Predicting virus Fitness: Towards a structure-based computational model.

Predicting the impact of new emerging virus mutations is of major interest in surveillance and for understanding the evolutionary forces of the pathogens. The SARS-CoV-2 surface spike-protein (S-protein) binds to human ACE2 receptors as a critical step in host cell infection. At the same time, S-protein binding to human antibodies neutralizes the virus and prevents interaction with ACE2. Here we combine these two binding properties in a simple virus fitness model, using structure-based computation of all possible mutation effects averaged over 10 ACE2 complexes and 10 antibody complexes of the S-protein (∼380,000 computed mutations), and validated the approach against diverse experimental binding/escape data of ACE2 and antibodies. The ACE2-antibody selectivity change caused by mutation (i.e., the differential change in binding to ACE2 vs. immunity-inducing antibodies) is proposed to be a key metric of fitness model, enabling systematic error cancelation when evaluated. In this model, new mutations become fixated if they increase the selective binding to ACE2 relative to circulating antibodies, assuming that both are present in the host in a competitive binding situation. We use this model to categorize viral mutations that may best reach ACE2 before being captured by antibodies. Our model may aid the understanding of variant-specific vaccines and molecular mechanisms of viral evolution in the context of a human host.

Computational Insight into Substrate-Induced Conformational Changes in Methionyl-tRNA Synthetase of Mycobacterium Tuberculosis.

Tuberculosis caused by Mycobacterium tuberculosis (M.tb) has killed millions worldwide. Antibiotic resistance leads to the ineffectiveness of the current therapies. Aminoacyl tRNA synthetase (aaRS) class of proteins involved in protein synthesis are promising bacterial targets for developing new therapies. Here, we carried out a systematic comparative study on the aaRS sequences from M.tb and human. We listed important M.tb aaRS that could be explored as potential M.tb targets alongside the detailed conformational space analysis of methionyl-tRNA synthetase (MetRS) in apo- and substrate-bound form, which is among the proposed targets. Understanding the conformational dynamics is central to the mechanistic understanding of MetRS, as the substrate binding leads to the conformational changes causing the reaction to proceed. We performed the most complete simulation study of M.tb MetRS for 6 microseconds (2 systems × 3 runs × 1 microsecond) in the apo and substrate-bound states. Interestingly, we observed differential features, showing comparatively large dynamics for the holo simulations, whereas the apo structures became slightly compact with reduced solvent exposed area. In contrast, the ligand size decreased significantly in holo structures possibly to relax ligand conformation. Our findings correlate with experimental studies, thus validating our protocol. Adenosine monophosphate moiety of the substrate exhibited quite higher fluctuations than the methionine. His21 and Lys54 were found to be the important residues forming prominent hydrogen bond and salt-bridge interactions with the ligand. The ligand-protein affinity decreased during simulations as computed by MMGBSA analysis over the last 500 ns trajectories, which indicates the conformational changes upon ligand binding. These differential features could be further explored for designing new M.tb inhibitors.

In silico docking based screening of constituents from Persian shallot as modulators of human glucokinase.

Purpose: Small molecule glucokinase (GK) modulators not only decrease fasting and basal plasma sugar contents but also progress glucose tolerance. The hydro-ethanolic extract of the Persian shallot (Allium hirtifolium Boiss.) decreased blood glucose, improved plasma insulin and amplified GK action. The present study was proposed to screen phytoconstituents from Persian shallot as human GK activators using in silico docking studies. Methods: A total of 91 phytoconstituents reported in Persian shallot (A. hirtifolium Boiss.) were assessed in silico for the prediction of drug-like properties and molecular docking investigations were carried out with human GK using AutoDock vina with the aim of exploring the binding interactions between the phytoconstituents and GK enzyme followed by in silico prediction of toxicity. Results: Almost all the phytoconstituents tested showed good pharmacokinetic parameters for oral bioavailability and drug-likeness. In the docking analysis, cinnamic acid, methyl 3,4,5-trimethoxy benzoate, quercetin, kaempferol, kaempferol 3-O-ß-D-glucopyranosyl-(1- > 4)-glucopyranoside, 5-hydroxy-methyl furfural, ethyl N-(O-anisyl) formimidate, 2-pyridinethione and ascorbic acid showed appreciable hydrogen bond and hydrophobic type interactions with the allosteric site residues of the GK enzyme. Conclusion: These screened phytoconstituents may serve as promising hit molecules for further development of clinically beneficial and safe allosteric activators of the human GK enzyme.

Understanding Factors Impacting Coronavirus Disease 2019 Vaccine Hesitancy in a Rural Surgical Clinic.

