Zeina Hobaika

Saint Joseph University | USJ · Life and Earth Sciences Department

Long oligomer sequences, rich in guanine and cytosine, such as c-kit1 and the HIV-1 LTR-III sequence, are prevalent in oncogenes and retroviruses and play crucial roles in cancer. Understanding the conformational dynamics of such guanine quadruplexes and identifying druggable regions are therefore essential for developing new inhibition strategies....

Lignocellulosic is a carbon source biomass composed of cellulose, hemicelluloses, and lignin, which are strongly associated with each other. This fact makes them hardly degradable by produced microbial enzymes when introduced to compost piles. To address this problem, a primary single or combined pretreatment method of this biomass allows for the s...

Poultry waste is rich in organic matter, which allows its treatment by the process of anaerobic digestion (AD) to reinforce economic and environmental green strategies. The aim of this study is to assess the technical feasibility of poultry waste AD in semi-continuous mode and to intensify methane production by co-digestion with physico-chemical sl...

Poultry waste are rich in organic matter, allowing its use as substrates for biogas production by anaerobic digestion (AD). The major difficulty in the anaerobic digestion of this protein-rich waste is the ammonia inhibition. Different results of biochemical methane potential (BMP) were obtained after the mesophilic anaerobic digestion of different...

Several fecal and enteric pathogens are present within the primary organic raw materials that are introduced to compost piles. These pathogens may compete with the existing microbiota and limit their efficiency, yielding only partial decomposition of the final compost. These pathogens also affect the process kinetics and persist in the final compos...

Grape seeds are the wineries’ main by-products, and their disposal causes ecological and environmental problems. In this study seeds from the pomace waste of autochthonous grape varieties from Lebanon, Obeidi (white variety) and Asswad Karech (red variety) were used for a multi-step biomass fractionation. For the first step, a lipid extraction was...

Focusing on the Middle East and North Africa (MENA) region, which comprises some of the world’s richest countries next to some of the poorest, this book offers excellent insights into the discriminatory consequences of the COVID-19 pandemic. With a geographic focus on the MENA region, the multidisciplinary case studies collected in this edited vol...

Following our previous work (Chem. Sci. 2021, 12, 4889−4907), we study the structural dynamics of the SARS-CoV-2 Main Protease dimerization interface (apo dimer) by means of microsecond adaptive sampling molecular dynamics simulations (50 μs) 10 using the AMOEBA polarizable force field (PFF). This interface is structured by a complex H-bond network...

Following our previous work (Chem. Sci., 2021, 12, 4889 – 4907), we study the structural dynamics of the SARS-CoV-2 Main Protease dimerization interface (apo dimer) by means of microsecond adaptive sampling molecular dynamics simulations (50 microseconds) using the AMOEBA polarizable force field (PFF). This interface is structured by a complex H-bo...

Following our previous work (Chem. Sci., 2021, 12, 4889 – 4907), we study the structural dynamics of the SARS-CoV-2 Main Protease dimerization interface (apo dimer) by means of microsecond adaptive sampling molecular dynamics simulations (50 microseconds) using the AMOEBA polarizable force field (PFF). This interface is structured by a complex H-bo...

Treatment and management of lactoserum from dairy industry has become a global issue. In fact, generated effluents have high organic loads (lactose, protein, vitamin, minerals ... etc.) constituting a major source of environmental pollution. In a sustainable green approach, anaerobic digestion is considered a promising solution for the treatment of...

The HIV-1 integrase (IN) is a major target for the design of novel anti-HIV inhibitors. Among these, three inhibitors which embody a halobenzene ring derivative (HR) in their structures are presently used in clinics. High-resolution X-ray crystallography of the complexes of the IN-viral DNA transient complex bound to each of the three inhibitors sh...

The HIV-1 integrase (IN) is a major target for the design of novel anti-HIV inhibitors. Among these, three inhibitors which embody a halobenzene ring derivative (HR) in their structures are presently used in clinics. High-resolution X-ray crystallography of the complexes of the IN-viral DNA transient complex bound to each of the three inhibitors sh...

Using polarizable (AMOEBA) and non-polarizable (CHARMM) force fields, we compare the relative free energy stability of two extreme conformations of the HIV-1 NCp7 nucleocapsid that had been previously experimentally advocated to prevail in solution. Using accelerated sampling techniques, we show that they differ in stability by no more than 0.75-1....

