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Ecology
Published in Paul Pumpens, Single-Stranded RNA Phages, 2020
The inactivation kinetics of the phages MS2, fr, and GA were compared by the UV254, singlet oxygen 1O2, free chlorine, and chlorine dioxide ClO2 treatment (Sigstam et al. 2013). The genome damage was quantified by PCR, and protein damage was assessed by quantitative matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS). The ClO2 caused great variability in the inactivation kinetics between viruses and was the only treatment that did not induce genome damage. The inactivation kinetics were similar for all viruses when treated with disinfectants possessing a genome-damaging component, namely, free chlorine, 1O2, and UV254. On the protein level, the UV254 subtly damaged the MS2 and fr coat proteins, whereas the GA coat remained intact. The 1O2 oxidized a methionine residue in the MS2 coat but did not affect the other two phages. The molecular dynamics simulations indicated that the degradation was dictated by the solvent-accessible surface area of the individual amino acids. These data explained clearly why closely related phages could exhibit drastically different inactivation kinetics (Sigstam et al. 2013).
Predicting Stability in Rheologically Modified Systems
Published in Laba Dennis, Rheological Proper ties of Cosmetics and Toiletries, 2017
The van der Waals force is itself a function of three fundamental field contributors; the London dispersion force, the Keesom force, and the hydrogen bonding (acid-base) energy (19). It is likely that Keesom force and hydrogen bonding are in fact perturbations of the primary symmetrical London field (20). Keesom's inductive polarization stretches the London (electronic spin) field elliptically. The elongated van der Waals field exposes more “sticky surface” (21) for increased cohesion. Hydrogen bonding induces even more elongation in an elastic fashion and occurs in response to a bonding partner. These specific contributors to cohesive energy and structure are often treated empirically as “solvent interaction parameters/' “solvent cavity areas,” or “solvent accessible surface area,” in order of preciseness.
Transscleral Drug Delivery to the Retina and Choroid
Published in Glenn J. Jaffe, Paul Ashton, P. Andrew Pearson, Intraocular Drug Delivery, 2006
We and others have shown that transscleral delivery may be a viable modality of delivering drugs to the posterior segment (3–6). The sclera has a large and accessible surface area, and a high degree of hydration that renders it conducive to water-soluble substances. It is also hypocellular and thus has few proteolytic enzymes or protein-binding sites that can degrade or sequester drugs. The fact that scleral permeability does not appreciably decline with age (4) is serendipitous for the treatment of chronic diseases such as diabetic retinopathy and age-related macular degeneration, which affect older persons.
Molecular docking and dynamics study to explore phytochemical ligand molecules against the main protease of SARS-CoV-2 from extensive phytochemical datasets
Published in Expert Review of Clinical Pharmacology, 2021
Shafi Mahmud, Mohasana Akter Mita, Suvro Biswas, Gobindo Kumar Paul, Maria Meha Promi, Shamima Afrose, Robiul Hasan, Sharmin Sultana Shimu, Shahriar Zaman, Salah Uddin, Trina Ekawati Tallei, Talha Bin Emran, Abu Saleh
The solvent-accessible surface area of the protein-ligand complexes was explored to check for any deviation in the protein surface area. The higher SASA profile co-relates with the extension of the protein volume whereas the lower SASA profile relates with the truncated nature of the protein. The SASA profile for all complexes initially had a higher profile, where control and apo system were mostly higher in the maximum simulation segment. After 80–100 ns time both apo and control systems exceeded the SASA value from the screened complexes, which defines the expansion of the apo and control complexes. Flemichin A, delta-oleanolic acid complexes had stable SASA profile from the very beginning while emodin 1-O-beta-D-glucoside tend to stable after 70–80 ns time. The higher trend of SASA in emodin 1-O-beta-D-glucoside at the beginning phase might be responsible for the enlargement of the surface area of this complex at the primary phase [Figure 3(b)].
Identifying novel sphingosine kinase 1 inhibitors as therapeutics against breast cancer
Published in Journal of Enzyme Inhibition and Medicinal Chemistry, 2020
Faez Iqbal Khan, Dakun Lai, Razique Anwer, Iffat Azim, Mohd Kalim Ahmad Khan
The solvent accessible surface area (SASA) is characterised by the region of a protein that is accessible to solvent molecules. The average SASA values for SphK1, SphK1–PF-543, SphK1–ZINC06823429, SphK1–ZINC95421070, and SphK1–ZINC95421501 were also observed during the 100 ns MD simulations. The average SASA values for SphK1, SphK1–PF-543, SphK1–ZINC06823429, SphK1–ZINC95421070, and SphK1–ZINC95421501 were found to be 171.74 nm2, 171.96 nm2, 168.93 nm2, 170.01 nm2, and 171.82 nm2, respectively (Table 4). The average SASA values were comparable for all the systems except a slight decrease in SASA found in case of SphK1–ZINC06823429 and SphK1–ZINC95421070. No significant changes in SASA values were reported upon binding of PF-543 and ZINC95421501 in the active pocket of SphK1 (Figure 7). It can be inferred that the internal residues in the SphK1 are not accessible to solvent because of binding of PF-543 and ZINC95421501. The free energy of solvation of SphK1, SphK1–PF-543, SphK1–ZINC06823429, SphK1–ZINC95421070, and SphK1–ZINC95421501 was also calculated during SASA calculations. The average free energy of solvation of SphK1, SphK1–PF-543, SphK1–ZINC06823429, SphK1–ZINC95421070, and SphK1–ZINC95421501 was found to be 264.63 kJ/mol/nm2, 252.64 kJ/mol/nm2, 255.25 kJ/mol/nm2, 249.01 kJ/mol/nm2, and 268.47 kJ/mol/nm2, respectively (Table 4, Figure 8).
Development of tibulizumab, a tetravalent bispecific antibody targeting BAFF and IL-17A for the treatment of autoimmune disease
Published in mAbs, 2019
Robert J. Benschop, Chi-Kin Chow, Yu Tian, James Nelson, Barbra Barmettler, Shane Atwell, David Clawson, Qing Chai, Bryan Jones, Jon Fitchett, Stacy Torgerson, Yan Ji, Holly Bina, Ningjie Hu, Mahmoud Ghanem, Joseph Manetta, Victor J. Wroblewski, Jirong Lu, Barrett W. Allan
The crystal structure of the Fv domain of ixekizumab was used for structural modeling of its surface properties, including hydrophobicity and charge distribution. Homology models of mutants were generated in the Molecular Operating Environment (MOE) (Chemical Computing Group, Montreal, Canada), based on the crystal structure and subject to the same analysis. Solvent accessible surface area (SASA) and surface exposure (%) for each residue were calculated based on the static model structure using the protein properties analysis module (MOE). Spatial aggregation propensity (SAP) was computed according to the method in the BIOVIA Discovery Studio 4.0 software (San Diego, CA). Environment setting of Amber10: EHT force field was applied before electrostatic potential computing by BIOVIA Discovery Studio 4.0 software.