Dra. Gerli-Candia, Lorena

2017, Dra. Gerli-Candia, Lorena, Pacheco, A., Salgado-Morán, G., Ramírez-Tagle, R., Glossman-Mitnik, D., Misra, A., de Carvalho-Alcântara, A.

Nonsteroidal anti-inflammatory drugs (NSAIDs) are among the most frequently prescribed drugs and have multiple therapeutic uses. These drugs are predominantly used for the treatment of musculoskeletal diseases because of their analgesic, antipyretic, and antiplatelet activities. Oxicams constitute an interesting class of organic compounds and have been investigated in the search for new analgesic and anti-inflammatory drugs. In the present work, a theoretical investigation of the molecular structure and spectroscopic properties of a series of five oxicams in different solvents was performed using density functional theory (DFT) methods. The geometric optimizations of the oxicams were carried out using the M06 density functional and the CBSB7 basis set. The infrared data were all obtained at the same theoretical level. The UV-Vis absorption and NMR data of some oxicams were calculated using the DFT and CBSB3 basis sets. The analysis of structural parameters, particularly the bond length and spectroscopic data, indicated that interactions occurred between the hydrogen bond types for 4-meloxicam, isoxicam, and normeloxicam. Stereoelectronic interactions caused by the substitution of alkyl groups caused the bond lengths to elongate. Similarly, the substitution of heteroatoms, such as nitrogen, sulfur, or oxygen, increased the bond lengths and angular stresses.

2023, Dra. Gerli-Candia, Lorena, Rasul, Hezha, Vinay-Thomas, Noel, Ghafour, Dlzar, Aziz, Bakhtyar, Salgado, Guillermo, Mendoza-Huizar, L.

The largest threat to civilization since the Second World War is the spread of the new coronavirus disease (COVID-19). Therefore, there is an urgent need for innovative therapeutic medicines to treat COVID-19. Reusing bio-actives is a workable and efficient strategy in the battle against new epidemics because the process of developing new drugs is time-consuming. This research aimed to identify which herbal remedies had the highest affinity for the receptor and assess a variety of them for potential targets to suppress the SARS-CoV-2 Mpro. The use of AutoDock Vina for structure-based virtual screening was done first due to the importance of protein interactions in the development of drugs. Molecular docking was used in the comparative study to assess 89 different chemicals from medicinal herbs. To anticipate their effectiveness against the primary protease of SARS-CoV-2, more analysis was done on the ADMET profile, drug-likeness, and Lipinski’s rule of five. The next step involved three replicas of 100 ns-long molecular dynamics simulations on the potential candidates, which were preceded by calculations of the binding free energy of MM-GBSA. The outcomes showed that Achyrodimer A, Cinchonain Ib, Symphonone F, and Lupeol acetate all performed well and had the highest 6LU7 binding affinities. Using RMSD, RMSF, and protein-ligand interactions, the stability of the protein-ligand complex was assessed. The studies indicate that bioactive substances obtained from herbal medicines may function as a COVID-19 therapeutic agent, necessitating additional wet lab research to confirm their therapeutic potential, efficacy, and pharmacological capacity against the condition.

2016, Dra. Gerli-Candia, Lorena, Sadiki, Y., Bouzzine, S., Bejjit, L., Salgado-Morán, Guillermo, Hamidi, M., Bouachrine, M., Serein-Spirau, F., Lère-Porte, J., Marc-Sotiropoulos, J., Glossman-Mitnik, D.

In this paper, theoretical study using density functional theory (DFT) method (B3LYP level with 6-31G(d,p)) of four novel low band gap acceptor–donor organic materials based on thiophene and phenyl and linked to cyanoacrylic acid as acceptor group are investigated. Different electron side groups were introduced to investigate their effects on the electronic structure; the HOMO, LUMO, gap energy, ionization potentials, electron affinities and open circuit voltage (Voc) of these compounds have been calculated and reported in this paper. The electronic absorption and emission spectra of these dyes are studied by time-dependent density functional theory calculations. A systematic theoretical study of such compound has not been reported as we know. Thus, our aim is first, to explore their electronic and spectroscopic properties on the basis of the DFT quantum chemical calculations. We think that the presented study of structural, electronic and optical properties for these compounds could help in designing more efficient functional photovoltaic organic materials.

