Article
Biochemistry & Molecular Biology
Saeed Ullah, Muhammad Waqas, Sobia Ahsan Halim, Imtiaz Khan, Asaad Khalid, Ashraf N. Abdalla, Hafiz A. Makeen, Aliya Ibrar, Ajmal Khan, Ahmed Al-Harrasi
Summary: This research aims to explore new structural leads for the treatment of type 2 diabetes mellitus by targeting the key carbohydrate catabolic enzyme, alpha-glucosidase. The tested compounds exhibited more potent inhibitory activities on alpha-glucosidase compared to the marketed drug, acarbose. In vitro kinetics studies and in silico molecular docking and simulations supported the findings of the research.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Biochemistry & Molecular Biology
B. S. Ravindranath, S. Vishnu Vinayak, Vivek Chandra Mohan
Summary: Chlamydia felis is a major cause of chronic conjunctivitis in cats without respiratory infections, with zoonotic potential. The emergence of antimicrobial resistance to antibiotics targeting rRNA has complicated the diagnosis and treatment of chlamydial infections, posing challenges for research in this field.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biochemistry & Molecular Biology
Shirin Mollazadeh, Farzin Hadizadeh, Ricardo J. Ferreira
Summary: The study found that the stereochemistry of 1,4-dihydropyridines (DHPs) affects their binding ability with P-glycoprotein (P-gp) and can also impact the permeation and accumulation of drugs in cell membranes. Therefore, the stereochemistry should not be overlooked during the development of novel 1,4-dihydropyridine derivatives.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2021)
Article
Biochemistry & Molecular Biology
Loretta Akakpo, Edward Ntim Gasu, Jehoshaphat Oppong Mensah, Lawrence Sheringham Borquaye
Summary: This study used molecular docking and molecular dynamics simulations to explore the inhibitory activity of some natural products against Plasmodium falciparum dihydrofolate reductase (PfDHFR). Two compounds were found to have stable binding and could be considered as potential antifolate agents.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
Gozde Yalcin-Ozkat, Ronak H. Ersan, Mahmut Ulger, Seda T. Ulger, Serdar Burmaoglu, Ilkay Yildiz, Oztekin Algul
Summary: The increase in drug-resistant strains of Mycobacterium tuberculosis has driven researchers to seek new drug targets. In this study, the antitubercular activity of benzimidazole derivatives was experimentally determined, and molecular docking studies revealed their interaction with the DprE1 enzyme.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
Tanusree Mookherjee, Angshuman Bagchi, Rita Ghosh
Summary: This study reveals a possible molecular mechanism of how the peptide circPPP1R12A can promote cancer by interfering with the Mst pathway. The peptide was found to bind to Mst1/2 proteins, preventing their interactions with Sav1 and inhibiting the activation of the Mst pathway.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Article
Chemistry, Applied
Masoomeh Naseri, Ali Niazi, Kowsar Bagherzadeh, Elahe Konoz, Hamid Reza Samadikhah
Summary: An ultrasensitive electrochemical aptasensor based on modified glassy carbon electrode was developed to detect tetracycline in food samples. Molecular docking and molecular dynamic simulations were used to study the affinity and stability of antibiotics-aptamers complexes. The aptasensor, using kanamycin-specific aptamer, achieved a wide dynamic linear range and low limit of detection for tetracycline in milk samples.
Article
Biochemistry & Molecular Biology
Mahmoud A. A. Ibrahim, Alaa H. M. Abdelrahman, Esraa A. A. Badr, Nahlah Makki Almansour, Othman R. Alzahrani, Muhammad Naeem Ahmed, Mahmoud E. S. Soliman, Mohamed Ahmed Naeem, Ahmed M. Shawky, Peter A. Sidhom, Gamal A. H. Mekhemer, Mohamed A. M. Atia
Summary: In this study, the potential ABCG2 inhibitors NPACT00968 and NPACT01545 were identified through computational screening. Molecular dynamics simulations showed that these two compounds exhibited stable binding to ABCG2 transporter. The results suggest that further experimental investigations are warranted.
MOLECULAR DIVERSITY
(2022)
Article
Chemistry, Physical
Nazanin Dehdasht-Heidari, Behzad Shareghi, Sadegh Farhadian, Lida Momeni
Summary: This study investigates the interaction between safranal and pepsin under physiological conditions, revealing that safranal can alter the structure and function of pepsin, with non-covalent reactions playing a critical role in this interaction.
JOURNAL OF MOLECULAR LIQUIDS
(2021)
Review
Engineering, Chemical
Renata Mikstacka, Zbigniew Dutkiewicz
Summary: CYP1B1 is an important enzyme involved in cardiovascular diseases, hormone-related cancers, and anti-cancer drug resistance. Inhibition of CYP1B1 activity is a potential strategy for cancer prevention and treatment. Research on CYP1B1 in cancer mainly focuses on its interactions with substrates and inhibitors, with computational methods being a key tool for studying these molecular interactions.
