Interfacial Tension-Temperature-Pressure-Salinity Relationship for the Hydrogen-Brine System under Reservoir Conditions: Integration of Molecular Dynamics and Machine Learning.

Hydrogen (H2) underground storage has attracted considerable attention as a potentially efficient strategy for the large-scale storage of H2. Nevertheless, successful execution and long-term storage and withdrawal of H2 necessitate a thorough understanding of the physical and chemical properties of H2 in contact with the resident fluids. As capillary forces control H2 migration and trapping in a subsurface environment, quantifying the interfacial tension (IFT) between H2 and the resident fluids in the subsurface is important. In this study, molecular dynamics (MD) simulation was employed to develop a data set for the IFT of H2-brine systems under a wide range of thermodynamic conditions (298-373 K temperatures and 1-30 MPa pressures) and NaCl salinities (0-5.02 mol·kg-1). For the first time to our knowledge, a comprehensive assessment was carried out to introduce the most accurate force field combination for H2-brine systems in predicting interfacial properties with an absolute relative deviation (ARD) of less than 3% compared with the experimental data. In addition, the effect of the cation type was investigated for brines containing NaCl, KCl, CaCl2, and MgCl2. Our results show that H2-brine IFT decreases with increasing temperature under any pressure condition, while higher NaCl salinity increases the IFT. A slight decrease in IFT occurs when the pressure increases. Under the impact of cation type, Ca2+ can increase IFT values more than others, i.e., up to 12% with respect to KCl. In the last step, the predicted IFT data set was used to provide a reliable correlation using machine learning (ML). Three white-box ML approaches of the group method of data handling (GMDH), gene expression programming (GEP), and genetic programming (GP) were applied. GP demonstrates the most accurate correlation with a coefficient of determination (R2) and absolute average relative deviation (AARD) of 0.9783 and 0.9767%, respectively.

Intradermal Immunization of Soluble Influenza HA Derived from a Lethal Virus Induces High Magnitude and Breadth of Antibody Responses and Provides Complete Protection In Vivo.

Immunogens mimicking the native-like structure of surface-exposed viral antigens are considered promising vaccine candidates. Influenza viruses are important zoonotic respiratory viruses with high pandemic potential. Recombinant soluble hemagglutinin (HA) glycoprotein-based protein subunit vaccines against Influenza have been shown to induce protective efficacy when administered intramuscularly. Here, we have expressed a recombinant soluble trimeric HA protein in Expi 293F cells and purified the protein derived from the Inf A/Guangdong-Maonan/ SWL1536/2019 virus which was found to be highly virulent in the mouse. The trimeric HA protein was found to be in the oligomeric state, highly stable, and the efficacy study in the BALB/c mouse challenge model through intradermal immunization with the prime-boost regimen conferred complete protection against a high lethal dose of homologous and mouse-adapted InfA/PR8 virus challenge. Furthermore, the immunogen induced high hemagglutinin inhibition (HI) titers and showed cross-protection against other Inf A and Inf B subtypes. The results are promising and warrant trimeric HA as a suitable vaccine candidate.

SARS-CoV-2 envelope protein attain Kac mediated dynamical interaction network to adopt 'histone mimic' at BRD4 interface.

