Article
Thermodynamics
Nikolaos Kateris, Rui Xu, Hai Wang
Summary: This study investigates the binding energies and HOMO-LUMO energy gaps of metal-aromatic complexes using density functional theory calculations. The results show that the binding of metals with aromatic compounds can significantly reduce their energy gaps.
COMBUSTION AND FLAME
(2023)
Article
Chemistry, Physical
Sania Bibi, Sehrish Sarfaraz, Muhammad Yar, Muhammad Iqbal Zaman, Abdul Niaz, Ayesha Khan, Muhammad Ali Hashmi, Khurshid Ayub
Summary: Density functional theory and Time Dependent Density functional theory calculations were used to study the interaction between sulfide ion and different functionalized single wall carbon nanotubes. The results showed that the sidewall functionalized COOH+NH2-SWCNT has a higher sensing ability towards sulfide ion.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Chemistry, Physical
Fazilath A. Basha, F. Liakath Ali Khan, S. Muthu, M. Raja
Summary: This study investigates the structural, wavefunctional, electronic, and charge transfer properties of 8-Quinolinesulfonamide using DFT tools, including the analysis of monomer and dimer forms. Calculated energies of HOMO and LUMO represent electron excitation properties, while MEP analysis identifies electrophilic and nucleophilic sites. Spectroscopic wavenumbers, UV-Visible spectrum, natural bond orbital analysis, as well as druglikeness and molecular docking studies were also conducted.
COMPUTATIONAL AND THEORETICAL CHEMISTRY
(2021)
Article
Chemistry, Physical
S. Janani, Hemamalini Rajagopal, S. Muthu, S. Aayisha, M. Raja
Summary: In this study, spectroscopic investigations were used to characterize 1-Benzyl-4-(N-Boc-amino)piperidine, and its molecular structure, vibrational frequencies, conformational preferences were studied using Density Functional Theory. The compound's anticancer activity and performance on different protein targets were also investigated, along with other properties such as HOMO-LUMO bandgap energy and electron excitation analysis.
JOURNAL OF MOLECULAR STRUCTURE
(2021)
Article
Chemistry, Physical
Shyama Charan Mandal, Frank Abild-Pedersen
Summary: The design of heterogeneous catalysts can be accelerated by identifying relevant descriptors that link binding and activation energies to reactivity. This study investigated scaling relations between binding energies of various hydrocarbon-based adsorbates on different Pt surfaces and metal binding energies estimated via the alpha-scheme model. The findings show that the binding energies of certain groups of adsorbates can be used to predict the binding energies of more complex hydrocarbon-based adsorbates.
Article
Chemistry, Physical
Ravi Trivedi, Vikash Mishra
Summary: In this study, the structural stability and electronic properties of transition metal doped germanium cages were investigated using density functional theory. It was found that 4d transition metals result in more stable structures compared to 3d transition metals, and different charge transfer mechanisms were observed.
JOURNAL OF MOLECULAR STRUCTURE
(2021)
Article
Chemistry, Physical
Ying Gao, Chenglin Sun, Tan Su
Summary: In this study, the stability of TADF devices was improved by introducing tert-butyl and phenyl into the peripheral position of carbazole. The TADF property was judged through specific HOMO-LUMO overlap calculation. By designing positional isomers combining tert-Butyl-substituted carbazole with different acceptors, potential TADF emitters were identified based on HOMO-LUMO overlap calculation. The results suggest that HOMO-LUMO overlap can be used to identify promising synthetic motifs for TADF candidates among structural isomers.
JOURNAL OF MOLECULAR STRUCTURE
(2023)
Article
Biochemistry & Molecular Biology
Ahmed M. Deghady, Rageh K. Hussein, Abdulrahman G. Alhamzani, Abeer Mera
Summary: This study conducted a descriptive investigation on 1-(4-Hydroxyphenyl)-3-phenylprop-2-en-1-one compound using density functional theory, revealing its high chemical reactivity and antibacterial activity through quantum chemical parameters and molecular docking. The optimized molecular structure and computed vibrational frequencies were validated with experimental data, showing a significant role of the carbonyl group in the molecule's strong antibacterial activity.
Article
Biochemistry & Molecular Biology
B. Keshav Rao
Summary: In this study, the stability and electronic properties of bio-hybrid molecules were investigated using first-principles density functional theory. The interactions between a (ZnO) (12) nano-cluster and arginine/aspartic acid showed higher stability, providing insights for the development of drugs for wound healing and bone dysfunction treatment.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biology
Moola M. Nyambe, Edet F. Archibong, Kazhila C. Chinsembu
Summary: This study presents electronic structure calculations of xerantholide, a sesquiterpene lactone with anti-gonorrhea and anti-plasmodium activities. The interaction of xerantholide with Neisseria gonorrhoeae carbonic anhydrase was observed through molecular docking, and a biomimetic model study was also conducted. The results suggest that xerantholide has potential as an inhibitor for Neisseria gonorrhoeae carbonic anhydrase.
