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In Silico Antisickling Evaluation of 3, 4-Dihydroxybenzeoic Acid Isolated from Ficus

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In Silico Antisickling Evaluation of 3, 4-Dihydroxybenzeoic Acid Isolated from Ficus Electronic Research Journal of Engineering, Computer and Applied Sciences ISSN: 2709-3700 www.erjsciences.info Volume 3 (2021) In silico Antisickling evaluation of 3, 4-dihydroxybenzeoic acid isolated from Ficus. thonningii leaf Ijoma Kingsley Ikechukwu1 Department of Pure and Industrial Chemistry, Nnamdi Azikiwe University, Awka, Anambra State, Nigeria Email: [email protected] Ajiwe Vincent Department of Pure and Industrial Chemistry, Nnamdi Azikiwe University, Awka, Anambra State, Nigeria Abstract: Molecular docking and molecular dynamic simulation studies were performed on 3, 4- dihydroxybenzeoic acid isolated from Ficus thonningii leaf a known antisickling plant used in Eastern Nigeria in the management of Sickle Cell Disease patients. The Harbone method was used for extraction, whereas a combination of column chromatography and flash chromatography was used for the isolation and purification of the active principal of the leaf extract, a combination of H-NMR, C-13 NMR, COSY, TOCSY, HSQC and HMBC was used to elucidate the structure of the pure isolate. Binding affinity of -5.8kcal/mol from the molecular docking assay indicates that 3, 4-dihydroxybenzeoic acid binds to sickle Deoxyhemoglobin and was sufficient enough to interfere with the processes that trigger sickle hemoglobin polymerization in vitro. The molecular dynamic simulation analysis of the binding site amino acid residue was performed at 500 ps and it further confirmed the possible Hemoglobin allosteric effect of 3, 4-dihydroxybenzeoic acid as an effector ligand because of the observed perturbation and variations in the Holo and Apo simulations studies of Root Mean Square Deviation (RMSD), Radius of Gyration (Rg) and Solvent Accessible Surface Area (SASA), Electrostatic internal energy and van der Waal (VDW) interactions. Keywords: Sickle Hemoglobin, Molecular docking, Molecular dynamics, Antisickling Introduction: Sickle cell hemoglobin (HbS) results from a point mutation in which a neutral hydrophobic Valine residue is substituted for a negatively charged Glutathione at the β6 position of normal adult hemoglobin (HbA). As a consequence, deoxygenated molecules aggregate into fibers, which form elongated bundles. These result in alteration of hemoglobin function, and reduce the flexibility of the erythrocytes (Eaton, and Hofrichter, 1987). The crystal structure of deoxy HbS was solved at 3.0 Å resolutions by Love and co- workers in a unit cell arrangement that is believed to correspond closely to the arrangement within the fiber, (Padlan and Love, 1985; Padlan and Love, 1985) using crystals grown in low ionic strength solutions containing polyethylene glycol. The low ionic strength HbS structure shows small but significant differences from that of HbA, particularly in a hinge like displacement of the β chain α helices, which are involved in intermolecular contact (Padlan and 1 Corresponding author 113 Electronic Research Journal of Engineering, Computer and Applied Sciences ISSN: 2709-3700 www.erjsciences.info Volume 3 (2021) Love, 1985; Padlan and Love, 1985). The HbS crystal structure is usually obtained under ionic strength conditions that approximate physiological conditions (Perutz, 1968 and Prabhakaran and Johnson, 1993), thus, it is important to evaluate the stability of regions that participate as contact sites and energy of association between HbS molecules and HbS molecules-ligands interactions. Molecular dynamics has been highly successful in simulating the various motions within protein structures (McCammon and Harvey, 1987). Understanding the magnitudes and time scales of atomic fluctuations in proteins is essential for characterizing the internal motions that play important roles in their biological activity. The inter subunit contacts of the four Hb subunits within the Hb tetramer are stabilized by many weak nonbonded interactions. Thus, we have compared molecular dynamics simulations of DeOxyHbS (Holo) and DeOxyHbs-FTH2 (Apo), and have studied the fluctuations in Root mean square deviation, radius of gyration, solvent accessible surface area as well as the potential energy and van der waal interactions between Apo and Holo simulations, because several researches have established that the capability of biomolecules to prevent in vitro polymerization depends on tendency and efficiency to bind to the complimentary contact region/site of deoxyHbS monomers (Bianchi 2007, Abdulmalik et al.,2005); modification of amino acid residues that contribute to the three dimensional structures of HbS contact region and other critical sites (Oyewole, 2008); and Stabilization of the R (relaxed) state of HbS molecule (Ibraheem 2010; Chikezie, 