Interface mimicry, achieved by recognition of host-pathogen interactions, is the basis by which pathogen proteins can hijack the host machinery. The envelope (E) protein of SARS-CoV-2 is reported to mimic the histones at the BRD4 surface via establishing the structural mimicry; however, the underlying mechanism of E protein mimicking the histones is still elusive. To explore the mimics at dynamic and structural residual network level an extensive docking, and MD simulations were carried out in a comparative manner between complexes of H3-, H4-, E-, and apo-BRD4. We identified that E peptide is able to attain an 'interaction network mimicry', as its acetylated lysine (Kac) achieves orientation and residual fingerprint similar to histones, including water-mediated interactions for both the Kac positions. We identified Y59 of E, playing an anchor role to escort lysine positioning inside the binding site. Furthermore, the binding site analysis confirms that E peptide needs a higher volume, similar to the H4-BRD4 where both the lysine's (Kac5 and Kac8) can accommodate nicely, however, the position of Kac8 is mimicked by two additional water molecules other than four water-mediated bridging's, strengthening the possibility that E peptide could hijack host BRD4 surface. These molecular insights seem pivotal for mechanistic understanding and BRD4-specific therapeutic intervention. KEY POINTSMolecular mimicry is reported in hijacking and then outcompeting the host counterparts so that pathogens can rewire their cellular function by overcoming the host defense mechanism.The molecular recognition process is the basis of molecular mimicry. The E peptide of SARS-CoV-2 is reported to mimic host histone at the BRD4 surface by utilizing its C-terminally placed acetylated lysine (Kac63) to mimic the N-terminally placed acetylated lysine Kac5GGKac8 histone (H4) by interaction network mimicry identified through microsecond molecular dynamics (MD) simulations and post-processing extensive analysis.There are two steps to mimic: firstly, tyrosine residues help E to anchor at the BRD4 surface to position Kac and increase the volume of the pocket. Secondary, after positioning of Kac, a common durable interaction network N140:Kac5; Kac5:W1; W1:Y97; W1:W2; W2:W3; W3:W4; W4:P82 is established between Kac5, with key residues P82, Y97, N140, and four water molecules through water mediate bridge. Furthermore, the second acetylated lysine Kac8 position and its interaction as polar contact with Kac5 were also mimicked by E peptide through interaction network P82:W5; W5:Kac63; W5:W6; W6:Kac63.The binding event at BRD4/BD1 seems an induced-fit mechanism as a bigger binding site volume was identified at H4-BRD4 on which E peptide attains its better stability than H3-BRD4.We identified the tyrosine residue Y59 of E that acts like an anchor on the BRD4 surface to position Kac inside the pocket and attain the interaction network by using aromatic residues of the BRD4 surface.Communicated by Ramaswamy H. Sarma.

Multi-Material Additive Manufacturing of High Temperature Polyetherimide (PEI)-Based Polymer Systems for Lightweight Aerospace Applications.

Rapid innovations in 3-D printing technology have created a demand for multifunctional composites. Advanced polymers like amorphous thermoplastic polyetherimide (PEI) can create robust, lightweight, and efficient structures while providing high-temperature stability. This work manufactured ULTEM, a PEI-based polymer, and carbon-fiber-infused ULTEM multi-material composites with varying layering patterns (e.g., AAABBB vs. ABABAB) using fused filament fabrication (FFF). The microstructure of fractured surfaces and polished cross-sections determined that the print quality of layers printed closer to the heated bed was higher than layers closer to the top surface, primarily due to the thermal insulating properties of the material itself. Mechanical properties of the multi-material parts were between those of the single-material parts: an ultimate tensile strength and elastic modulus of 59 MPa and 3.005 GPa, respectively. Multi-material parts from the same filaments but with different layering patterns showed different mechanical responses. Prints were of higher quality and demonstrated a higher elastic modulus (3.080 GPa) when consecutive layers were printed from the same filament (AAABBB) versus parts with printed layers of alternating filaments (ABABAB), which showed a higher ultimate strength (62.04 MPa). These results demonstrate the potential for creatively designing multi-material printed parts that may enhance mechanical properties.

FÓ§rster resonance energy transfer (FRET) between CdSe quantum dots and ABA phosphorus(V) corroles.

In this article, highly fluorescent phosphorus(V) corrole was synthesised which was then combined with CdSe quantum dots (QDs) in order to study Förster resonance energy transfer (FRET) mechanism between CdSe QDs (donor) and phosphorus corrole (acceptor). Spectral overlap between QD's emission profile and corrole's absorption profile was found to be significant enough to result into Förster resonance energy transfer (FRET). The UV-vis spectrum experienced increase in the absorption bands on addition of phosphorus corrole to CdSe QDs suggesting QD-corrole conjugation. In the steady state fluorescence measurements, emission spectrum observed quenching in the fluorescence intensity of prepared CdSe QDs on addition of phosphorus corrole. Likewise, in case of time-resolved fluorescence measurements it was noticed that the CdSe QD's lifetime was greatly quenched by the presence of a corrole acceptor. Stern-Volmer plot was made to show quenching in this case was dynamic in nature. Based on the results of UV-vis, steady state and time-resolved fluorescence measurements the plausible mechanism behind such observations is considered to be FRET.