COMPUTATIONAL BIOLOGY AND CHEMISTRY
(2022)
Article
Chemistry, Physical
Kimihiko Hirao, Takahito Nakajima, Bun Chan
Summary: The study extended Slater's transition state concept to approximate total energy differences using three orbital energies; numerical validation showed accurate reproduction of Delta SCF values; while the current method has some limitations, it contributes to an improved understanding of SCF-type orbital theories.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Multidisciplinary
Ismail Celik, Meryem Erol, Gulcan Kuyucuklu
Summary: In this study, the antimicrobial activities of synthesized 2-(substituted)oxazolo[4,5-b]pyridine derivatives against various bacteria, fungi, and drug-resistant isolates were investigated. Molecular docking and dynamics simulations were performed to evaluate the interactions at the DNA gyrase enzyme ATP binding site. The predicted ADME profiles of the compounds were compliant with Lipinski and other restrictive rules.
NEW JOURNAL OF CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Fortunatus C. Ezebuo, Ikemefuna C. Uzochukwu
Summary: Schistosomiasis is a neglected disease with significant health impact in tropical and subtropical regions. Current treatment options using praziquantel or oxamniquine have limitations due to resistance or tolerance. This study used molecular docking and dynamics simulations to predict potential antischistosomal drugs, with tolmetin and diflunisal showing promising binding energies.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Integrative & Complementary Medicine
Akachukwu Ibezim, Emmanuel Onah, Ebubechukwu N. Dim, Fidele Ntie-Kang
Summary: This study explores the repositioning of approved drugs for psoriasis treatment by docking them against anti-psoriatic targets, revealing that some antiviral and anticancer drugs may have anti-psoriatic effects with high binding affinity.
BMC COMPLEMENTARY MEDICINE AND THERAPIES
(2021)
Article
Biology
Ralf Schmauder, Thomas Eick, Eckhard Schulz, Guenther Sammler, Elmar Voigt, Guenter Mayer, Holger Ginter, Guenter Ditze, Klaus Benndorf
Summary: By using a microfluidic chip-based technique, we have developed a method for studying ion currents and fluorescence signals in order to measure the kinetics of channel activation and deactivation, as well as ligand binding and unbinding. This approach allows for the rapid generation of concentration-activation relationships and activation kinetics, while minimizing the effects of interference.
COMMUNICATIONS BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Elena Sthephanie Castro-Silva, Martiniano Bello, Martha Cecilia Rosales-Hernandez, Jose Correa-Basurto, Maricarmen Hernandez-Rodriguez, Daniel Villalobos-Acosta, Juan Vicente Mendez-Mendez, Alan Estrada-Perez, Jesus Murillo-Alvarez, Mauricio Munoz-Ochoa
Summary: This study found that fucosterol extracted from an algal source has inhibitory effects on A beta(1-42) aggregation, which could potentially prevent the development of Alzheimer's disease.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2021)
Article
Biochemistry & Molecular Biology
M. J. Fragoso-Vazquez, D. Mendez-Luna, M. C. Rosales-Hernandez, G. R. Luna-Palencia, A. Estrada-Perez, Benedicte Fromager, I Vasquez-Moctezuma, J. Correa-Basurto
Summary: The study evaluated the hybrid compound Gln-VPA using various methods, showing its anti-proliferative effects and inhibition of glutaminase activity in HeLa cells. LC-MS metabolomics studies indicated that Gln-VPA and DON have different biological targets in the cell death mechanism.
MOLECULAR DIVERSITY
(2021)
Article
Biochemistry & Molecular Biology
Alberto Martinez-Munoz, Jose Correa-Basurto, Martiniano Bello
Summary: In this study, the mechanism of how indomethacin forms complexes with folate-G4-PAMAM dendrimer was explored using ligand diffusion molecular dynamic simulations (LDMDSs) and molecular mechanics-generalized-born surface area (MMGBSA) approach. The results showed that the folate-G4-PAMAM dendrimer can bind indomethacin more effectively, indicating better encapsulation.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Correction
Multidisciplinary Sciences
Leonardo David Herrera-Zuniga, Liliana Marisol Moreno-Vargas, Luck Ballaud, Jose Correa-Basurto, Diego Prada-Gracia, David Pastre, Patrick A. Curmi, Jean Michel Arrang, Rachid C. Maroun
SCIENTIFIC REPORTS
(2021)
Article
Chemistry, Medicinal
David Mendez-Luna, Loreley Araceli Morelos-Garnica, Juan Benjamin Garcia-Vazquez, Martiniano Bello, Itzia Irene Padilla-Martinez, Manuel Jonathan Fragoso-Vazquez, Alfonso Duenas Gonzalez, Nuria De Pedro, Jose Antonio Gomez-Vidal, Humberto Lubriel Mendoza-Figueroa, Jose Correa-Basurto
Summary: The study designed and synthesized three new compounds with high affinity for the GPER binding site, which showed growth inhibitory activity in cancer cell lines without side effects. In silico studies revealed the binding modes and energetic features of the compounds on GPER, indicating potential for new compounds with growth inhibitory activities against nonconventional GPER cell models.
