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  1. Bundhun A, Abdallah HH, Ramasami P, Schaefer HF
    J Phys Chem A, 2010 Dec 23;114(50):13198-212.
    PMID: 21090692 DOI: 10.1021/jp1078955
    A systematic investigation of the X-Ge-CY(3) (X = H, F, Cl, Br, and I; Y = F, Cl, Br, and I) species is carried out using density functional theory. The basis sets used for all atoms (except iodine) in this work are of double-ζ plus polarization quality with additional s- and p-type diffuse functions, and denoted DZP++. Vibrational frequency analyses are performed to evaluate zero-point energy corrections and to determine the nature of the stationary points located. Predicted are four different forms of neutral-anion separations: adiabatic electron affinity (EA(ad)), zero-point vibrational energy corrected EA(ad(ZPVE)), vertical electron affinity (EA(vert)), and vertical detachment energy (VDE). The electronegativity (χ) reactivity descriptor for the halogens (X = F, Cl, Br, and I) is used as a tool to assess the interrelated properties of these germylenes. The topological position of the halogen atom bound to the divalent germanium center is well correlated with the trend in the electron affinities and singlet-triplet gaps. For the expected XGeCY(3) structures (X = H, F, Cl, Br, and I; Y = F and Cl), the predicted trend in the electron affinities is well correlated with simpler germylene derivatives (J. Phys. Chem. A 2009, 113, 8080). The predicted EA(ad(ZPVE)) values with the BHLYP functional range from 1.66 eV (FGeCCl(3)) to 2.20 eV (IGeCF(3)), while the singlet-triplet splittings range from 1.28 eV (HGeCF(3)) to 2.22 eV (FGeCCl(3)). The XGeCY(3) (Y = Br and I) species are most often characterized by three-membered cyclic systems involving the divalent germanium atom, the carbon atom, and a halogen atom.
  2. Cheurfa M, Abdallah HH, Allem R, Noui A, Picot-Allain CMN, Mahomoodally F
    Food Chem Toxicol, 2019 Jan;123:98-105.
    PMID: 30292622 DOI: 10.1016/j.fct.2018.10.002
    Aqueous and ethanol extracts prepared from leaves of Olea europaea L. were evaluated for in vitro antioxidant and in vivo hypocholesterolemic effect. The result of administration of O. europaea leaf extracts on serum total cholesterol, triglyceride, high-density lipoprotein (HDL), low-density lipoprotein (LDL), and very low-density lipoprotein (VLDL) in hypercholesterolaemic mice was evaluated. In addition, rutin and luteolin, reported to occur naturally in O. europaea leaves, were docked against HMG-CoA reductase, the rate-limiting enzyme in cholesterol metabolism. Mice treated with both extracts showed reduced total cholesterol (246.6 and 163.4 mg/dl, for mice groups treated with respective extracts) and LDL (150.16 and 81.28 mg/dl, for mice groups treated with respective extracts) levels as compared to the hypercholesterolaemic group (total cholesterol 253.00 mg/dl and LDL 160.00 mg/dl). Mice treated with aqueous extract (200 mg/kg body weight) showed significantly reduced triglyceride and VLDL levels as compared to the group treated with atorvastatine. HDL level of mice administered with O. europaea aqueous extract was comparable to the atorvastatine-treated group. The ethanol extract of O. europeae leaves was a potent antioxidant (IC50 69.15 mg/ml, % inhibition 54.98, 82.63 mg ascorbic acid equivalent/g extract, 7.53 mol of Fe2+/g extract, and % inhibition 49.71, for the DPPH, β-carotene bleaching, total antioxidant capacity, FRAP, and ferric thiocyanate assays, respectively). Docking studies revealed that rutin showed higher binding affinity with HMG-CoA reductase as compared to luteolin. Data gathered from this study support the development of a prophylactic biomedicine from O. europaea leaves for the management of hypercholesterolemia and atherosclerosis.
  3. Scior T, Abdallah HH, Salvador-Atonal K, Laufer S
    Curr Comput Aided Drug Des, 2020;16(3):327-339.
    PMID: 32507104 DOI: 10.2174/1573409915666191010104527
    BACKGROUND: The relatedness between the linear equations of thermodynamics and QSAR was studied thanks to the recently elucidated crystal structure complexes between sulfonamide pterin conjugates and dihydropteroate synthase (DHPS) together with a published set of thirty- six synthetic dapsone derivatives with their reported entropy-driven activity data. Only a few congeners were slightly better than dapsone.