Structure-based pharmacophore mapping and virtual screening of natural products to identify polypharmacological inhibitor against c-MET/EGFR/VEGFR-2.

Three receptor tyrosine kinases (RTKs), c-MET, EGFR, and VEGFR-2 have been identified as potential oncogenic targets involved in tumor development, metastasis, and invasion. Designing inhibitors that can simultaneously interact with multiple targets is a promising approach, therefore, inhibiting these three RTKs with a single chemical component might give an effective chemotherapeutic strategy for addressing the disease while limiting adverse effects. The in-silico methods have been developed to identify the polypharmacological inhibitors particularly for drug repurposing and multitarget drug design. Here, to find a viable inhibitor from natural source against these three RTKs, structure-based pharmacophore mapping and virtual screening of SN-II database were carried out. The filtered compound SN00020821, identified as Cedeodarin, from different computational approaches, demonstrated good interactions with all the three targets, c-MET/EGFR/VEGFR-2, with interaction energies of -42.35 kcal/mol, -49.32 kcal/mol and -44.83 kcal/mol, respectively. SN00020821displayed stable key interactions with critical amino acids of all the three receptors' kinase catalytic domains including "DFG motif" explored through the MD simulations. Furthermore, it also met the ADMET requirements and was determined to be drug-like as predicted from the Lipinski's rule of five and Veber's rule. Finally, SN00020821 provides a novel molecular scaffold that could be investigated further as a polypharmacological anticancer therapeutic candidate that targets the three RTKs.Communicated by Ramaswamy H. Sarma.

A common Matrix metalloproteinase 8 promoter haplotype enhances the risk for hypertension via diminished interactions with nuclear factor kappa B.

OBJECTIVES: Matrix metalloproteinase 8 (MMP8) has a prominent role in collagen turnover in blood vessels and vascular remodeling. The contribution of regulatory single nucleotide polymorphisms in MMP8 to cardiovascular diseases is unclear. We aimed to delineate the influence of MMP8 promoter variations on hypertension. METHODS: A case-control study in unrelated individuals ( n  = 2565) was carried out. Resequencing of the MMP8 proximal promoter, linkage disequilibrium analysis, genotyping of variants and regression analyses were performed. MMP8 promoter-reporter constructs were generated and expressed in human vascular endothelial cells under various conditions. RESULTS: We identified four single nucleotide polymorphisms (SNPs) in the promoter region of MMP8 : -1089A/G (rs17099452), -815G/T (rs17099451), -795C/T (rs11225395), -763A/T (rs35308160); these SNPs form three major haplotypes. Hap3 (viz., GTTT haplotype) carriers showed significant associations with hypertension in two geographically distinct human populations (e.g., Chennai: odds ratio [OR] = 1.47, 95% confidence interval [CI] = 1.16-1.86, P  = 2 × 10 -3 ; Chandigarh: OR = 1.85, 95% CI = 1.21-2.81, P  = 4 × 10 -3 ). Hap3 carriers also displayed elevated systolic blood pressure, diastolic blood pressure and mean arterial pressure levels. Hap3 promoter-reporter construct showed lower promoter activity than the wild-type (Hap1) construct. In silico analysis and molecular dynamics studies predicted diminished binding of the transcription factor nuclear factor kappa B (NF-κB) to the functional -815T allele of Hap3 compared to the -815G wild-type allele; this prediction was validated by in-vitro experiments. Hap3 displayed impaired response to tumor necrosis factor-alpha treatment, possibly due to weaker binding of NF-κB. Notably, MMP8 promoter haplotypes were identified as independent predictors of plasma MMP8 and endothelial dysfunction markers (von Willebrand factor and endothelin-1) levels. CONCLUSION: MMP8 promoter GTTT haplotype has a functional role in reducing MMP8 expression during inflammation via diminished interaction with NF-κB and in enhancing the risk of hypertension.

Effect of Reinforcements and 3-D Printing Parameters on the Microstructure and Mechanical Properties of Acrylonitrile Butadiene Styrene (ABS) Polymer Composites.