Article
Multidisciplinary Sciences
Yudibeth Sixto-Lopez, Jose Correa-Basurto, Martiniano Bello, Bruno Landeros-Rivera, Jose Antonio Garzon-Tiznado, Sarita Montano
Summary: The SARS-CoV-2 virus has three lineages circulating worldwide, two of which have been found with three mutations among the Mexican population; these mutations significantly affect the structural behavior of the S protein and its binding with inhibitors; further experimental studies are needed to explore the clinical implications of these effects.
SCIENTIFIC REPORTS
(2021)
Review
Biochemistry & Molecular Biology
Leticia Guadalupe Fragoso-Morales, Jose Correa-Basurto, Martha Cecilia Rosales-Hernandez
Summary: Alzheimer's disease is a major human dementia characterized by memory loss associated with oxidative stress in brain cells. Overexpression of NADPH oxidase in AD leads to the production of large amounts of reactive oxygen species, damaging brain cells and vasculature, making it a potential therapeutic target for AD.
Article
Cell Biology
Yudibeth Sixto-Lopez, Emilie Marhuenda, Juan Benjamin Garcia-Vazquez, Manuel Jonathan Fragoso-Vazquez, Martha Cecilia Rosales-Hernandez, Oscar Zacarias-Lara, David Mendez-Luna, Jose Antonio Gomez-Vidal, David Cornu, Bakalara Norbert, Jose Correa-Basurto
Summary: Glioblastoma multiforme accounts for 70% of primary malignancies of the central nervous system, with a median survival after treatment of around 15 months. Research has identified HDAC inhibitors as showing antiproliferative properties in 3D cultures, suggesting they may be a key target for future therapeutic studies.
CELLULAR AND MOLECULAR NEUROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Ozvaldo Linares-Anaya, Alcives Avila-Sorrosa, Francisco Diaz-Cedillo, Luis Angel Gil-Ruiz, Jose Correa-Basurto, Domingo Salazar-Mendoza, Adrian L. Orjuela, Jorge Ali-Torres, Maria Teresa Ramirez-Apan, David Morales-Morales
Summary: Two benzo[d][1,3]azoles 2-substituted with benzyl- and allyl-sulfanyl groups, BTA-1 and BMZ-2, showed promising cytotoxic activities against six human cancer cell lines in vitro. BMZ-2 exhibited comparable inhibitory effects to tamoxifen in some cases and displayed low cytotoxicity against healthy cells. Computational molecular docking studies revealed the affinity and possible interactions of both compounds with the tamoxifen binding site on ER alpha and GPER receptors.
Article
Multidisciplinary Sciences
R. Flores-Mejia, M. J. Fragoso-Vazquez, L. G. Perez-Blas, A. Parra-Barrera, S. S. Hernandez-Castro, A. R. Estrada-Perez, J. Rodrigues, E. Lara-Padilla, A. Ortiz-Morales, J. Correa-Basurto
Summary: The study investigates the chemical structure, cytotoxicity, and antiproliferative effects of G4-PAMAM, as well as its intracellular localization in the HMC-1 and K-562 cell lines. The results show that G4-PAMAM generates multivalent mass spectrum values and exhibits antiproliferative activity in both tumor cell lines. Additionally, the dendrimers were found in the cytoplasm and nucleus of the studied tumor cells.
SCIENTIFIC REPORTS
(2021)
Article
Genetics & Heredity
Elvia C. Mendoza-Caamal, Francisco Barajas-Olmos, Elaheh Mirzaeicheshmeh, Ian Ilizaliturri-Flores, Carlos A. Aguilar-Salinas, Donaji V. Gomez-Velasco, Isabel Ciceron-Arellano, Adriana Resendiz-Rodriguez, Angelica Martinez-Hernandez, Cecilia Contreras-Cubas, Sergio Islas-Andrade, Carlos Zerrweck, Humberto Garcia-Ortiz, Lorena Orozco
Summary: This study identified two novel variants of DYRK1B associated with AOMS3, demonstrating classic dominant autosomal inheritance with full penetrance. It also revealed age-dependent variable expressivity, with different metabolic phenotypes appearing at different stages of life. Early diagnosis and intervention for monogenic forms of metabolic diseases are important to prevent symptoms and complications.