The Human Immunodeficiency Virus Type 1 nucleocapsid 7 (NCp7) is a multi-functional protein formed by N-terminal and C-terminal domains surrounding two Zn-fingers, linked by a stretch of basic residues, which play a key role in the viral replica-tion. We report the first NCp7 polarizable molecular dynamics (MD) study using the AMOEBA force field co...

The Human Immunodeficiency Virus Type 1 nucleocapsid 7 (NCp7) is a multi-functional protein formed by N-terminal and C-terminal domains surrounding two Zn-fingers, linked by a stretch of basic residues, which play a key role in the viral replica-tion. We report the first NCp7 polarizable molecular dynamics (MD) study using the AMOEBA force field co...

Three integrase strand transfer inhibitors are in intensive clinical use, raltegravir (RAL), elvitegravir (EVG) and dolutegravir (DTG). The onset of integrase resistance mutations limits their therapeutic efficiency. As put forth earlier, the drug affinity for the intasome could be improved by targeting preferentially the retroviral nucleobases, wh...

The HIV-1 integrase (IN) is a major target for the design of novel anti-HIV inhibitors. Among these, three inhibitors which embody a halobenzene ring derivative (HR) in their structures are presently used in clinics. High-resolution X-ray crystallography of the complexes of the IN-viral DNA transient complex bound to each of the three inhibitors sh...

Three Integrase (IN) strand transfer inhibitors are in intensive clinical use, raltegravir, elvitegravir anddolutegravir. However, the onset of IN resistance mutations limits their therapeutic efficiency. As put forth earlier, the drug affinity for the intasome could be improved by targeting preferentially the retroviralnucleobases, which are littl...

Three Integrase (IN) strand transfer inhibitors are in intensive clinical use, raltegravir, elvitegravir anddolutegravir. However, the onset of IN resistance mutations limits their therapeutic efficiency. As put forth earlier, the drug affinity for the intasome could be improved by targeting preferentially the retroviralnucleobases, which are littl...

Organic waste generation is constantly increasing due to industrialization and various treatment processes. Nowadays, anaerobic digestion, as a green technology, is widely used to convert organic waste, into methane, and subsequently, into bioenergy. In this study, our main objective was to evaluate the feasibility of applying anaerobic digestion t...

Coffee is one of the most popular beverages in the world. Over 50% of this mass is discarded after use, becoming a significant waste source known as spent coffee grounds (SCG). SCG usage as a raw material for biogas production emerges with great potential. In this study, we investigated the biochemical composition of SCG and its potential as a gree...

In the present study, nine different varieties of deseeded grape pomace were analyzed for the biochemical composition of the raw material (total solids, volatile matter, total chemical oxygen demand, cellulose, hemicellulose, lignin, total soluble compounds and polyphenols). The biological methane potential of the substrates was assessed in batch a...

To optimize the anaerobic digestion of grape pomace under mesophilic conditions, continuous digesters were operated at different hydraulic retention times (HRT) (30, 20, 15 and 10 days) equivalent to organic loading rates (OLR) of 2.5, 3.7, 5.7 and 7.3 kg COD m(-3) d(-1), respectively. At HRTs of 30 and 20 days, steady state conditions were observe...

The present invention relates to a novel monoclonal antibody, or the derived compounds or functional fragments of same, capable of binding to HIV-1 Integrase (IN). More particularly, the invention relates to a monoclonal antibody, termed 4C6, which reacts with a specific epitope on the catalytic core domain of the IN molecule as well as their use f...

The lignocellulosic structure of grape pomace requires the use of pretreatments facilitating microbial decomposition of the matter and enhancing methane production. In this study, the effects of various pretreatments (freezing, alkaline treatment using NaOH and NH3, acid treatment using HCl, ultrasounds and pulsed electric fields) were investigated...

In the context of the SIBFA polarizable molecular mechanics/dynamics (PMM/PMD) procedure, we report the calibration and a series of validation tests for the 1,2,4-triazole-3-thione (TZT) heterocycle. TZT acts as the chelating group of inhibitors of di-zinc metallo-beta-lactamases (MBL), an emerging class of Zn-dependent bacterial enzymes, which by...

A correct representation of the short-range contributions such as exchange-repulsion (Erep) and charge-transfer (Ect) is essential for the soundness of separable, anisotropic polarizable molecular mechanics potentials. Within the context of the SIBFA procedure, this is aimed at by explicit representations of lone pairs in their expressions. It is n...