Fused filament fabrication (FFF) systems utilize a wide variety of commercially available filaments, including Acrylonitrile Butadiene Styrene (ABS), as well as their variants. However, the effect of filament composition, reinforcements (chopped fibers and nanotubes), and 3-D printing variables on the microstructure and thermomechanical behavior is not well understood, and systematic studies are needed. In this work, different types of ABS materials with and without carbon fiber and carbon nanotube reinforcements were printed with multiple print layer heights. The microstructure, elastic behavior, tensile behavior, and fracture toughness of 3-D printed materials were characterized. ABS material systems printed at a low print layer height of 0.1 mm outperformed those printed at a larger height of 0.2 mm. Carbon nanotube reinforcements result in significant improvement in the strength and elastic modulus of ABS materials. Printed coupons of ABS with carbon nanotubes achieve an ultimate strength of 34.18 MPa, while a premium grade ABS coupon achieved 28.75 MPa when printed with the same print layer heights. Samples of ABS with chopped carbon fiber show an ultimate strength of 27.25 MPa, due primarily to the significant porosity present in the filament. Elastic moduli and fracture toughness measured using dynamic and mechanical methods show similar trends as a function of layer height. The effects of different materials, reinforcements, and printing parameters on the microstructure and mechanical properties are discussed in detail.

Design and synthesis of amino acid derivatives of substituted benzimidazoles and pyrazoles as Sirt1 inhibitors.

Owing to its presence in several biological processes, Sirt1 acts as a potential therapeutic target for many diseases. Here, we report the structure-based designing and synthesis of two distinct series of novel Sirt1 inhibitors, benzimidazole mono-peptides and amino-acid derived 5-pyrazolyl methylidene rhodanine carboxylic acid. The compounds were evaluated for in vitro enzyme-based and cell-based Sirt1 inhibition assay, and cytotoxic-activity in both liver and breast cancer cells. The tryptophan conjugates i.e.13h (IC50 = 0.66 µM, ΔG bind = -1.1 kcal mol-1) and 7d (IC50 = 0.77 µM, ΔG bind = -4.4 kcal mol-1) demonstrated the maximum efficacy to inhibit Sirt1. The MD simulation unveiled that electrostatic complementarity at the substrate-binding-site through a novel motif "SLxVxP(V/F)A" could be a cause of increased Sirt1 inhibition by 13h and 13l over Sirt2 in cell-based assay, as compared to the control Ex527 and 7d. Finally, this study highlights novel molecules 7d and 13h, along with a new key hot-spot in Sirt1, which could be used as a starting lead to design more potent and selective sirtuin inhibitors as a potential anticancer molecule.

Characterizing (un)binding mechanism of USP7 inhibitors to unravel the cause of enhanced binding potencies at allosteric checkpoint.

The ability to predict the intricate mechanistic behavior of ligands and associated structural determinants during protein-ligand (un)binding is of great practical importance in drug discovery. Ubiquitin specific protease-7 (USP7) is a newly emerging attractive cancer therapeutic target with bound allosteric inhibitors. However, none of the inhibitors have reached clinical trials, allowing opportunities to examine every aspect of allosteric modulation. The crystallographic insights reveal that these inhibitors have common properties such as chemical scaffolds, binding site and interaction fingerprinting. However, they still possess a broader range of binding potencies, ranging from 22 nM to 1,300 nM. Hence, it becomes more critical to decipher the structural determinants guiding the enhanced binding potency of the inhibitors. In this regard, we elucidated the atomic-level insights from both interacting partners, that is, protein-ligand perspective, and established the structure-activity link between USP7 inhibitors by using classical and advanced molecular dynamics simulations combined with linear interaction energy and molecular mechanics-Poisson Boltzmann surface area. We revealed the inhibitor potency differences by examining the contributions of chemical moieties and USP7 residues, the involvement of water-mediated interactions, and the thermodynamic landscape alterations. Additionally, the dissociation profiles aided in the establishment of a correlation between experimental potencies and structural determinants. Our study demonstrates the critical role of blocking loop 1 in allosteric inhibition and enhanced binding affinity. Comprehensively, our findings provide a constructive expansion of experimental outcomes and show the basis for varying binding potency using in-silico approaches. We expect this atomistic approach to be useful for effective drug design.

Additive Manufacturing and Characterization of Metal Particulate Reinforced Polylactic Acid (PLA) Polymer Composites.