Article
Chemistry, Inorganic & Nuclear
Talis Uelisson da Silva, Everton Tomaz da Silva, Karina de Carvalho Pougy, Camilo Henrique da Silva Lima, Sergio de Paula Machado
Summary: A combination of DFT calculations, docking studies, and MD simulations was used to investigate the inhibition of nitric oxide synthase by indazole-3-carboxylic acid and its metal complexes. The results indicated that the strength of the M-OH2 bond decreases with higher biological activity, and the M-ONO- interaction is more effective than M-H2O.
INORGANIC CHEMISTRY COMMUNICATIONS
(2022)
Article
Chemistry, Applied
Lang Chen, Han Yang, Linna Jiao, Pei Pu, Xin Zheng, Guizhao Liang
Summary: In this study, a peptide (VAGTWYSL) derived from 8-LG was screened to inhibit the antigenicity of 8-LG and its mechanism of action was explored. The inhibitory effect of the peptide on the antigenicity of 8-LG was found to be influenced by different experimental conditions, possibly through hydrophobic forces, hydrogen bonds, and structural changes to reduce the allergenicity of 8-LG.
Article
Biochemical Research Methods
Seshu Vardhan, Suban K. K. Sahoo
Summary: The SARS-CoV-2 Omicron variant BA.2 is designated as a variant of concern by the WHO due to its high transmission rate and pathogenicity. Our study compares BA.2 with other variants and investigates the structural changes caused by mutations. We find that certain polyphenols can effectively interact with the Omicron variants, suggesting potential use in combating the virus.
PHYTOCHEMICAL ANALYSIS
(2023)
Article
Biochemistry & Molecular Biology
Dorota Kowalska, Joanna Dolzonek, Krzysztof Zamojc, Sergey A. Samsonov, Martyna Maszota-Zieleniak, Joanna Makowska, Piotr Stepnowski, Anna Bialk-Bielinska, Dariusz Wyrzykowski
Summary: Human serum albumin (HSA) plays a crucial role in binding low-molecular-weight compounds and facilitating their distribution in living organisms. This study investigates the impact of counter-ions, such as [B (CN)4]- and [C(CN)3]-, on the affinity of [IM1-12]+ towards HSA. Experimental methods and computational approaches are used to analyze protein-ligand interactions and the thermal stability of resulting complexes. The findings provide valuable insights into the presence of globular proteins and ionogenic compounds in the environment and living organisms.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Chemistry, Physical
Laila H. Abdel-Rahman, Shaaban K. Mohamed, Youness El Bakri, Sajjad Ahmad, Chin-Hung Lai, Amer A. Amer, Joel T. Mague, Ehab M. Abdalla
Summary: A new thiazolidine derivative was successfully synthesized and characterized, showing a layered crystal structure with high affinity intermolecular complex formation through hydrogen bonding interactions.
JOURNAL OF MOLECULAR STRUCTURE
(2021)
Article
Chemistry, Physical
Maria Lbadaoui-Darvas, Giovanni Garberoglio, Katerina S. Karadima, M. Natalia D. S. Cordeiro, Athanasios Nenes, Satoshi Takahama
Summary: This comprehensive review explores methods and applications of molecular simulations of interfacial systems, providing detailed insights into techniques and challenges in solid and fluid surfaces. The review also summarizes methods for estimating macroscopic properties of interfaces and extracting information about fluctuating liquid surfaces, demonstrating their application in atmospheric science, material science, and biophysics. The main goals are to guide practical questions in software, force fields, and select appropriate analysis methods, while highlighting the potential for molecular simulations to advance our understanding in applied science.
MOLECULAR SIMULATION
(2023)
Article
Chemistry, Medicinal
Michael Gonzalez-Durruthy, Riccardo Concu, Laura F. Osmari Vendrame, Mirkos Ortiz Martins, Ivana Zanella, Juan Manuel Ruso, Maria Natalia Dias Soeiro Cordeiro
Summary: This study combined molecular docking approaches and DFT ab initio simulations to investigate the key interactions of cyclodextrins (CDs) with potential pharmacological relevance and the multidrug resistance P-gp protein. The findings provide valuable insights into the CD docking mechanism and the role of P-gp in drug delivery.
CURRENT TOPICS IN MEDICINAL CHEMISTRY
(2023)
Article
Pharmacology & Pharmacy
Abhishek Ghosh, Parthasarathi Panda, Amit Kumar Halder, Maria Natalia D. S. Cordeiro
Summary: This study systematically investigates the structural requirements for antiviral properties of some aryl benzoyl hydrazide derivatives using various computational tools. The results provide important guidelines for the design and development of novel antiviral agents against RNA viruses, including influenza, HIV-1, hepatitis C, and coronaviruses.
