Article
Chemistry, Medicinal
Lina S. Prieto Cardenas, Karen A. Arias Soler, Diana L. Nossa Gonzalez, Wilson E. Rozo Nunez, Agobardo Cardenas-Chaparro, Pablo R. Duchowicz, Jovanny A. Gomez Castano
Summary: In this study, virtual methods were used to evaluate naphthoquinone derivatives with unknown antiprotozoal activity, and QSAR models were developed to predict antiparasitic and toxicity activities. Most evaluated ligands showed good antiparasitic activity, with triazole derivatives exhibiting the best affinity with different macromolecular targets. Additionally, most of the compounds were found to be suitable for oral administration according to the ADME results.
Review
Biochemistry & Molecular Biology
Lenci K. Vazquez-Jimenez, Antonio Moreno-Herrera, Alfredo Juarez-Saldivar, Alonzo Gonzalez-Gonzalez, Eyra Ortiz-Perez, Alma D. Paz-Gonzalez, Isidro Palos, Esther Ramirez-Moreno, Gildardo Rivera
Summary: Parasitic diseases caused by protozoa are major public health problems in developing countries. The glycolysis pathway, particularly triose phosphate isomerase (TIM), has been identified as a promising target for developing new antiprotozoal drugs. In this review, the design strategies, structure-activity relationship, and binding modes of TIM inhibitors against various protozoa are discussed. Benzothiazole, benzoxazole, benzimidazole, and sulfhydryl derivatives are highlighted as effective TIM inhibitors. The development of new TIM inhibitors as antiprotozoal drugs is an important pharmaceutical strategy with potential for new therapies for these ancient parasitic diseases.
CURRENT MEDICINAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Wesam S. Qayed, Rafaela S. Ferreira, Jose Rogerio A. Silva
Summary: This study evaluated the targets of SARS-CoV-2 for a set of FDA-approved drugs using computational modeling techniques. Six FDA-approved drugs were identified as promising candidates for anti-SARS-CoV-2 activity, and their binding patterns and affinity were compared to native protein inhibitors. The findings provide molecular-level insights for identifying or designing novel drugs to combat COVID-19.
Article
Chemistry, Physical
Saliha Alyar, Hamit Alyar, Ummuhan Ozdemir Ozmen, Okan Aktas, Kelime Erdem
Summary: New Schiff bases derived from FDA-approved sulfa drugs (L1-L4) were successfully synthesized and characterized using analytical methods such as elemental composition, 1H NMR, 13C NMR, FT-IR, and LC-MS. The anticancer activities of the synthesized ligands were assessed against three human cancer cell lines, and the compound L1 showed the highest anticancer activity. In silico ADME characteristics of the compounds were estimated, and the interactions between the synthesized sulfa compounds and the MDM2 protein were determined, indicating their potential as anticancer medicine candidates.
JOURNAL OF MOLECULAR STRUCTURE
(2023)
Article
Biochemistry & Molecular Biology
Daniel Pushparaju Yeggoni, Shreya Dubey, Yusuf Zamal Mohammad, Aparna Rachamallu, Rajagopal Subramanyam
Summary: The study investigated the interaction between the phytochemical stigmasterol and human serum albumin under physiological conditions, revealing anti-inflammatory and anti-cancer properties of stigmasterol. Stigmasterol bound to a specific subdomain of HSA, altering the protein's secondary structure. Molecular docking and dynamic simulation further supported the binding mechanism between HSA and stigmasterol.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Chemistry, Medicinal
Fatima Doganc, Ismail Celik, Gokcen Eren, Marcel Kaiser, Reto Brun, Hakan Goker
Summary: A series of monocationic new guanidinobenzimidazole derivatives were synthesized and evaluated for their antiparasitic activity against four parasites in vitro. Two compounds showed promising activity against P. Falciparum, and molecular docking studies were conducted to understand the interactions between DNA minor groove and these compounds. All compounds exhibited theoretical ADME profiles conforming to Lipinski's and Ghose's restrictive rules.
