specific towards pathogenic Salmonella paratyphi A were generated via whole-cell SELEX. The aptamer was conjugated onto quantum dot (QD) that served as the molecular beacon and graphene oxide (GO) was used as a fluorescence quencher. Thus the proposed method enables detection of target pathogen using FRET-based assay. Further interaction of aptamer with pathogen protein DNA gyrase was explored using classical molecular dynamics simulation.

Application of real sample analysis and biosensing: Synthesis of new naphthyl derived chemosensor for detection of Al3+ ions.

A new chemosensor (NANH) based on naphthyl moiety was synthesized with good selectivity and sensitivity towards Al3+ ions via the inhibition by operating through dual mechanisms like photo-induced electron transfer (PET) and excited-state intramolecular proton transfer (ESIPT). The synthesized NANH was validated by various techniques such as 1H, 13C NMR and mass spectrum. While prominent fluorescent enhancement was observed from the NANH upon binding with Al3+ ions, however, other metal ions have not responded in the emission spectrum. Detection limit and association constant of NANH for Al3+ were calculated as 1.2 × 10-7 M and 4.09 × 104 M-1 by using fluorescence titration method. Binding ratio (1:1) of NANH with Al3+ ions were proved by Job's plot and DFT studies. Furthermore, aluminium in variety of water samples was determined, and NANH could be used for biosensing of Al3+ in living cells.

Comparative study of stability and transport of molecules through cyclic peptide nanotube and aquaporin: a molecular dynamics simulation approach.

The structural stability and transport properties of the cyclic peptide nanotube (CPN) 8 × [Cys-Gly-Met-Gly]2 in different phospholipid bilayers such as POPA (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidic acid), POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine), POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine), POPG (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol) and POPS (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoserine) with water have been investigated using molecular dynamics (MD) simulation. The hydrogen bonds and non-bonded interaction energies were calculated to study the stability in different bilayers. One µs MD simulation in POPA lipid membrane reveals the stability of the cyclic peptide nanotube, and the simulations at various temperatures manifest the higher stability of 8 × [Cys-Gly-Met-Gly]2. We demonstrated that the presence of sulphur-containing amino acids in CPN enhances the stability through disulphide bonds between the adjacent rings. Further, the water permeation coefficient of the CPN is calculated and compared with human aquaporin-2 (AQP2) channel protein. It is found that the coefficients are highly comparable to the AQP2 channel though the mechanism of water transport is not similar to AQP 2; the flow of water in the CPN is taking place as a two-line 1-2-1-2 file fashion. In addition to that, the transport behavior of Na+ and K+ ions, single water molecule, urea and anti-cancer drug fluorouracil were investigated using pulling simulation and potential of mean force calculation. The above transport behavior shows that Na+ is trapped in CPN for a longer time than other molecules. Also, the interactions of the ions and molecules in Cα and mid-Cα plane were studied to understand the transport behavior of the CPN. AbbreviationsAQP2Aquaporin-2CPNCyclic peptide nanotubeMDMolecular dynamicsPOPA1-Palmitoyl-2-oleoyl-sn-glycero-3-phosphatidic acidPOPE1-Palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolaminePOPG1-Palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerolPOPS1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoserineCommunicated by Ramaswamy H. Sarma.

Molecular Mechanism of T-2 Toxin-Induced Cerebral Edema by Aquaporin-4 Blocking and Permeation.

The present study aimed to reveal the molecular mechanism of T-2 toxin-induced cerebral edema by aquaporin-4 (AQP4) blocking and permeation. AQP4 is a class of aquaporin channels that is mainly expressed in the brain, and its structural changes lead to life-threatening complications such as cardio-respiratory arrest, nephritis, and irreversible brain damage. We employed molecular dynamics simulation, text mining, and in vitro and in vivo analysis to study the structural and functional changes induced by the T-2 toxin on AQP4. The action of the toxin leads to disrupted permeation of water and permeation coefficients are found to be affected, from the native (2.49 ± 0.02 × 10-14 cm3/s) to toxin-treated AQP4 (7.68 ± 0.15 × 10-14 cm3/s) channels. Furthermore, the T-2 toxin forms strong electrostatic interactions at the binding site and pushes the key residues (Ala210, Phe77, Arg216, and His201) outward at the selectivity filter. Also, the role of a histidine residue in the AQP4 channel was identified by alchemical transformation and umbrella sampling methods. Alchemical free-energy perturbation energy for H201A ↔ A201H, which was found to be 3.07 ± 0.18 kJ/mol, indicates the structural importance of the histidine residue at 201. In addition, histopathology and expression of AQP4 in the Mus musculus brain tissues show the damaged and altered expression of the protein. Text mining reveals the co-occurrence of genes/proteins associated with the AQP4 expression and T-2 toxin-induced cell apoptosis, which leads to cerebral edema.

Combined Inhibitory Effects of Citrinin, Ochratoxin-A, and T-2 Toxin on Aquaporin-2.

Aquaporins form a large family of transmembrane protein channel that facilitates selective and fast water transport across the cell membrane. The inhibition of aquaporin channels leads to many water-related diseases such as nephrogenic diabetes insipidus, edema, cardiac arrest, and stroke. Herein, we report the molecular mechanism of mycotoxins (citrinin, ochratoxin-A, and T-2 mycotoxin) inhibition of aquaporin-2 (AQP2) and arginine vasopressin receptor 2. Molecular docking, molecular dynamics simulations, quantum chemical calculations, residue conservation-coupling analysis, sequence alignment, and in vivo studies were utilized to explore the binding interactions between the mycotoxins and aquaporin-2. Theoretical studies revealed that the electrostatic interactions induced by the toxins pulled the key residues (187Arg, 48Phe, 172His, and 181Cys) inward, hence reduced the pore diameter and water permeation. The permeability coefficient of the channel was reduced from native ((3.32 ± 0.75) × 10-14 cm3/s) to toxin-treated AQP2 ((1.08 ± 0.03) × 10-14 cm3/s). The hydrogen bonds interruption and formation of more hydrogen bonds with toxins also led to the reduced number of water permeation. Further, in vivo studies showed renal damages and altered level of aquaporin expression in mycotoxin-treated Mus musculus. Furthermore, the multiple sequence alignments among the model organism along with evolutionary coupling analysis provided the information about the interdependences of the residues in the channel.