FRONTIERS IN PHARMACOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Shirley A. R. Sancha, Nikoletta Szemeredi, Gabriella Spengler, Maria-Jose U. Ferreira
Summary: In order to overcome multidrug resistance in cancer chemotherapy, lycorine, a major Amaryllidaceae alkaloid isolated from Pancratium maritimum, was derivatized to obtain 31 new compounds. These compounds showed significant activity in the study of anticancer drug resistance.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Riccardo Concu, Maria Natalia Dias Soeiro Cordeiro, Martin Perez-Perez, Florentino Fdez-Riverola
Summary: This study developed a novel multi-target machine learning (MTML) quantitative structure-activity relationship (QSAR) model for predicting interactions between different drugs and enzyme targets. The model was based on a large dataset of drug-enzyme pairs and used topological drug features and artificial neural network (ANN) multi-layer perceptron (MLP). The validated model showed an overall accuracy of over 96%. To maximize its diffusion, a public and accessible web-based tool was developed for users to make their own predictions.
Article
Biology
Soumya Mitra, Amit Kumar Halder, Nilanjan Ghosh, Subhash C. Mandal, M. Natalia D. S. Cordeiro
Summary: Non-alcoholic fatty liver disease (NAFLD) is a major health hazard globally, and there are limited treatment options available. This study used cheminformatics and molecular modeling techniques to investigate the structural requirements of 3-benzamidobenzoic acid derivatives for their potency towards Farnesoid X receptor (FXR), providing important guidelines for designing novel FXR partial agonists for the management of NAFLD.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Review
Pharmacology & Pharmacy
Amit Kumar Halder, Soumya Mitra, Maria Natalia D. S. Cordeiro
Summary: This article reviews the recent developments in the design of multi-target drugs for the treatment of major depressive disorders. Case studies focusing on design strategies and challenges are discussed. The authors suggest exploring potential biological targets and utilizing computational modeling techniques for further research.
EXPERT OPINION ON DRUG DISCOVERY
(2023)
Article
Biochemistry & Molecular Biology
Catia A. Bonito, Ricardo J. Ferreira, Maria-Jose U. Ferreira, Jean-Pierre Gillet, M. Natalia D. S. Cordeiro, Daniel J. V. A. dos Santos
Summary: In this study, the impact of four P-gp mutations on drug-binding and efflux-related signal-transmission mechanism was evaluated. The repacking of the transmembrane helices induced by mutations and ligands indicates P-gp's sensitivity to perturbations in the transmembrane region. Changes in drug-binding were observed as a consequence of transmembrane helices repacking, but were not always correlated with alterations in ligand binding mode and affinity. The changes in drug efflux are mostly related to changes in drug specificity rather than effects on signal-transmission mechanism.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Chemistry, Multidisciplinary
Catia A. Bonito, Ricardo J. Ferreira, Maria-Jose. U. Ferreira, Fernando Duraes, Emilia Sousa, Jean-Pierre Gillet, M. Natalia D. S. Cordeiro, Daniel J. V. A. dos Santos
Summary: A medicinal chemistry study combined in silico and in vitro methodologies to identify and characterize putative allosteric drug-binding sites (aDBSs) at the interface of the transmembrane-and nucleotide-binding domains (TMD-NBD) of P-glycoprotein. Two aDBSs were identified using in silico fragment-based molecular dynamics and were characterized in terms of size, polarity, and lining residues. Several compounds from a small library of thioxanthone and flavanone derivatives were found to decrease verapamil-stimulated ATPase activity, indicating allosteric efflux modulation in P-glycoprotein. Molecular docking and dynamics simulations provided insights into the binding mode of flavanone derivatives as allosteric inhibitors.
Article
Biochemistry & Molecular Biology
Catarina A. Madeira, Carolina Anselmo, Joao M. Costa, Catia A. Bonito, Ricardo J. Ferreira, Daniel J. . V. A. Santos, Ronald J. Wanders, Joao B. Vicente, Fatima V. Ventura, Paula Leandro
Summary: Medium chain acyl-CoA dehydrogenase (MCAD) deficiency is caused by mutations in the ACADM gene, leading to impaired function and/or structure of MCAD. This study investigates the effects of amino acid substitutions on FAD incorporation and finds that most variants result in reduced FAD content, but some can be rescued by cofactor supplementation, indicating the importance of cofactor availability for MCAD function.
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE
(2023)
Editorial Material
Biochemistry & Molecular Biology
Maria-Jose U. Ferreira
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Environmental Sciences
Amit Kumar Halder, Ana S. Moura, M. Natalia D. S. Cordeiro
Summary: Manufactured substances known as endocrine disrupting chemicals (EDCs) released in the environment can cause severe eco and cytotoxicity at relatively low doses. This study introduces a new multitasking quantitative structure-toxicity relationship (QSTR) modeling approach for predicting the ecotoxicity of EDCs against 170 biological species. The developed QSTR models display high accuracies, and a multitasking consensus modeling approach further improves the predictive ability.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)