Structural and thermodynamic properties of conserved water molecules in Mpro native: A combined approach by MD simulation and Grid Inhomogeneous Solvation Theory

The new viral strains of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) are continuously rising, becoming more virulent, and transmissible. Therefore, the development of new antiviral drugs is essential. Due to its significant role in the viral life cycle of SARS-CoV-2, the main protease (Mpro) enzyme is a leading target for antiviral drug design. The Mpro monomer consists of domain DI, DII, and DI-DII interface. Twenty-one conserved water molecules (W4-W24) are occupied at these domains according to multiple crystal structure analyses. The crystal and MD structures reveal the presence of eight conserved water sites in domain DI, DII and remaining in the DI-DII interface. Grid-based inhomogeneous fluid solvation theory (GIST) was employed on MD structures of Mpro native to predict structural and thermodynamic properties of each conserved water site for focusing to identify the specific conserved water molecules that can easily be displaced by proposed ligands. Finally, MD water W13 is emerged as a promising candidate for water mimic drug design due to its low mean interaction energy, loose binding character with the protein, and its involvement in a water-mediated H-bond with catalytic His41 via the interaction Thr25(OG)---W13---W---His41(NE2). In this context, water occupancy, relative interaction energy, entropy, and topologies of W13 are thermodynamically acceptable for the water displacement method. Therefore, the strategic use of W13's geometrical position in the DI domain may be implemented for drug discovery against COVID disease by designing new ligands with appropriately oriented chemical groups to mimic its structural, electronic, and thermodynamic properties.

The Reliability and Validity of a Portable Three-Dimensional Scanning System to Measure Leg Volume

(1) Background: The study examined the reliability (test-retest, intra- and inter-day) and validity of a portable 3D scanning method when quantifying human leg volume. (2) Methods: Fifteen males volunteered to participate (age, 24.6 ± 2.0 years; stature, 178.9 ± 4.5 cm; body mass, 77.4 ± 6.5 kg; mean ± standard deviation). The volume of the lower and upper legs was examined using a water displacement method (the criterion) and two consecutive 3D scans. Measurements were taken at baseline, 1 h post-baseline (intra-day) and 24 h post-baseline (inter-day). Reliability and validity of the 3D scanning method was assessed using Bland-Altman limits of agreement and Pearson's product moment correlations. (3) Results: With respect to the test-retest reliability, the 3D scanning method had smaller systematic bias and narrower limits of agreement (±1%, and 3-5%, respectively) compared to the water displacement method (1-2% and 4-7%, respectively), when measuring lower and upper leg volume in humans. The correlation coefficients for all reliability comparisons (test-retest, intra-day, inter-day) would all be regarded as 'very strong' (all 0.94 or greater). (4) Conclusions: The study's results suggest that a 3D scanning method is a reliable and valid method to quantify leg volume.

Noninvasive Measurements of Breast Cancer-Related Lymphedema

Breast cancer-related lymphedema (BCRL) presents as swelling in the arm, hand, trunk, or breast at varying times after completion of breast cancer treatment. Its reported incidence varies widely in part due to its dependence on the type and extent of the treatment, co-present pre-treatment risk factors, and the criteria used to define its presence. Central to this issue is the quantitative measures that are variously used to specify lymphedema thresholds for its detection and tracking over time and during treatment. The goal of this paper is to discuss these issues and the methods available for the non-invasive quantitative assessment of BCRL. Operational principles and advantages and limitations of the various methods and their clinical history of use and effectiveness are discussed. 

The role of arm volumes evaluation in the functional outcome and patient satisfaction following surgical repair of the brachial plexus traumatic injuries

OBJECTIVE

Brachial plexus injuries are among the most complex injuries of the peripheral nervous system and among the most devastating injuries overall. In complete lesions, functional priorities include the reinnervation of the musculocutaneous and axillary nerves for proximal functions restoration. Three major nerves - radial, median, and ulnar - and the corresponding muscles remain denervated, which results in subsequent muscle atrophy. This study was aimed at the evaluation of arm volumes in surgically treated patients with brachial plexus injuries, in correlation with the type of palsy, recovery and associated factors.

METHODS

The study included 36 patients with brachial plexus injuries who were surgically treated in our institution over a 15-year-long period. The evaluation of arm and arm segments volumes was carried out using water displacement testing, based on the Archimedes principle.

RESULTS

Statistically significant differences were noted between the operated arm and the healthy arm in all of the measured segments (hands, forearms and upper arms), as well as between the patients with complete and upper palsy, and in correlation with the shoulder abduction recovery.