Affordable commercial desktop 3-D printers and filaments have introduced additive manufacturing to all disciplines of science and engineering. With rapid innovations in 3-D printing technology and new filament materials, material vendors are offering specialty multifunctional metal-reinforced polymers with unique properties. Studies are necessary to understand the effects of filament composition, metal reinforcements, and print parameters on microstructure and mechanical behavior. In this study, densities, metal vol%, metal cross-sectional area %, and microstructure of various metal-reinforced Polylactic Acid (PLA) filaments were characterized by multiple methods. Comparisons are made between polymer microstructures before and after printing, and the effect of printing on the metal-polymer interface adhesion has been demonstrated. Tensile response and fracture toughness as a function of metal vol% and print height was determined. Tensile and fracture toughness tests show that PLA filaments containing approximately 36 vol% of bronze or copper particles significantly reduce mechanical properties. The mechanical response of PLA with 12 and 18 vol% of magnetic iron and stainless steel particles, respectively, is similar to that of pure PLA with a slight decrease in ultimate tensile strength and fracture toughness. These results show the potential for tailoring the concentration of metal reinforcements to provide multi-functionality without sacrificing mechanical properties.

Preoperative COVID-19 Testing for Elective Ophthalmological Procedure in a Tertiary Health Care Centre: Our Experience During the Pandemic.

BACKGROUND: To study the prevalence of coronavirus infection among asymptomatic patients requiring eye surgery and the role of screening in prevention of spread of infection among the healthcare workers. DESIGN: The prospective observational study was conducted in the Ophthalmology department of a tertiary care center in Delhi from September 2020 to December 2020. SETTING: Patients requiring elective ophthalmological procedures in a tertiary care hospital were screened for coronavirus using the RT-PCR method. Testing methods and results were documented. RESULTS: Among the 218 asymptomatic patients posted for elective surgery in that period, 16 (7.3%) were found to be positive for COVID-19. Those who tested positive were advised home isolation and surgery was postponed for the next 14 days. No complications were reported in these patients. One health-care worker also tested positive for COVID-19 during our study period. CONCLUSION: In our study, 1 out of 14 asymptomatic patients were found to be carriers for the novel virus. Asymptomatic COVID-infected patients may lead to transmission of the virus inside the hospital among the visiting patients and hospital staff while they have no adverse effect on the surgery and its outcome.

Is Interferon α-2b 1 MillionIU/mL Truly Better Than Tacrolimus 0.03% for Steroid-Resistant VKC ?: Our 2-Year Experience at a Tertiary Health-Care Centre.

PURPOSE: To compare the efficacy of eye-drop interferon (IFN) α-2b 1 millionIU/mL with eye-ointment tacrolimus 0.03% in refractory vernal keratoconjunctivitis (VKC). MATERIALS AND METHODS: Fifty patients with VKC refractory to conventional treatment with topical corticosteroids and antihistamines after 4 weeks of regular use were selected retrospectively. Patients were divided into two groups depending on whether they received eye-ointment tacrolimus 0.03% three times a day or eye-drop IFN alpha-2b 1 millionIU/mL three times a day and were followed up for 24 months. The main outcome measures were total subjective symptom score (TSSS) and total objective ocular score (TOSS). RESULTS: Mean baseline TSSS was 7.24±1.98 in Group A (tacrolimus group) and 7.84±1.82 in Group B (IFN group), and it reduced to 1.12±0.83 in Group A and 0.62±0.41 in Group B at 6 months, which was statistically significant compared to the baseline score (p<0.05) as well as between the two groups. Mean baseline TOSS was 6.72±2.07 in Group A and 6.56±2.04 in Group B, and it improved to 1 month onwards to 1.52±0.87 in Group A and 1.0±0.71 in Group B at 6 months, which was statistically significant compared to the baseline score (p<0.05) as well as between the two groups. Side effects like stinging and burning sensations were seen in the tacrolimus group only. CONCLUSION: Our study suggests that while both eye-drop IFN α-2b 1 millionIU/mL and eye-ointment tacrolimus eye ointment 0.03% are both safe and effective steroid-sparing agents in steroid-resistant VKC. IFN α-2b results in greater improvement in subjective symptoms and objective signs, has fewer side effects in long term and is better tolerated as compared to tacrolimus.

Sentiment analysis on the impact of coronavirus in social life using the BERT model.