The development and the use of vegetal biomasses as energy source are currently encouraged worldwide, as part of a sustainable valorization of biomass resources in a future bio-based economy. In this context, anaerobic digestion is one of the key elements in the current energy transition. In our research, we have focused on the byproducts of winema...

The Human Immunodeficiency Virus-1 integrase is responsible for the covalent insertion of a newly synthesized double-stranded viral DNA into the host cells, and is an emerging target for antivirus drug design. Raltegravir (RAL) and elvitegravir (EVG) are the first two integrase strand transfer inhibitors used in therapy. However, treated patients e...

Grape harvest date is determined according to the technological and phenolic maturities. These parameters were calculated for different red grape (Vitis vinifera L.) varieties (Cabernet Sauvignon, Merlot, Syrah, Cabernet Franc) over four years () (642 samples). Titratable acidity and sugar content of the grapes were used to determine the technologi...

Anaerobic digestion (AD) of agricultural wastes represents a key element in the implementation of a sustainable approach contributing to green energy applications and to waste valorization as biogas and fertilizer sources. In our research, we have focused on the byproducts of winemaking, in particular grape pomace (GP). Our recent results demonstra...

HIV-1 integrase (IN) inserts viral DNA in the host cells in two steps: the 3'-processing (3'-P) and the strand transfer (ST). The efficiency of the first integrase strand transfer inhibitors (INSTIs) raltegravir (RAL) and elvitegravir (EVG) is limited by the rapid occurrence of integrase mutations. However, the recently approved dolutegravir (DTG)...

Food byproducts valorization practices have gained much attention lately as a means of sustainable management, which can increase the profit for local economies. So far, these materials constitute an underexploited source for the recovery and production of natural compounds for food and other multiple industrial applications. The annual production...

Our work aims to perform a green valorization of vine shoots, effective on economic, industrial, environmental, safety and health levels. In fact, applying the principles of green chemistry on the extraction of phenolic compounds from vine shoots helps minimize the environmental and health impact resulting from the use of solvents in chemical produ...

In this study, we have estimated the biogas and methane production from grape pomace (variety Cabernet Franc). The physical and chemical characteristics of the raw material were determined, and the structural polysaccharides were identified and analyzed by the Van Soest method. Batch anaerobic digestions were carried out to assess the methane produ...

Our work aims to perform a green valorization of vine shoots, effective on economic, industrial, environmental, safety and health levels. In fact, applying the principles of green chemistry on the extraction of phenolic compounds from vine shoots helps minimize the environmental and health impact resulting from the use of solvents in chemical produ...

Food byproducts valorization practices have gained much attention lately as a means of sustainable management, which can increase the profit for local economies. So far, these materials constitute an underexploited source for the recovery and production of natural compounds for food and other multiple industrial applications. The annual production...

We recently reported that viral DNA could be the primary target of raltegravir (RAL), an efficient anti-HIV-1 drug, which acts by inhibiting integrase. To elucidate this mechanism, we conducted a comparative analysis of RAL and TB11, a diketoacid abandoned as an anti-HIV-1 drug for its weak efficiency and marked toxicity, and tested the effects of...

The development and the use of vegetal biomasses as energy source are currently encouraged in the European Union in the context of the European Directive 2003/30/CE. Anaerobic digestion is a promising and potent approach for the sustainable valorization of biomass resources in a future bio-based economy. In our research, we have focused on the by-p...

The extraction of polyphenols from vine shoots was conducted with conventional solid liquid (CSL) processes and innovative technologies such as high-voltage electrical discharges (HVED), pulsed electric fields (PEF) and ultrasounds (US). Several solvents and extraction techniques were tested and their conditions optimized by response surface method...

Integrase (IN) is the retroviral enzyme that catalyzes integration of viral cDNA into the infected cell chromosome. Integration involves two steps: the 3' processing (3'P) of viral DNA in the cytoplasm and the strand transfer (ST) in the nucleus. The DKA (diketoacid) related compounds raltegravir (RAL), elvitegravir (EVG) and dolutegravir have been...

These studies summarize our major findings in terms of vine shoots and grape pomace valorization. Conventional and innovative processes were used for phenolic compounds (PC) extraction. Vine shoots are abundant pruning wastes. Few studies were conducted on PC extraction from these byproducts. As to grape pomaces, these are the major (62%) winemakin...