    OBJECTIVE: Our study aimed at demonstrating the applicability of thermodynamic QSAR and to shed light on the mechanistic aspects of sulfone binding to DHPS.

    METHODS: To this end ligand docking to DHPS, quantum mechanical properties, 2D- and 3D-QSAR as well as Principle Component Analysis (PCA) were carried out.

    RESULTS: The short aryl substituents of the docked pterin-sulfa conjugates were outward oriented into the solvent space without interacting with target residues which explains why binding enthalpy (ΔH) did not correlate with potency. PCA revealed how chemically informative descriptors are evenly loaded on the first three PCs (interpreted as ΔG, ΔH and ΔS), while chemically cryptic ones reflected higher dimensional (complex) loadings.

    CONCLUSION: It is safe to utter that synthesis efforts to introduce short side chains for aryl derivatization of the dapsone scaffold have failed in the past. On theoretical grounds we provide computed evidence why dapsone is not a pharmacodynamic lead for drug profiling because enthalpic terms do not change significantly at the moment of ligand binding to target.

  4. Mustafa SF, Maarof H, Ahmed R, Abdallah HH
    J Mol Model, 2016 Dec;22(12):290.
    PMID: 27866329
    Diffusion at the atomic or molecular level is a source of many physical, chemical, and biological processes taking place in plentiful materials. This work is an endeavor toward investigating the diffusional behavior of two different type of guests, hexadecane-1,16-diol and hexadecane enclathration in urea tunnel architecture, whereby the correlation of the diffusion mechanism with the guest's structural and conformational properties is explored. To carry out this study, molecular dynamics simulation approach is adopted. It is found that hexadecane-1,16-diol exhibit slower diffusion with an average diffusion coefficient value [Formula: see text], where hexadecane diffuse more rapidly with an average diffusion coefficient value [Formula: see text]. It is also observed that the structural properties influence the guest's travel distance and torsion angle distribution of the trans and gauche conformational proportion. Furthermore, the observed high energy barrier accounted for hexadecane-1,16-diol and low energy barrier for hexadecane along urea tunnel systems was analyzed. The comparison of our obtained results are in close agreement with the available experimental measurements, i.e., gauche proportion properties between two different guest molecules correlate well with Raman spectroscopy investigation on α,ω-dihalogenoalkane/urea inclusion compounds. Our calculations also successfully endorse the structure-property relation between the two systems.
  5. Abdallah HH, Mavri J, Repič M, Lee VS, Wahab HA
    Int J Mol Sci, 2012;13(2):1269-83.
    PMID: 22408390 DOI: 10.3390/ijms13021269
    Genistein, daidzein, glycitein and quercetin are flavonoids present in soybean and other vegetables in high amounts. These flavonoids can be metabolically converted to more active forms, which may react with guanine in the DNA to form complexes and can lead to DNA depurination. We assumed two ultimate carcinogen forms of each of these flavonoids, diol epoxide form and diketone form. Density functional theory (DFT) and Hartree-Fock (HF) methods were used to study the reaction thermodynamics between active forms of flavonoids and DNA guanine. Solvent reaction field method of Tomasi and co-workers and the Langevin dipoles method of Florian and Warshel were used to calculate the hydration free energies. Activation free energy for each reaction was estimated using the linear free energy relation. Our calculations show that diol epoxide forms of flavonoids are more reactive than the corresponding diketone forms and are hence more likely flavonoid ultimate carcinogens. Genistein, daidzein and glycitein show comparable reactivity while quercetin is less reactive toward DNA.
  6. Abdulla MH, Sattar MA, Abdullah NA, Khan MA, Abdallah HH, Johns EJ
    Eur J Pharmacol, 2009 Jun 10;612(1-3):69-74.