Objective: Evaluate patient hesitancy about the coronavirus disease 2019 (COVID-19) vaccine. Patients and Methods: English and Spanish pre-and post-video surveys were completed by patients at rural surgery clinics. The surveys consisted of 25 or 21 five-point Likert statements, respectively. Paired difference t-tests and independent sample t-tests were performed. Results: Ninety-four patients completed the surveys: 137 females (73%) and 51 (27%) males; 113 patients were Hispanic (64%); 63 patients were white (36%). The pre-video survey showed that the top two factors influencing patients were: preference for wearing masks over vaccination (n = 185; x¯ = 3.55) and not trusting the effectiveness of the vaccine (n = 186; x¯ = 3.01). Patients agreed that the video made them want to talk to their family about getting vaccinated (n = 176; x¯ = 3.14) and made them appreciate that they can get really sick from COVID-19 (n = 177; x¯ = 3.14). After watching the video, women of childbearing age (WCBA; n = 65; x¯ = 3.20) agreed more that the video made them want to get the COVID-19 vaccine than non-WCBA (n = 59; x¯ = 2.37; p = 0.0123). Women of childbearing age (n = 66; x¯ = 3.32) also agreed more that the video made them appreciate that they can get really sick from the COVID virus than non-WCBA (n = 60; x¯ = 2.58; p = 0.0254). Post-video statements showed that patients agreed that the video was easy to understand, they liked the video, and the video was helpful. Conclusions: There is room to better inform patients in a rural setting, especially WCBA, about COVID-19 illness and vaccination through video testimonies. Surgeons are uniquely positioned to offer effective recommendations, to increase vaccination rates, and address vaccine hesitancy.

Modelling SARS-CoV-2 spike-protein mutation effects on ACE2 binding.

The binding affinity of the SARS-CoV-2 spike (S)-protein to the human membrane protein ACE2 is critical for virus function. Computational structure-based screening of new S-protein mutations for ACE2 binding lends promise to rationalize virus function directly from protein structure and ideally aid early detection of potentially concerning variants. We used a computational protocol based on cryo-electron microscopy structures of the S-protein to estimate the change in ACE2-affinity due to S-protein mutation (ΔΔGbind) in good trend agreement with experimental ACE2 affinities. We then expanded predictions to all possible S-protein mutations in 21 different S-protein-ACE2 complexes (400,000 ΔΔGbind data points in total), using mutation group comparisons to reduce systematic errors. The results suggest that mutations that have arisen in major variants as a group maintain ACE2 affinity significantly more than random mutations in the total protein, at the interface, and at evolvable sites. Omicron mutations as a group had a modest change in binding affinity compared to mutations in other major variants. The single-mutation effects seem consistent with ACE2 binding being optimized and maintained in omicron, despite increased importance of other selection pressures (antigenic drift), however, epistasis, glycosylation and in vivo conditions will modulate these effects. Computational prediction of SARS-CoV-2 evolution remains far from achieved, but the feasibility of large-scale computation is substantially aided by using many structures and mutation groups rather than single mutation effects, which are very uncertain. Our results demonstrate substantial challenges but indicate ways forward to improve the quality of computer models for assessing SARS-CoV-2 mutation effects.

Leishmaniasis diagnosis: an update on the use of parasitological, immunological and molecular methods.

Diagnosis of leishmaniasis has always been a major challenge as its clinical features resemble some other commonly occurring diseases such as tuberculosis, typhoid, and malaria. Reliable laboratory methods become important for differential diagnosis. Demonstration of the parasites in stained preparations of bone marrow and splenic aspirates being risky and invasive is still the gold standard for diagnosis. Serological tests utilizing rapid immunochromatographic formats or rK39 in enzyme linked immune sorbent assay, immunoblotting, direct agglutination test have complications related to high proportions of positive asymptomatic individuals and the inability to diagnose a relapse. Among the molecular techniques, polymerase chain reaction is the most commonly used technique that is successfully implied for diagnosis. This review provides updated information on the recent developments in the field of diagnosis in leishmaniasis, various methods utilized with their advantages and limitations.

Purification and characterisation of a xylose-specific mitogenic lectin from Fusarium sambucinum.