CONCLUSIONS

Previous studies were mainly focused on the functional outcome and quality of life; although related to both, arm volumes in patients with brachial plexus injuries were not analyzed before. Significant differences between the operated arm and the healthy arm volumes, as well as between the various types of palsy, found in the present study should trigger further prospective research in relation to neurophysiology, useful functional recovery and quality of life.

Validity and Reliability of Three-Dimensional Imaging for Measuring Breast Cancer-Related Lymphedema in the Upper Limb: A Cross-Sectional Study

Background: In the past, measurement of upper limb lymphedema was done by water displacement (WD), which is frequently cited as the gold standard. For various reasons, however, the use of WD is restricted in clinical settings. A more precise and easy-to-use method would be favorable. The high precision of three-dimensional (3D) imaging in comparison to WD has already been reported for healthy subjects. The aim of this study is to determine the validity and reliability of 3D imaging by comparing it to the WD method in women with unilateral upper limb lymphedema. Methods and Results: Thirty-nine women with unilateral breast cancer-related lymphedema (BCRL) were included, of which 37 completed two volume measurement techniques (3D and WD) on the BCRL and contralateral healthy arm. Slightly larger volumes were measured by the WD method in healthy arms (+9.8 mL; p = 0.058) and also in BCRL arms (+18.5 mL; p < 0.001). All measurements were performed twice by the same researcher to evaluate reliability. There was no significant difference between the two measurements for healthy arms (p = 0.323) or BCRL arms (p = 0.807) in 3D imaging. Bland-Altman plots showed a high limit of agreement between the single measurements. 3D imaging had a high intrarater reliability (Intraclass Correlation Coefficient = 0.999). Conclusion: Results show that 3D imaging is an innovative method for measuring upper limb volume in BCRL patients. Even though image processing is time consuming, 3D imaging combines high reproducibility with high precision. By software automation, this technique could easily be integrated into clinical routine. It is for this reason that we would recommend implementing the Vectra 3D imaging technique for measurement of BCRL.

Ultrasonography as the Gold Standard for In Vivo Volumetric Determination of Chemically-induced Mammary Tumors

BACKGROUND/AIM

In this study, we evaluated the dimensions and volume of rat mammary tumors and the association of these variables with tumor invasiveness.

MATERIALS AND METHODS

Tumors were measured by caliper and ultrasonography. Volume was determined by water displacement and by application of four formulas using tumor length (L), width (W) and depth (D) or tumor weight.

RESULTS

Results confirmed the data obtained in our previous work, where we verified that mammary tumors grow as oblate spheroids.

CONCLUSION

The determination of mammary tumor volume by applying the formula V=(4/3)×π×(L/2)×(L/2)×(D/2) is the best way to evaluate tumor volume in vivo. Beyond volume evaluation by water displacement, the determination on the basis of tumor weight is the most accurate way to evaluate tumor volume after animal sacrifice or tumor excision. According to our results, it is not possible to predict if a tumor is invasive or non-invasive by its dimensions, volume or weight. Future work in chemically-induced mammary cancer should use ultrasonography and water displacement or tumor weight to determine tumor volume in vivo and after animal sacrifice or tumor excision, respectively.

Breast volumetric analysis for aesthetic planning in breast reconstruction: a literature review of techniques

BACKGROUND

Accurate volumetric analysis is an essential component of preoperative planning in both reconstructive and aesthetic breast procedures towards achieving symmetrization and patient-satisfactory outcome. Numerous comparative studies and reviews of individual techniques have been reported. However, a unifying review of all techniques comparing their accuracy, reliability, and practicality has been lacking.

METHODS

A review of the published English literature dating from 1950 to 2015 using databases, such as PubMed, Medline, Web of Science, and EMBASE, was undertaken.

RESULTS

Since Bouman's first description of water displacement method, a range of volumetric assessment techniques have been described: thermoplastic casting, direct anthropomorphic measurement, two-dimensional (2D) imaging, and computed tomography (CT)/magnetic resonance imaging (MRI) scans. However, most have been unreliable, difficult to execute and demonstrate limited practicability. Introduction of 3D surface imaging has revolutionized the field due to its ease of use, fast speed, accuracy, and reliability. However, its widespread use has been limited by its high cost and lack of high level of evidence. Recent developments have unveiled the first web-based 3D surface imaging program, 4D imaging, and 3D printing.

CONCLUSIONS

Despite its importance, an accurate, reliable, and simple breast volumetric analysis tool has been elusive until the introduction of 3D surface imaging technology. However, its high cost has limited its wide usage. Novel adjunct technologies, such as web-based 3D surface imaging program, 4D imaging, and 3D printing, appear promising.