    PMID: 19356722 DOI: 10.1016/j.ejphar.2009.03.064
    This study set out to investigate the impact of chronic cumulative blockade of angiotensin II and adrenoceptors in WKY and SHR and to explore how the renovascular responses to adrenergic and angiotensin II receptor agonists may be interdependent. Rats were treated with either losartan, carvedilol or losartan+carvedilol for 7 days and on day eight, animals were pentobarbitone anaesthetized and prepared for renal haemodynamic study. Dose-response relationships were determined in terms of reduction/elevation in the magnitude of renal blood flow in response to intrarenal arterial injection of dopamine, phenylephrine and isoprenaline. Renal vascular responses were blunted in WKY and SHR treated with either losartan or carvedilol as compared to their untreated counterparts (P<0.05). In the combined treated rats, the vascular responses to isoprenaline and phenylephrine were restored to levels observed in the untreated rats, but the renal vasoconstrictor responses to dopamine decreased (P<0.05) in both WKY and SHR. There was a reduction of (P<0.05) in the magnitude of the isoprenaline induced renal vasodilation in all SHR as compared to WKY groups. The data obtained showed that the renal vascular action of dopamine, phenylephrine and isoprenaline depended on an intact renin-angiotensin system (RAS) in WKY and SHR. Treatment with losartan or carvedilol blunted the renal vasoconstrictor/vasodilator responses to sympathomimetics which was attenuated with the combined treatment. These observations using chronic blockade of adrenergic and angiotensin receptors demonstrated that there was a long standing interdependency between the RAS and sympathetic nervous system (SNS) in determining the responsiveness of the renal vasculature of normal and hypertensive rats.
  7. Al Azzam KM, Abdallah HH, Halim HN, Ahmad MA, Shaibah H
    Sci Pharm, 2015 06 22;83(4):683-98.
    PMID: 26839848 DOI: 10.3797/scipharm.1501-15
    The current work reports an extended theoretical study from our previous experimental work for the enantioselective extraction of amlodipine enantiomers in a biphasic recognition chiral extraction system (BRCES) consisting of hydrophobic D-diisopropyl tartrate dissolved in organic phase (n-decanol) and hydrophilic hydroxypropyl-β-cyclodextrin (HP-β-CD) in aqueous phase (acetate buffer) which preferentially recognize the R-enantiomer and S-enantiomer, respectively. The calculations were simulated using a semi-empirical PM3 method as a part of the Gaussian09 software package and were used to optimize the structures of the hosts, guests, and host-guest complexes in the gas phase without any restrictions. It was found that HP-β-CD has the strongest recognition ability among the three β-CD derivatives studied, namely HP-β-CD, hydroxyethyl-β-cyclodextrin (HE-β-CD), and methylated-β-cyclodextrin (Me-β-CD), due to the large interaction energies (Ecomp = -14.3025 kcal/ mol), while D-diisopropyl tartrate has the strongest ability among the four tartaric acid derivatives studied namely; L-diisopropyl tartrate, D-diisopropyl tartrate, L-diethyl tartrate, and D-diethyl tartrate (Ecomp = -5.9964 kcal/ mol). The computational calculations for the enantioselective partitioning of amlodipine enantiomers rationalized the reasons for the different behaviors for this extraction. The present theoretical results may be informative to scientists who are devoting themselves to developing models for their experimental parts or for enhancing the hydrophobic drug solubility in drug delivery systems.
  8. Zengin G, Abdallah HH, Dogan A, Mollica A, Aumeeruddy-Elalfi Z, Mahomoodally MF
    Food Chem Toxicol, 2018 Jan;111:423-431.
    PMID: 29198858 DOI: 10.1016/j.fct.2017.11.055
    The potentiality of bioactive phenolic compounds may result in plant extracts having multiple biological activities. The aim of this study was to investigate into the biological activities of the methanolic, ethyl acetate, and water extracts of Tchihatchewia isatidea Boiss, an endemic medicinal plant of Turkey. The phenolic compositions of the extracts were confirmed using RP-HPLC. Extracts were screened for their potential antioxidant through a panoply of assays; their anti-diabetic potential, and plausible inhibitory activity against tyrosinase and acetylcholinesterase. Molecular modelling methods were also used to assess the docking properties of phenolic compounds on tyrosinase. The major and most abundant compounds were rosmarinic acid (570 ± 14 μg/g extract in the methanolic extract), ferrulic acid (336 ± 6 μg/g extract in the methanolic extract), (+)-catechin (340 ± 4 μg/g extract in the water extract), apigenin (182 ± 4 μg/g extract in the methanolic extract), and epicatechin (188 ± 12 μg/g extract in the water extract). Radical scavenging, reducing capacity, and metal chelating activities were detected in the extracts, with preponderance activity observed in the methanolic extract. In conclusion, the potential clinical applications observed during this study may provide new insights into the molecular aspect particularly for neuroprotective and anti-diabetic mechanisms involving oxidative stress.