2020, Anbazhakan, K., Sadasivam, K., Praveena, R., Salgado, Guillermo, Cardona, Wilson, Glossman- Mitnik, Daniel, Gerli-Candia, Lorena

Derivatives of parent molecules possess similar structural activity which makes them to be the topic of equal interest. In the present work, a naturally occurring acid eugenol and its co derivatives allyl-2-methoxy-4-nitrophenol and 5-Allyl-3-nitrobenzene-1,2-diol are theoretically investigated for their antioxidant role using density functional theory (DFT). Becke’s exchange correlation functional B3LYP and Minnesota functional M062X along with the basis set 6-311++G(d,p) are used to investigate the structural property through geometry optimization, frontier molecular orbital analysis, electrostatic potential analysis, and molecular descriptive parameters. Electron donating capability of the molecules is analyzed using frontier molecular orbital analysis and molecular descriptors. Molecular surface potential analysis facilitated to locate highest and lowest potential regions in these molecules. Hydrogen atom abstraction property (radical scavenging property) of the molecules is studied with the help of hydrogen atom transfer mechanism.

2020, Meneses Olmedo, Lorena Maribel, Cuesta Hoyos, Sebastián, Salgado Moran, Guillermo, Cardona Villada, Wilson, Gerli-Candia, Lorena, Mendoza Huizar, Luis H.

In this study, a computational DFT study was performed to propose a new acid catalyzed mechanism to produce 5HMF from D-Fructose and D-Tagatose. The reactivity and selectivity towards 5HMF formation were analyzed, and the results revealed both saccharides present higher selectivity towards 5HMF with the first dehydration occurring on oxygen 2. Fructose seems to be more reactive than tagatose, although the dehydration process of the different hydroxyl groups on tagatose produces more unstable structures, which can undergo several side reactions. The new mechanism is proposed eliminating the tautomerization step and lowering the activation free energy of the second dehydration step in 21 kcal/mol.

2023, Rasul, Hezha, Khdr-Sabir, Dana, Aziz, Bakhtyar, Salgado, Guillermo, Mendoza-Huizar, L., Belhassan, Assia, Gerli-Candia, Lorena, Cardona-Villada, Wilson, Vinay-Thomas, Noel, Dlzar D. Ghafour

A bacterial biofilm is a cluster of bacterial cells embedded in a self-produced matrix of extracellular polymeric substances such as DNA, proteins, and polysaccharides. Several diseases have been reported to cause by bacterial biofilms, and difficulties in treating these infections are of concern. This work aimed to identify the inhibitor with the highest binding affinity for the receptor protein by screening various inhibitors obtained from Azorella species for a potential target to inhibit dispersin B. This work shows that azorellolide has the highest binding affinity (− 8.2 kcal/mol) among the compounds tested, followed by dyhydroazorellolide, mulinone A, and 7-acetoxy-mulin-9,12-diene which all had a binding affinity of − 8.0 kcal/mol. To the best of our knowledge, this is the first study to evaluate and contrast several diterpene compounds as antibacterial biofilm chemicals. Methods: Here, molecular modelling techniques tested 49 diterpene compounds of Azorella and six FDA-approved antibiotics medicines for antibiofilm activity. Since protein-like interactions are crucial in drug discovery, AutoDock Vina was initially employed to carry out structure-based virtual screening. The drug-likeness and ADMET properties of the chosen compounds were examined to assess the antibiofilm activity further. Lipinski’s rule of five was then applied to determine the antibiofilm activity. Then, molecular electrostatic potential was used to determine the relative polarity of a molecule using the Gaussian 09 package and GaussView 5.08. Following three replica molecular dynamic simulations (using the Schrodinger program, Desmond 2019-4 package) that each lasted 100 ns on the promising candidates, binding free energy was estimated using MM-GBSA. Structural visualisation was used to test the binding affinity of each compound to the crystal structure of dispersin B protein (PDB: 1YHT), a well-known antibiofilm compound.

2021, Meneses, Lorena, Cuesta Hoyos, Sebastián, Salgado Morán, Guillermo, Muñoz C., Patricio, Gerli-Candia, Lorena, Mendoza Huizar, Luis H., Belhassan, Assia

In the present study, we performed a computational study to gain insights on the binding mode and high affinity of pregabalin, its inactive isomer (R-pregabalin) and gabapentin when modulating voltage-gated calcium channels. Quantum chemical descriptors were evaluated at two different levels of theory (ωB97XD and B3LYP-D3) for the three molecules. The results show that the three ligands have similar quantum chemical descriptors, suggesting that the affinity is governed by the binding pose and the ability to access the pocket. The binding mode analysis of pregabalin indicates that it is interacting with 12 residues (6 hydrogen bonds) including Arg217, which is key to pregabalin action mechanism. Our results suggest that the electrostatic interactions and the hydrogen bonds between pregabalin and Arg217 could explain its high affinity, highlighting the importance of Arg217 in the pharmacological action.