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Shalini Mathpal, Tushar Joshi, Priyanka Sharma, Tanuja Joshi, Hemlata Pundir, Veena Pande, Subhash Chandra
Summary: This research aims to identify new drug candidates for the inhibition of the Main protease enzyme of COVID-19 using in silico techniques. By performing molecular docking and molecular dynamics simulation, four potential drugs were discovered among 3180 FDA-approved drugs. These findings provide important leads for the development of novel drugs against COVID-19.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biochemistry & Molecular Biology
Francesco Madeddu, Jessica Di Martino, Michele Pieroni, Davide Del Buono, Paolo Bottoni, Lorenzo Botta, Tiziana Castrignano, Raffaele Saladino
Summary: This study used computational methods to analyze the interaction between two new antitumor drug molecules and hTop1p enzyme. The results showed that these two compounds have a similar inhibitory mechanism to CPT and may have potential antitumor activity.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Endocrinology & Metabolism
Sahar Aldosari, Chukwuebuka Egbuna, Hind Albadrani, Alaa Alshareeda, Kingsley C. Patrick-Iwuanyanwu, Adedokun A. Kamoru, Sikiru O. Imodoye, Eugene N. Onyeike, Sadaf Jahan, Johra Khan
Summary: This study performed molecular docking simulation and ADMET investigations on selected bioactive compounds to identify potential inhibitors/therapeutics against cancer caused by JAK2-STAT5 dysregulation. The top-performing compounds, including hypericin, withanolide, tomatidine, silymarin, baicalin, and diosmin, showed promising binding energies and potential as lead compounds for new drug discovery.
JOURNAL OF BIOLOGICAL REGULATORS AND HOMEOSTATIC AGENTS
(2023)
Article
Biochemistry & Molecular Biology
Gurusamy Sankararaj Senthilkumar, Murugesan Sankarganesh, Jeyaraj Dhaveethu Raja, Paul Raj Adwin Jose, Arumugam Sakthivel, Thayalaraj Christopher Jeyakumar, Radhakrishnan Nandini Asha
Summary: In this study, a novel bidentate morpholine-based Schiff base ligand and its copper(II) and zinc(II) complexes were synthesized and characterized using multiple analytical techniques. The results showed that the ligand and complexes possessed a 1:1 stoichiometric ratio, with the azomethine nitrogen and morpholine ring nitrogen atoms in the ligand coordinating with the metal ions. Furthermore, the Cu(II) and Zn(II) complexes exhibited a square pyramidal geometry. In vitro experiments demonstrated that the Cu(II) and Zn(II) complexes were able to bind to DNA and exhibited good antimicrobial and antioxidant activities. These findings are of significance for the development of new metal complexes and their applications.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biochemistry & Molecular Biology
Leena Hussein Bajrai, Aiah M. Khateb, Maha M. Alawi, Hashim R. Felemban, Anees A. Sindi, Vivek Dhar Dwivedi, Esam Ibraheem Azhar
Summary: This study demonstrates the potential of a diverse set of glycosylated flavonoids as inhibitors of Mtb CYP121. The findings provide a basis for further experimental validation and development of therapies for drug-resistant Mtb strains.
Article
Biochemistry & Molecular Biology
Tanveer A. A. Wani, Ahmed H. H. Bakheit, Seema Zargar, Nojood Altwaijry, Mashooq Ahmad Bhat, Hamad M. M. Alkahtani, Lamees S. S. Al-Rasheed
Summary: The presence of the p-aryl/cyclohexyl ring in the N-(4-aryl/cyclohexyl)-2-(pyridine-4-yl carbonyl) hydrazine carbothioamide derivative (2C) enhances its antifungal properties. This study investigates the interaction of 2C with BSA using spectroscopic methods and molecular docking. The results demonstrate a strong binding interaction between BSA and 2C through hydrogen and van der Waals forces, with binding constants ranging from 2.91 x 10(5) to 1.29 x 10(5).
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Sanda Nastasia Moldovean, Diana-Gabriela Timaru, Vasile Chis
Summary: The D2 dopamine receptor plays a crucial role in modulating dopamine release and radiopharmaceutical ligands are used to quantify dopaminergic pathways in the living human brain. This study used molecular dynamics simulations and QM calculations to investigate the interaction mechanisms and binding affinities between three synthetic compounds and the D2 receptor.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Cell Biology
Tanveer A. A. Wani, Seema Zargar
Summary: One of the top priorities in medicinal chemistry is the discovery of new molecules that have potential as anticancer agents. Compounds that interact with DNA, such as groove binders, alkylators, and intercalators, have shown promise as chemotherapeutic drugs for cancer treatment. This study focused on the anticancer drug 1,3,5-Tris(4-carboxyphenyl)benzene (H3BTB), which binds to DNA through groove binding and has demonstrated significant cytotoxic potential against breast and cervical cancer cell lines. Computational studies, including molecular docking and molecular dynamics simulations, supported the minor groove binding of H3BTB-DNA complex. This research will contribute to further empirical investigation into the synthesis of metallic and non-metallic derivatives of H3BTB and their potential as bioactive molecules for cancer treatment.