Nowadays, the whole world is confronting an infectious disease called the coronavirus. No country remained untouched during this pandemic situation. Due to no exact treatment available, the disease has become a matter of seriousness for both the government and the public. As social distance is considered the most effective way to stay away from this disease. Therefore, to address the people eagerness about the Corona pandemic and to express their views, the trend of people has moved very fast towards social media. Twitter has emerged as one of the most popular platforms among those social media platforms. By studying the same eagerness and opinions of people to understand their mental state, we have done sentiment analysis using the BERT model on tweets. In this paper, we perform a sentiment analysis on two data sets; one data set is collected by tweets made by people from all over the world, and the other data set contains the tweets made by people of India. We have validated the accuracy of the emotion classification from the GitHub repository. The experimental results show that the validation accuracy is ≈ 94%.

Elucidation of Structural Determinants Delineates the Residues Playing Key Roles in Differential Dynamics and Selective Inhibition of Sirt1-3.

Sirt1-3 are the most studied sirtuins, playing a key role in caloric-dependent epigenetic modifications. Since they are localized in distinct cellular compartments and act differently under various pathological conditions, selective inhibition would be a promising strategy to understand their biological function and to discover effective therapeutics. Here, sirtuin's inhibitor Ex527* is used as a probe to speculate the possible root cause of selective inhibition and differential structural dynamics of Sirt1-3. Comparative energetics and mutational studies revealed the criticality of residues I279 and I316 for the Sirt1 selectivity toward Ex527*. Furthermore, essential dynamics and residue network analysis revealed that the side-chain reorientation in residue F190 due to nonconserved residue Y191 played a major role in the formation of an extended selectivity pocket in Sirt2. These changes at the dynamical and residual level, which impact the internal wiring significantly, might help in rationally designing selective inhibitors against Sirt1-3.

Identification of potential molecules against COVID-19 main protease through structure-guided virtual screening approach.

The pandemic caused by novel coronavirus disease 2019 (COVID-19) infecting millions of populations worldwide and counting, has demanded quick and potential therapeutic strategies. Current approved drugs or molecules under clinical trials can be a good pool for repurposing through in-silico techniques to quickly identify promising drug candidates. The structural information of recently released crystal structures of main protease (Mpro) in APO and complex with inhibitors, N3, and 13b molecules was utilized to explore the binding site architecture through Molecular dynamics (MD) simulations. The stable state of Mpro was used to conduct extensive virtual screening of the aforementioned drug pool. Considering the recent success of HIV protease molecules, we also used anti-protease molecules for drug repurposing purposes. The identified top hits were further evaluated through MD simulations followed by the binding free energy calculations using MM-GBSA. Interestingly, in our screening, several promising drugs stand out as potential inhibitors of Mpro. However, based on control (N3 and 13b), we have identified six potential molecules, Leupeptin Hemisulphate, Pepstatin A, Nelfinavir, Birinapant, Lypression and Octreotide which have shown the reasonably significant MM-GBSA score. Further insight shows that the molecules form stable interactions with hot-spot residues, that are mainly conserved and can be targeted for structure- and pharmacophore-based designing. The pharmacokinetic annotations and therapeutic importance have suggested that these molecules possess drug-like properties and pave their way for in-vitro studies.Communicated by Ramaswamy H. Sarma.

Essential functional molecules associated with SARS-CoV-2 infection: Potential therapeutic targets for COVID-19.

The whole world is still suffering substantially from the coronavirus disease 2019 (COVID-19) outbreak. Several protein-based molecules that are associated with the Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which are essential for its functionality, survival, and pathogenesis have been identified and are considered as potential therapeutic targets. These protein-based molecules are either structural/non-structural components of SARS-CoV-2 or host factors, which play a crucial role in this infection. Developing drug molecules against these essential functional molecules to hinder their regular functioning and associated physiological pathways could be promising for successful clinical management of this novel coronavirus infection. The review aims to highlight the functional molecules that play crucial roles in SARS-CoV-2 pathogenesis. We have emphasized how these potential druggable targets could be beneficial in tackling the COVID-19 crisis.

A Common Tag Nucleotide Variant in MMP7 Promoter Increases Risk for Hypertension via Enhanced Interactions With CREB (Cyclic AMP Response Element-Binding Protein) Transcription Factor.