2011; Oyewole, 2008). Similarly, it has been shown that any innocuous agent that can be bound to the region involved in sickling should alter the binding site significantly enough to prevent the formation of rods, i.e., prevent sickling (Schoenborn, 1965). Finch et al.,1973; Josephs et al.,1976; Fermi et al.,1984 and Magdoff-Fairchild et al.,1972 showed that in vitro; the sickling fibers are rods composed of four, six or eight monofilaments which are helically wound around each other, each monofilament being a string of stacked hemoglobin molecules. This suggests that sickling is not simply caused by a single complementary site, but that other molecular binding sites play a significant role. Interference with any of these contact points might, therefore, prevent sickling. Certain anesthetics and some other relatively chemically inert gases bind to myoglobin and hemoglobin (Schoenborn, 1976). The use of traditional medicine can’t fade out in the treatment and management of an array of diseases in the African continent. Several studies demonstrated the anti-sickling property of various extracts (Pauline, 2013) and the bioactivity of plant extracts is attributed to the presence of phytochemicals (Ijoma and Ajiwe, 2017; Ijoma et al.,2017; Ijoma et al.,2016). The antisickling characterization of Ficus species have been reported (Mpiana et al.,2008) Protein aggregation is a complex biological process associated with various diseases, including neurodegenerative diseases such as Alzheimer and Parkinson, as well as sickle cell disease (SCD), a red blood cell disorder (Horwish, 2002; Sami et al.,2017; Ross et al.,2004). Understanding the thermodynamics and the molecular mechanisms of protein aggregation is, therefore, critical for the development of therapeutic strategies and the design of protein aggregation inhibitors. From a molecular perspective, protein aggregation depends on a complex balance of electrostatic and hydrophobic interactions mediated by water and osmolytes (Bellissent-Funel et al.,2016; Ball, 2017), which in turn, influence protein function. A remarkable example concerns the human hemoglobin mutant, HbS, or sickle cell Hb, responsible for SCD (Pauling et al.,1949; Ingram, 1956; Murayama, 1966; Padlan and Love, 1985; Padlan and Love, 1985; Harrington et al.,1997; Eaton and Hofrichter., 1987; Eaton and Hofrichter, 1990; Noguchi and Schechter, 1985). The molecule of Hb is formed by 4 polypeptide chains, 114 Electronic Research Journal of Engineering, Computer and Applied Sciences ISSN: 2709-3700 www.erjsciences.info Volume 3 (2021) specifically, 2α chains and 2β chains (Petruz, 1970). HbS differs from normal adult HbA by a single amino acid, namely, the substitution of Glu (charged) in the 6th position of the β polypeptide chains, by Val (hydrophobic) (Ingram, 1956). This substitution, associated with the mutation of a single nucleotide in the gene for the β-chain6, has great biological implications, being responsible for the polymerization of Deoxy- HbS into 14-stranded helical fibers, which distort the shape of erythrocytes, causing several problems associated with vaso-occlusion (Eaton and Hofrichter, 1987; Eaton and Hofrichter, 1990; Rees et al.,2010; Ware et al.,2017). This mutated Val-β6 has its hydrophobic side chain lodged in a pocket of a neighbor HbS tetramer, formed by several hydrophobic residues, noteworthy, but not exclusive, Ala-β70, Phe-β85, and Leu-β88, as well as Heme (Padlan and Love, 1985; Padlan and Love, 1985; Harrington et al.,1997). Furthermore, since the replaced Glu-β6 → Val-β6 are at the Hb surface, the structure of Deoxy-HbS is not significantly perturbed, relative to that of Deoxy-HbA (Padlan and Love, 1985; Padlan and Love, 1985; Harrington et al.,1997; Perutz et al.,1986). HbS polymerization is characterized by a delay time (Adachi and Asakura, 1978; Adachi and Asakura, 1979; Adachi and Asakura, 1982) and is believed to occur via a double nucleation mechanism, initiated by the formation of HbS fibers (homogeneous nucleation), followed by fiber growth, though nucleation of additional polymers on the surface of existing ones (heterogeneous nucleation) (Ferrone et al.,1985 and Ferrone et al.,1985). Furthermore, it was proposed that homogenous nucleation proceeds through a two-step mechanism where metastable dense clusters play the role of nucleation precursors (Galkin et al.,2007). Thus, delaying or preventing the formation of such precursors could represent a possible solution to hemoglobin gelation. Taxonomy: FICUS THONNINGII Kingdom: Plantae Phylum: Tracheophyta Class: Magnoliopsida Order: Rosales Family: Moraceae Genus: Ficus L. Species: Ficus thonningii Blume (Global Biodiversity Information Facility Secretariat, 2019, Roskov et al.,2020) 115 Electronic Research Journal of Engineering, Computer and Applied Sciences ISSN: 2709-3700 www.erjsciences.info Volume 3 (2021) Plate1:
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