Article
Biochemistry & Molecular Biology
Tanuja Joshi, Hemlata Pundir, Subhash Chandra
Summary: In this study, FDA-approved drugs were screened and analyzed to identify potential inhibitors of the essential enzyme CaDHFR in Candida albicans. Paritaprevir, Lumacaftor, and Rifampin showed promising interaction with CaDHFR, suggesting their potential as novel antifungal agents. These drugs could be further explored for repurposing in the treatment of candidiasis.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Chemistry, Medicinal
Alfredo Juarez-Saldivar, Nuria E. Campillo, Eyra Ortiz-Perez, Alma D. Paz-Gonzalez, Emma Saavedra, Gildardo Rivera
Summary: In this study, three ontology-based approaches were used to compare the proteomes of five species of protozoa, leading to the identification of 12 potential drug targets for the development of new broad-spectrum antiprotozoal drugs.
MEDICINAL CHEMISTRY
(2023)
Article
Genetics & Heredity
Karina Janett Juarez-Rendon, Manuel Alejandro Castro-Garcia, Diddier Giovanni Prada-Ortega, Gildardo Rivera, Luz Maria Ruiz-Godoy, Virginia Isabel Enriquez-Carcamo, Miguel Angel Reyes-Lopez
Summary: This study identified five unreported gene variants in the HOXC13 and HOXD13 genes and suggested that two of these variants may be a risk factor for the development of cervical cancer.
Article
Infectious Diseases
Jose Vazquez-Villanueva, Karina Vazquez, Ana Veronica Martinez-Vazquez, Alfredo Wong-Gonzalez, Jesus Hernandez-Escareno, Omar Cabrero-Martinez, Wendy Lizeth Cruz-Pulido, Abraham Guerrero, Gildardo Rivera, Virgilio Bocanegra-Garcia
Summary: This study analyzed 336 samples from a bovine slaughterhouse and found that 83.3% of the samples were positive for E. coli infection. The study revealed that these E. coli isolates exhibited resistance to multiple antibiotics and carried various virulence factors and resistance genes. Therefore, E. coli poses a threat to public health.
Review
Chemistry, Medicinal
Timoteo Delgado-Maldonado, Antonio Moreno-Herrera, Gerard Pujadas, Lenci K. Vazquez-Jimenez, Alonzo Gonzalez-Gonzalez, Gildardo Rivera
Summary: New antiviral therapeutics are essential in combating emerging and re-emerging viral diseases like dengue and Zika. Non-structural protein with methyltransferase activity is a promising target for drug development due to its critical role in virus replication. Various drug strategies have identified potential methyltransferase inhibitors that can bind to the active site. This review analyzes different types of inhibitors and discusses the potential for developing effective antiviral drugs against dengue and Zika.
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Luca De Angelis, Graham C. Haug, Gildardo Rivera, Soumen Biswas, Ammar Al-Sayyed, Hadi Arman, Oleg Larionov, Michael P. Doyle
Summary: One important reaction of 1,2,3-triazines is the inverse electron demand Diels-Alder (IEDDA) cycloaddition with a dienophile, which proceeds through nucleophilic addition to the triazine followed by N-2 loss and cyclization. Previous studies have not provided a comprehensive understanding of the site of nucleophilic addition on the triazine. This study investigated the C-, N-, H-, O-, and S-nucleophilic additions on 1,2,3-triazine and 1,2,3-triazine-1-oxide frameworks and revealed the differentiation of addition at the 4- and 6-positions. Computational studies further examined the factors influencing the outcomes of these reactions.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Organic
Soumen Biswas, Luca De Angelis, Gildardo Rivera, Hadi Arman, Michael P. Doyle
Summary: 1,2,3-Triazine 1-oxides are highly effective substrates for inverse electron demand Diels-Alder reactions. These stable heterocyclic compounds, formed from vinyldiazoacetates via reaction with tert-butyl nitrite, undergo clean nucleophilic addition reactions with amidines to form pyrimidines, with beta-ketocarbonyl compounds and related nitrile derivatives to form polysubstituted pyridines, and with 3/5-aminopyrazoles to form pyrazolo[1,5-a]pyrimidines, in high yields. These reactions, catalyzed by bases, are rapid at room temperature and allow for a range of structural modifications.
Article
Polymer Science
Maria Jimena Martinez, Roi Naveiro, Axel J. Soto, Pablo Talavante, Shin-Ho Kim Lee, Ramon Gomez Arrayas, Mario Franco, Pablo Mauleon, Hector Lozano Ordonez, Guillermo Revilla Lopez, Marco Bernabei, Nuria E. Campillo, Ignacio Ponzoni
Summary: Artificial intelligence (AI) is revolutionizing the discovery of new materials, particularly in the field of virtual screening of chemical libraries. This study developed computational models that can predict the dispersancy efficiency of oil and lubricant additives, a critical property in their design. The proposed models combined machine learning techniques with visual analytics strategies in an interactive tool, aiding domain experts in decision-making. The best-performing model achieved a mean absolute error of 5.50±0.34 and a root mean square error of 7.56±0.47, demonstrating its effectiveness in predicting dispersancy efficiency.