ORPHANET JOURNAL OF RARE DISEASES
(2021)
Article
Chemistry, Medicinal
Astrid Rivera-Antonio, Martha Cecilia Rosales-Hernandez, Irving Balbuena-Rebolledo, Jose Martin Santiago-Quintana, Jessica Elena Mendieta-Wejebe, Jose Correa-Basurto, Juan Benjamin Garcia-Vazquez, Efren Venancio Garcia-Baez, Itzia I. Padilla-Martinez
Summary: A novel synthesis method for (E)-2-hydroxy-alpha-aminocinnamic acids was reported, demonstrating their antioxidant properties and ability to scavenge free radicals, inhibit MPO, with low cytotoxicity. The compounds show promising potential for further exploration as therapeutic agents for chronic diseases related to MPO activity.
Article
Medicine, Research & Experimental
Monserrat I. Morales-Rivera, Radames Alemon-Medina, Angelica Martinez-Hernandez, Josefina Gomez-Garduno, Elaheh Mirzaeicheshmeh, Nelly F. Altamirano-Bustamante, Ian Ilizaliturri-Flores, Elvia C. Mendoza-Caamal, Maria G. Perez-Guille, Raquel Garcia-Alvarez, Cecilia Contreras-Cubas, Federico Centeno-Cruz, Cristina Revilla-Monsalve, Humberto Garcia-Ortiz, Francisco Barajas-Olmos, Lorena Orozco
Summary: Genetic factors affecting metformin response variability have been poorly studied in the Latin American population, with a specific variant in the MATE1 gene being more common in Mexicans and possibly of Amerindian origin. This variant was associated with increased blood metformin levels, suggesting a potential need for pharmacogenetic considerations in populations with a high frequency of this risk genotype.
BIOMEDICINE & PHARMACOTHERAPY
(2021)
Article
Environmental Sciences
Maria del Carmen Cuevas-Diaz, Fernando Rafael Ramos-Morales, Alejandro Castro-Luna, Dinora Vazquez-Luna, Sergio Martinez-Hernandez, Oswaldo Guzman-Lopez, Joel Zavala-Cruz, Angel Ortiz-Ceballos
Summary: This study found that the tropical endogeic earthworm Pontoscolex corethrurus and oil palm bagasse can synergistically remove petroleum hydrocarbons from crude oil-contaminated soil effectively.
BULLETIN OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY
(2022)
Review
Neurosciences
Cindy Bandala, Jose Luis Cortes-Altamirano, Samuel Reyes-Long, Eleazar Lara-Padilla, Ian Ilizaliturri-Flores, Alfonso Alfaro-Rodriguez
Summary: The recent COVID-19 pandemic caused by SARS-CoV-2 has affected many countries and could potentially infect a significant portion of the world population. The virus enters cells through the ACE2 receptor and can cause respiratory and neurological symptoms, with potential long-term consequences for patients.
ACTA NEUROBIOLOGIAE EXPERIMENTALIS
(2021)
Article
Chemistry, Physical
B. P. Akhouri, R. Perween, J. R. Solana
Summary: Monte Carlo simulations are used to obtain the equation of state and internal energy of fluids with Mie n-m potentials, and its performance is tested against a third order perturbation theory. The theory is then applied to tune the potentials for real fluids and achieve accurate fit with experimental data.
MOLECULAR SIMULATION
(2024)
Article
Chemistry, Physical
Malaisamy Veerapandian, Nagarajan Hemavathy, Alagesan Karthika, Jayaraman Manikandan, Umashankar Vetrivel, Jeyaraman Jeyakanthan
Summary: This study investigates the conformational stability and flexibility of SpeB enzyme and its interactions with substrate. The research finds that neutral pH 7 and alkaline pH 11 are the optimal conditions for stable binding between SpeB and substrate.
MOLECULAR SIMULATION
(2024)
Article
Chemistry, Physical
Maipelo Nyepetsi, Olayinka A. Oyetunji, Foster Mbaiwa
Summary: Biodiesel, a potential alternative to fossil-based fuels, has limitations such as high viscosity, pour point, and cloud point. This study used ReaxFF molecular dynamics to investigate the decarboxylation of methyl palmitate using different catalysts. The presence of alpha-NiMoO4 and beta-NiMoO4 accelerated the reactions and resulted in higher quantities of stable products. Ni3Mo catalyst showed an initial rapid formation of products followed by a decrease. All reactions followed first-order kinetics, and the catalysts reduced the activation energies.
MOLECULAR SIMULATION
(2024)