  9. Scior T, Abdallah HH, Mustafa SFZ, Guevara-García JA, Rehder D
    Inorganica Chim Acta, 2021 May 01;519:120287.
    PMID: 33589845 DOI: 10.1016/j.ica.2021.120287
    In silico techniques helped explore the binding capacities of the SARS-CoV-2 main protease (Mpro) for a series of metalloorganic compounds. Along with small size vanadium complexes a vanadium-containing derivative of the peptide-like inhibitor N3 (N-[(5-methylisoxazol-3-yl)carbonyl]alanyl-l-valyl-N1-((1R,2Z)-4-(benzyloxy)-4-oxo-1-{[(3R)-2-oxopyrrolidin-3-yl] methyl }but-2-enyl)-l-leucinamide) was designed from the crystal structure with PDB entry code 6LU7. On theoretical grounds our consensus docking studies evaluated the binding affinities at the hitherto known binding site of Chymotrypsin-like protease (3CLpro) of SARS-CoV-2 for existing and designed vanadium complexes. This main virus protease (Mpro) has a Cys-His dyad at the catalytic site that is characteristic of metal-dependent or metal-inhibited hydrolases. Mpro was compared to the human protein-tyrosine phosphatase 1B (hPTP1B) with a comparable catalytic dyad. HPTP1B is a key regulator at an early stage in the signalling cascade of the insulin hormone for glucose uptake into cells. The vanadium-ligand binding site of hPTP1B is located in a larger groove on the surface of Mpro. Vanadium constitutes a well-known phosphate analogue. Hence, its study offers possibilities to design promising vanadium-containing binders to SARS-CoV-2. Given the favourable physicochemical properties of vanadium nuclei, such organic vanadium complexes could become drugs not only for pharmacotherapy but also diagnostic tools for early infection detection in patients. This work presents the in silico design of a potential lead vanadium compound. It was tested along with 20 other vanadium-containing complexes from the literature in a virtual screening test by docking to inhibit Mpro of SARS-CoV-2.
  10. Helal MH, Al-Mudaris ZA, Al-Douh MH, Osman H, Wahab HA, Alnajjar BO, et al.
    Int J Oncol, 2012 Aug;41(2):504-10.
    PMID: 22614449 DOI: 10.3892/ijo.2012.1491
    Molecules that target the deoxyribonucleic acid (DNA) minor groove are relatively sequence specific and they can be excellent carrier structures for cytotoxic chemotherapeutic compounds which can help to minimize side effects. Two novel isomeric derivatives of diaminobenzene Schiff base [N,N'-bis (2-hydroxy-3-methoxybenzylidene)-1,2-diaminobenzene (2MJ) and N,N'-bis(2-hydroxy-3-methoxybenzylidene)-1,3-diaminobenzene (2MH)] were analyzed for their DNA minor groove binding (MGB) ability using viscometry, UV and fluorescence spectroscopy, computational modeling and clonogenic assay. The result shows that 2MJ and 2MH are strong DNA MGBs with the latter being more potent. 2MH can form interstrand hydrogen bond linkages at its oxygens with N3 of adenines. Changing the 2-hydroxy-3-methoxybenzylidene binding position to the 1,3 location on the diaminobenzene structure (2MJ) completely removed any viable hydrogen bond formation with the DNA and caused significant decrease in binding strength and minor groove binding potency. Neither compound showed any significant cytotoxicity towards human breast, colon or liver cancer cell lines.
  11. Arshad A, Ahemad S, Saleem H, Saleem M, Zengin G, Abdallah HH, et al.
    Biomolecules, 2021 01 04;11(1).