Article
Chemistry, Medicinal
Alonzo Gonzalez-Gonzalez, Citlali Vazquez, Rusely Encalada, Emma Saavedra, Lenci K. K. Vazquez-Jimenez, Eyra Ortiz-Perez, Maria Laura Bolognesi, Gildardo Rivera
Summary: Phenothiazine derivatives have the potential to inhibit trypanothione reductase, an important antioxidant enzyme. A virtual screening of these derivatives identified compounds with higher affinity to the enzyme than the natural ligand trypanothione disulfide. Two compounds, ZINC1033681 and ZINC10213096, showed significant inhibition of parasite growth and acted as mixed-type inhibitors of recombinant TR. This study provides further insights into the potential of phenothiazine derivatives as TR inhibitors.
MOLECULAR INFORMATICS
(2023)
Review
Environmental Sciences
Alejandra Aguilar-Salazar, Ana Veronica Martinez-Vazquez, Guadalupe Aguilera-Arreola, Erick de Jesus de Luna-Santillana, Maria Antonia Cruz-Hernandez, Cesar Marcial Escobedo-Bonilla, Edgar Lara-Ramirez, Mario Sanchez-Sanchez, Abraham Guerrero, Gildardo Rivera, Virgilio Bocanegra-Garcia
Summary: This review aims to provide a comprehensive overview of the current dissemination and characterization of ESKAPE bacteria in surface water and wastewater sources, which display widespread antimicrobial resistance and have significant clinical implications globally.
Review
Chemistry, Medicinal
Carlos Gaona-Lopez, Ana Veronica Martinez-Vazquez, Juan Carlos Villalobos-Rocha, Karina Janett Juarez-Rendon, Gildardo Rivera
Summary: This article mainly discusses the issue of diarrhea caused by Giardia lamblia and points out its harm to children and adults worldwide. Although giardiasis is considered a major disease in low-income and developing countries, current migratory flows have caused an increase in giardiasis cases in high-income countries. This article focuses on the nucleolus of G. lamblia, discusses possible therapeutic targets, and describes some drugs under research that could be effective against this parasite.
Article
Infectious Diseases
Jessica L. Ortega-Balleza, Abraham Guerrero, Graciela Castro-Escarpulli, Ana Veronica Martinez-Vazquez, Maria Antonia Cruz-Hernandez, Erick de Jesus de Luna-Santillana, Erika Acosta-Cruz, Iram Pablo Rodriguez-Sanchez, Gildardo Rivera, Virgilio Bocanegra-Garcia
Summary: The global spread of antimicrobial resistance genes (ARGs) is a significant public health concern, driven primarily by the transfer of mobile genetic elements (MGEs). This study evaluated the whole genome of multidrug-resistant E. coli strains isolated from various sources, and identified numerous ARGs, plasmid replicons, and intact prophages. The findings highlight the high pathogenic potential of these E. coli strains and emphasize the need for monitoring.
TROPICAL MEDICINE AND INFECTIOUS DISEASE
(2023)
Review
Biochemistry & Molecular Biology
Shaila A. Shetu, Nneoma James, Gildardo Rivera, Debasish Bandyopadhyay
Summary: Pancreatic enzymes and hormones like insulin and glucagon are crucial for digestion and blood sugar regulation. However, pancreatic cancer, which often has no early detection method, is highly lethal due to the malfunctioning of the pancreas. The article explores various small molecule inhibitors that can effectively target and inhibit the proteins responsible for pancreatic cancer, shedding light on potential treatments for this dreadful disease.
CURRENT ISSUES IN MOLECULAR BIOLOGY
(2023)
Article
Chemistry, Medicinal
Ana Karen Estrada, Domingo Mendez-Alvarez, Alfredo Juarez-Saldivar, Edgar E. Lara-Ramirez, Ana Veronica Martinez-Vazquez, Juan Carlos Villalobos-Rocha, Isidro Palos, Eyra Ortiz-Perez, Gildardo Rivera
Summary: In this study, a ligand-based virtual screening method was used to identify 15 potential SGLT2 inhibitors from various databases. Molecular dynamics simulation analysis showed that spiroketal derivatives exhibited good stability.
MEDICINAL CHEMISTRY
(2023)