The CX bond in halobenzenes (XCl, Br) exhibits a dual character, being electron-deficient along the CX direction, and electron-rich on its flanks. We sought to amplify both features by resorting to electron-withdrawing and electron-donating substituents, respectively. This was done by quantum chemistry (QC) computations in the recognition sites of...

In light of their environmental and economic interests, food byproducts have been increasingly exploited and valorized for their richness in dietary fibers and antioxidants. Phenolic compounds are antioxidant bioactive molecules highly present in grape byproducts. Herein, the accelerated solvent extraction (ASE) of phenolic compounds from wet and d...

The C-X bond of halobenzenes (X=Cl, Br) has a dual character, its electron density being depleted in its prolongation and built-up on its sides. We have recently considered three protein or nucleic acid recognition sites of halobenzenes and quantified the energy gains that either electron-attracting substituents or electron-donating ones contribute...

The Human Immunodeficiency Virus-1 (HIV-1) integrase, responsible for the covalent insertion of the newly synthesized double-stranded viral DNA in the host cells, represents an important target of an intense pharmacological research. The first two integrase strand transfer inhibitors approved, by the Food and Drug Administration are raltegravir and...

The current work concerns the optimization process of phenolic compounds solid liquid extraction from grape byproducts at high temperatures and short incubation times. The effect of five experimental parameters (solid-liquid ratio, particle size, time, temperature and solvent mixture) mostly believed to affect the extraction process was undertaken....

02/2014; 5(4):351-360.

Halogenated compounds are gaining an increasing importance in medicinal chemistry and materials science. Ab initio quantum chemistry (QC) has unraveled the existence of a "sigma hole" along the CX (X = F, Cl, Br, I) bond, namely, a depletion of electronic density prolonging the bond, concomitant with a build-up on its sides, both of which are enha...

Integration of HIV DNA into host chromosome requires a 3'-processing (3'-P) and a strand transfer (ST) reactions catalyzed by virus integrase (IN). Raltegravir (RAL), commonly used in AIDS therapy, belongs to the family of IN ST inhibitors (INSTIs) acting on IN-viral DNA complexes (intasomes). However, studies show that RAL fails to bind IN alone,...

Binding of oligonucleotides to raltegravir. Titration data for LTR32 (black) and LTR34 (red) and corresponding Kds are obtained from fluorescence intensity in so called reverse experiments. The spectra of raltegravir recorded at different LTR34 concentrations are given in insert. (TIF)

UV-absorption analysis of oligonucleotides and raltegravir free and in complexes. (A) Spectra of RAL (80 µM, in red) and LTR32 (10 µM, in black) in phosphate buffer pH 6, I = 0.05, MgCl2 5 mM final concentration. (B) Spectra of RAL 20 µM, (black), in complex with LTR32 (1 µM, red), LTR32 (5 µM, blue) and LTR32 (10 µM, green). (TIF)

Aim HIV integrase (IN) is a privileged target for antiviral treatments. These induce the emergence of resistant strains, prompting the search of new drugs. To better understand the relationships between structure and function of IN and identify new anti-HIV inhibitors we prepared antibodies recognizing the IN a4 helix that binds viral DNA ends and...

Trois enzymes virales régissent le cycle réplicatif du VIH-1 : la transcriptase inverse, la protéase et l’intégrase (IN). Toutes trois sont des cibles privilégiées de médicaments anti-SIDA. IN du VIH-1 est une polynucléotidyltransférase de 288 acides aminés. Elle assure l’intégration du génome viral dans le génome cellulaire. La forme active de IN...

HIV-1 integrase (IN) catalyzes integration of viral DNA into cell DNA through 3'-processing of viral DNA and strand transfer reactions. To learn on binding of IN to DNAs and IN inhibition we applied spectroscopy (circular dichroism, fluorescence) in a simplified model consisting in a peptide analogue (K156) of alpha4 helix involved in recognition o...

HIV-1 integrase integrates retroviral DNA through 3′-processing and strand transfer reactions in the presence of a divalent cation (Mg2+ or Mn2+). The α4 helix exposed at the catalytic core surface is essential to the specific recognition of viral DNA. To define group determinants of recognition, we used a model composed of a peptide analogue of th...

Integrase (IN) of the type 1 human immunodeficiency virus (HIV-1) catalyzes the integration of viral DNA into host cellular DNA. We identified a bi-helix motif (residues 149-186) in the crystal structure of the catalytic core (CC) of the IN-Phe185Lys variant that consists of the alpha(4) and alpha(5) helices connected by a 3 to 5-residue turn. The...