A xylose-specific intracellular lectin, showing hemagglutination only with rabbit erythrocytes was purified from mycelium of Fusarium sambucinum which was designated as FSL. An array of anion exchange chromatography on Q-Sepharose and gel-exclusion chromatography on Sephadex G-100 resulted in 84.21% yield and 53.99-fold purification of lectin with specific activity of 169.53 titre/mg. Molecular weight of FSL determined by SDS-PAGE was 70.7 kDa, which was further confirmed by gel-exclusion chromatography. Native-PAGE analysis of FSL showed its monomeric nature. FSL was observed to be a glycoprotein containing 2.9% carbohydrate. Hapten inhibition profile of FSL displayed its strong affinity towards D-xylose (MIC 1.562 mM), L-fucose (MIC 6.25 mM), D-mannose (MIC 3.125 mM), fetuin (MIC 15.62 µg/mL), asialofetuin (MIC 125 µg/mL) and BSM (MIC 3.125 µg/mL). Affinity of FSL towards xylose is rare. FSL was found stable over a pH range 6.0-7.5 and upto 40 °C temperature. Hemagglutination activity of FSL remained unaffected by divalent ions. Lectin concentration of 5 µg/mL was found sufficient to stimulate proliferation of murine spleen cells and its concentration 75 µg/mL exhibited highest mitogenic potential. FSL exhibited maximum mitogenic stimulatory index of 14.35. The purification, characterisation and mitogenicity of F. sambucinum lectin has been reported first time.

Resolution of Cox mediated inflammation by Se supplementation in mouse experimental model of colitis.

UC a form of IBD is a chronic inflammatory disorder of large intestine, with unknown etiology. Reports suggest a critical role of COX-2 dependent prostaglandins (PGs) mediated inflammatory pathway in pathophysiology of UC. However, COX inhibition using NSAIDs exacerbate IBD and thus is not a viable solution. Currently, in DSS induced experimental colitis in mice, we have demonstrated that dietary Se supplementation (0.5ppm as sodium selenite) symptomatically resolves the signs of inflammation in a redox sensitive manner as compared to Se deficient (0.01ppm) conditions, as seen by modulation in oxidative stress markers, morphological changes, histopathological examinations, biochemical studies such as MPO activity, activity of intestinal markers enzymes as well as mRNA and expressions of various pro and anti-inflammatory factors such as, mPGES, hPGDS, TXAS, 15-PGDH, GPX-1 and GPX-2. These findings were validated and correlated with changes in the biophysical parameters such as membrane fluidity, electrical parameters (impedance), transport across the colonic tissue and FTIR. Current study not only concluded that Se at supranutritional concentrations by modulating the redox status relieves the signs of colitis by regulating COX dependent PG biosynthetic pathway, but also sheds light on the biophysical characterization of these inflammatory/resolution pathways involved in UC.

Radiofrequency Thermal Ablation Heat Energy Transfer in an Ex-Vivo Model.

Little work has been done to consider the temperature changes and energy transfer that occur in the tissue outside the vein with ultrasound-guided vein ablation therapy. In this experiment, a Ex-Vivo model of the human calf was used to analyze heat transfer and energy degradation in tissue surrounding the vein during endovascular radiofrequency ablation (RFA). A clinical vein ablation protocol was used to determine the tissue temperature distribution in 10 per cent agar gel. Heat energy from the radiofrequency catheter was measured for 140 seconds at fixed points by four thermometer probes placed equidistant radially at 0.0025, 0.005, and 0.01 m away from the RFA catheter. The temperature rose 1.5°C at 0.0025 m, 0.6°C at 0.005 m, and 0.0°C at 0.01 m from the RFA catheter. There was a clinically insignificant heat transfer at the distances evaluated, 1.4 ± 0.2 J/s at 0.0025 m, 0.7 ± 0.3 J/s at 0.0050 m, and 0.3 ± 0.0 J/s at 0.01 m. Heat degradation occurred rapidly: 4.5 ± 0.5 J (at 0.0025 m), 4.0 ± 1.6 J (at 0.0050 m), and 3.9 ± 3.6 J (at 0.01 m). Tumescent anesthesia injected one centimeter around the vein would act as a heat sink to absorb the energy transferred outside the vein to minimize tissue and nerve damage and will help phlebologists strategize options for minimizing damage.

Algal lectins as promising biomolecules for biomedical research.

Lectins are natural bioactive ubiquitous proteins or glycoproteins of non-immune response that bind reversibly to glycans of glycoproteins, glycolipids and polysaccharides possessing at least one non-catalytic domain causing agglutination. Some of them consist of several carbohydrate-binding domains which endow them with the properties of cell agglutination or precipitation of glycoconjugates. Lectins are rampant in nature from plants, animals and microorganisms. Among microorganisms, algae are the potent source of lectins with unique properties specifically from red algae. The demand of peculiar and neoteric biologically active substances has intensified the developments on isolation and biomedical applications of new algal lectins. Comprehensively, algal lectins are used in biomedical research for antiviral, antinociceptive, anti-inflammatory, anti-tumor activities, etc. and in pharmaceutics for the fabrication of cost-effective protein expression systems and nutraceutics. In this review, an attempt has been made to collate the information on various biomedical applications of algal lectins.