    PMID: 33406643 DOI: 10.3390/biom11010053
    Heliotropium is one of the most important plant genera to have conventional folklore importance, and hence is a potential source of bioactive compounds. Thus, the present study was designed to explore the therapeutic potential of Heliotropium crispum Desf., a relatively under-explored medicinal plant species. Methanolic extracts prepared from a whole plant of H. crispum were studied for phytochemical composition and possible in vitro and in silico biological properties. Antioxidant potential was assessed via six different assays, and enzyme inhibition potential against key clinical enzymes involved in neurodegenerative diseases (acetylcholinesterase (AChE) and butyrylcholinesterase (BChE)), diabetes (α-amylase and α-glucosidase), and skin problems (tyrosinase) was assayed. Phytochemical composition was established via determination of the total bioactive contents and reverse phase ultra-high performance liquid chromatography mass spectrometry (RP-UHPLC-MS) analysis. Chemical profiling revealed the tentative presence of 50 secondary metabolites. The plant extract exhibited significant inhibition against AChE and BChE enzymes, with values of 3.80 and 3.44 mg GALAE/g extract, respectively. Further, the extract displayed considerable free radical scavenging activity against DPPH and ABTS radicals, with potential values of 43.19 and 41.80 mg TE/g extract, respectively. In addition, the selected compounds were then docked against the tested enzymes, which have shown high inhibition affinity. To conclude, H. crispum was found to harbor bioactive compounds and showed potent biological activities which could be further explored for potential uses in nutraceutical and pharmaceutical industries, particularly as a neuroprotective agent.
  12. Saleem H, Khurshid U, Sarfraz M, Tousif MI, Alamri A, Anwar S, et al.
    Food Chem Toxicol, 2021 Aug;154:112348.
    PMID: 34144099 DOI: 10.1016/j.fct.2021.112348
    Suaeda fruticosa is an edible medicinal halophyte known for its traditional uses. In this study, methanol and dichloromethane extracts of S. fruticosa were explored for phytochemical, biological and toxicological parameters. Total phenolic and flavonoid constituents were determined by using standard aluminum chloride and Folin-Ciocalteu methods, and UHPLC-MS analysis of methanol extract was performed for tentative identification of secondary metabolites. Different standard methods like DPPH, ABTS, FRAP, CUPRAC, total antioxidant capacity (TAC), and metal chelation assays were utilized to find out the antioxidant potential of extracts. Enzyme inhibition studies of extracts against acetylcholinesterase, butyrylcholinesterase, tyrosinase, α-amylase and, α-glucosidase enzymes were also studied. Likewise, the cytotoxicity was also assessed against MCF-7, MDA-MB-231, and DU-145 cell lines. The higher phenolic and flavonoids contents were observed in methanol extracts which can be correlated to its higher radical scavenging potential. Similarly, 11 different secondary metabolites were tentatively identified by UHPLC profiling. Both the extract showed significant inhibition against all the enzymes except for α-glucosidase. Moreover, docking studies were also performed against the tested enzymes. In the case of cytotoxicity, both the samples were found moderately toxic against the tested cell lines. This plant can be explored further for its potential therapeutic and edible uses.
  13. Zengin G, Rodrigues MJ, Abdallah HH, Custodio L, Stefanucci A, Aumeeruddy MZ, et al.
    Comput Biol Chem, 2018 Dec;77:178-186.
    PMID: 30336375 DOI: 10.1016/j.compbiolchem.2018.10.005
    The genus Silene is renowned in Turkey for its traditional use as food and medicine. Currently, there are 138 species of Silene in Turkey, amongst which have been several studies for possible pharmacological potential and application in food industry. However, there is currently a paucity of data on Silene salsuginea Hub.-Mor. This study endeavours to access its antioxidant, enzyme inhibitory, and anti-inflammatory properties. Besides, reversed-phase high-performance liquid chromatography-diode array detector (RP-HPLC-DAD) was used to detect phenolic compounds, and molecular docking was performed to provide new insights for tested enzymes and phenolics. High amounts of apigenin (534 μg/g extract), ferulic acid (452 μg/g extract), p-coumaric acid (408 μg/g extract), and quercetin (336 μg/g extract) were detected in the methanol extract while rutin (506 μg/g extract) was most abundant in the aqueous extract. As for their biological properties, the methanol extract exhibited the best antioxidant effect in the DPPH and CUPRAC assays, and also the highest inhibition against tyrosinase. The aqueous extract was the least active enzyme inhibitor but showed the highest antioxidant efficacy in the ABTS, FRAP, and metal chelating assays. At a concentration of 15.6 μg/mL, the methanol extract resulted in a moderate decrease (25.1%) of NO production in lipopolysaccharide-stimulated cells. Among the phenolic compounds, epicatechin, (+)-catechin, and kaempferol showed the highest binding affinity towards the studied enzymes in silico. It can be concluded that extracts of S. salsuginea are a potential source of functional food ingredients but need further analytical experiments to explore its complexity of chemical compounds and pharmacological properties as well as using in vivo toxicity models to establish its maximum tolerated dose.