MMP (matrix metalloproteinase)-7-a potent extracellular matrix degrading enzyme-is emerging as a new regulator of cardiovascular diseases. However, potential contributions of MMP7 genetic variations to hypertension remain unknown. In this study, we probed for the association of a tag single-nucleotide polymorphism in the MMP7 promoter (-181A/G; rs11568818) with hypertension in an urban South Indian population (n=1501). The heterozygous AG genotype significantly increased risk for hypertension as compared with the wild-type AA genotype (odds ratio, 1.60 [95% CI, 1.25-2.06]; P=2.4×10-4); AG genotype carriers also displayed significantly higher diastolic blood pressure and mean arterial pressure than wild-type AA individuals. The study was replicated in a North Indian population (n=949) (odds ratio, 1.52 [95% CI, 1.11-2.09]; P=0.01). Transient transfection experiments using MMP7 promoter-luciferase reporter constructs revealed that the variant -181G allele conferred greater promoter activity than the -181A allele. Computational prediction and structure-based conformational and molecular dynamics simulation studies suggested higher binding affinity for the CREB (cyclic AMP response element-binding protein) to the -181G promoter. In corroboration, overexpression/downregulation of CREB and chromatin immunoprecipitation experiments provided convincing evidence for stronger binding of CREB with the -181G promoter. The -181G promoter also displayed enhanced responses to hypoxia and epinephrine treatment. The higher promoter activity of -181G allele translated to increased MMP7 protein level, and MMP7-181AG heterozygous individuals displayed elevated plasma MMP7 levels, which positively correlated with blood pressure. In conclusion, the MMP7 A-181G promoter polymorphism increased MMP7 expression under pathophysiological conditions (hypoxic stress and catecholamine excess) via increased interactions with CREB and enhanced the risk for hypertension in its carriers.

Molecular dynamics simulation reveals the possible druggable hot-spots of USP7.

The plasticity in Ubiquitin Specific Proteases (USP7) inducing conformational changes at important areas has highlighted an intricate mechanism, by which USP7 is regulated. Given the importance of USP7 in oncogenic pathways and immune-oncology, identification of USP7 inhibitors has attracted considerable interest. Despite substantial efforts, the discovery of deubiquitinases (DUBs) inhibitors, knowledge of their binding site and understanding the possible mechanism of action has proven particularly challenging. We disclose the most likely binding site of P5091 (a potent USP7 inhibitor), which reveal a cryptic allosteric site through extensive computational studies in an inhibitor dependent and independent manner. Overall, these findings demonstrate the tractability and druggability of USP7. Through a series of molecular dynamics simulations and detailed quantitative analysis, a dynamically stable allosteric binding site near catalytic center of the inactive state of USP7 (site partially absent in active state), along with two newly identified sites have been revealed, which opens the avenue for rational structure-guided inhibitor designing in USP7 specific-manner.

Computational modeling suggests impaired interactions between NKX2.5 and GATA4 in individuals carrying a novel pathogenic D16N NKX2.5 mutation.

NKX2.5, a homeobox containing gene, plays an important role in embryonic heart development and associated mutations are linked with various cardiac abnormalities. We sequenced the NKX2.5 gene in 100 congenital heart disease (CHD) patients and 200 controls. Our analysis revealed a total of 7 mutations, 3 in intronic region, 3 in coding region and 1 in 3' UTR. Of the above mutations, one mutation was found to be associated with tetralogy of fallot (TOF) and two (rs2277923 and a novel mutation, D16N) were strongly associated with VSD. A novel missense mutation, D16N (p-value =0.009744), located in the tinman (TN) region and associated with ventricular septal defect (VSD), is the most significant findings of this study. Computational analysis revealed that D16N mutation is pathogenic in nature. Through the molecular modeling, docking and molecular dynamics simulation studies, we have identified the location of mutant D16N in NKX2.5 and its interaction map with other partners at the atomic level. We found NKX2.5-GATA4 complex is stable, however, in case of mutant we observed significant conformational changes and loss of key polar interactions, which might be a cause of the pathogenic behavior. This study underscores the structural basis of D16N pathogenic mutation in the regulation of NKX2.5 and how this mutation renders the structural-functional divergence that possibly leading towards the diseased state.