  14. di Giacomo V, Chiavaroli A, Recinella L, Orlando G, Cataldi A, Rapino M, et al.
    Int J Mol Sci, 2020 05 18;21(10).
    PMID: 32443623 DOI: 10.3390/ijms21103575
    Cannabidiol (CBD) and cannabigerol (CBG) are Cannabis sativa terpenophenols. Although CBD's effectiveness against neurological diseases has already been demonstrated, nothing is known about CBG. Therefore, a comparison of the effects of these compounds was performed in two experimental models mimicking the oxidative stress and neurotoxicity occurring in neurological diseases. Rat astrocytes were exposed to hydrogen peroxide and cell viability, reactive oxygen species production and apoptosis occurrence were investigated. Cortexes were exposed to K+ 60 mM depolarizing stimulus and serotonin (5-HT) turnover, 3-hydroxykinurenine and kynurenic acid levels were measured. A proteomic analysis and bioinformatics and docking studies were performed. Both compounds exerted antioxidant effects in astrocytes and restored the cortex level of 5-HT depleted by neurotoxic stimuli, whereas sole CBD restored the basal levels of 3-hydroxykinurenine and kynurenic acid. CBG was less effective than CBD in restoring the levels of proteins involved in neurotransmitter exocytosis. Docking analyses predicted the inhibitory effects of these compounds towards the neurokinin B receptor. Conclusion: The results in the in vitro system suggest brain non-neuronal cells as a target in the treatment of oxidative conditions, whereas findings in the ex vivo system and docking analyses imply the potential roles of CBD and CBG as neuroprotective agents.
  15. Venugopala KN, Chandrashekharappa S, Pillay M, Abdallah HH, Mahomoodally FM, Bhandary S, et al.
    PLoS One, 2019;14(6):e0217270.
    PMID: 31163040 DOI: 10.1371/journal.pone.0217270
    Indolizines are heteroaromatic compounds, and their synthetic analogues have reportedly showed promising pharmacological properties. In this study, a series of synthetic 7-methoxy-indolizine derivatives were synthesised, characterised and evaluated for in vitro whole-cell anti-tuberculosis (TB) screening against susceptible (H37Rv) and multi-drug-resistant (MDR) strains of Mycobacterium tuberculosis (MTB) using the resazurin microplate assay method. The cytotoxicity was evaluated using the MTT assay. In silico molecular-docking study was conducted for compounds 5a-j against enoyl-[acyl-carrier] protein reductase, a key enzyme of the type II fatty acid synthesis that has attracted much interest for the development of novel anti-TB compounds. Thereafter, molecular dynamic (MD) simulation was undertaken for the most active inhibitors. Compounds 5i and 5j with the methoxy functional group at the meta position of the benzoyl group, which was at the third position of the indolizine nucleus, demonstrated encouraging anti-TB activity against MDR strains of MTB at 16 μg/mL. In silico studies showed binding affinity within the range of 7.07-8.57 kcal/mol, with 5i showing the highest binding affinity. Hydrogen bonding, π-π- interactions, and electrostatic interactions were common with the active site. Most of these interactions occurred with the catalytic amino acids (Pro193, Tyr158, Phe149, and Lys165). MD simulation showed that 5j possessed the highest binding affinity toward the enzyme, according to the two calculation methods (MM/PBSA and MM/GBSA). The single-crystal X-ray studies of compounds 5c and 5d revealed that the molecular arrangements in these two structures were mostly guided by C-H···O hydrogen-bonded dimeric motifs and C-H···N hydrogen bonds, while various secondary interactions (such as π···π and C-H···F) also contributed to crystal formation. Compounds 5a, 5c, 5i, and 5j exhibited no toxicity up to 500 μg/mL. In conclusion, 5i and 5j are promising anti-TB compounds that have shown high affinity based on docking and MD simulation results.
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