A5069895607- Computational Drug Discovery Methods
- Protein Structure and Dynamics
- Synthesis and biological activity
- Alzheimer's disease research and treatments
- Crystallization and Solubility Studies
- Research on Leishmaniasis Studies
- Diverse Scientific Research Studies
- DNA and Nucleic Acid Chemistry
- Hemoglobinopathies and Related Disorders
- Metal complexes synthesis and properties
- Natural Antidiabetic Agents Studies
- Monoclonal and Polyclonal Antibodies Research
- Antibiotic Resistance in Bacteria
- X-ray Diffraction in Crystallography
- Synthesis and Characterization of Heterocyclic Compounds
- Pharmacological Effects of Natural Compounds
- SARS-CoV-2 and COVID-19 Research
- Erythrocyte Function and Pathophysiology
- Biological Activity of Diterpenoids and Biflavonoids
- Vitamin C and Antioxidants Research
- Iron Metabolism and Disorders
- Phytochemistry and Bioactivity Studies
- Bacteriophages and microbial interactions
- Ethnobotanical and Medicinal Plants Studies
- Metabolomics and Mass Spectrometry Studies
Afe Babalola University
2014-2024
University of KwaZulu-Natal
2023
Obafemi Awolowo University
2017-2022
Forschungszentrum Jülich
2012-2022
Stadtwerke Jülich (Germany)
2014
German Research School for Simulation Sciences
2012-2013
Centre for Structural Systems Biology
2012
University of London
2010
We use state-of-the-art computer-aided drug design (CADD) techniques to identify prospective inhibitors of the main protease enzyme, 3CLpro severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing COVID-19. From our screening over one million compounds including approved drugs, investigational natural products, and organic compounds, a rescreening protocol incorporating enzyme dynamics via ensemble docking, we have been able range inhibitors. Importantly, some identified had...
Abstract Amyloid proteins are characterized by their tendency to aggregate into amyloid fibrils, which often associated with devastating diseases. Aggregation pathways typically involve unfolding or misfolding of monomeric and formation transient oligomers protofibrils before the final aggregation product is formed. The conformational dynamics polymorphic volatile nature these intermediates make characterization experimental techniques alone insufficient also require computational...
In this simulation study, we present a comparison of the secondary structure two major alloforms Alzheimer's peptide (Aβ(1-40) and Aβ(1-42)) on basis molecular dynamics (MD) simulations thea microsecond time scale using GROMOS96 force fields ffG43a2 ffG53a6. We observe force-field related differences in sampled conformations Aβ(1-40) Aβ(1-42), which characterize terms NMR chemical shifts calculated from MD trajectories validate against corresponding experimental results. From analysis, can...
The aggregation of amyloid-β protein (1-42) is studied at experimental concentrations using all-atom molecular dynamics simulations. We observe a fast into oligomers without significant changes in the internal structure individual proteins. process characterized terms transition networks.
We provide general AMBER force field (GAFF) parameters for 160 organic molecules including drugs, natural products, and steroids, which can be employed without further processing in molecular dynamics (MD) simulations using GROMACS. determined these based on quantum mechanical (QM) calculations involving geometry optimization at the HF6-31G* level of theory. For each molecule we a coordinate file three-dimensional structure, topology parameter file. The applicability was demonstrated by MD...
The biophysical and biological properties of unprecedented anti-HIV aptamers are presented. most active aptamer (1L) shows a significant affinity to the HIV protein gp120.
We use state-of-the-art computer-aided drug design (CADD) techniques to identify prospective inhibitors of the main protease enzyme, Mpro COVID-19 virus. With high-resolution X-ray crystallography structure this viral enzyme recently being solved, CADD provides a veritable tool for rapidly screening diverse sets compounds with aim identifying ligands capable forming energetically favorable complexes . From our 1,082,653 derived from ZINC, DrugBank, and in-house African natural product...
Bacterial and malaria co-infections are common in endemic countries thus necessitate co-administration of antibiotics antimalarials. There have long been anecdotal clinical reports interactions between penicillins antimalarial agents, but the nature mechanisms these remain to be investigated. In this study, we employed antimicrobial interaction testing methods study effect two antimalarials on antibacterial activity ampicillin vitro. Paper strip diffusion, a modified disc diffusion...
It is widely believed that Alzheimer's disease pathogenesis driven by the production and deposition of amyloid-β peptide (Aβ) in brain. In this study, we employ a combination silico vitro approaches to investigate inhibitory properties selected arginine-rich D-enantiomeric peptides (D-peptides) against amyloid aggregation. The D-peptides include D3, 12-residue with anti-amyloid potencies demonstrated vivo, RD2, scrambled sequence as well truncated RD2 variants. Using global optimization...
Abstract Amyloid‐β (Aβ) is a natively unfolded peptide found in all Alzheimer's disease patients as the major component of fibrillar plaques, which are recognized an important pathological hallmark disease. The binding copper to Aβ increases its neurotoxicity, Cu 2+ causes become redox active and decreases lag time associated with aggregation. In addition, pH factor that influences both aggregation rates binding. Hamiltonian replica exchange molecular dynamics (H‐REMD) simulations enable...
The increasing recognition of the biochemical importance glycosaminoglycans (GAGs) has in recent times made them center attention research investigations. It became evident that subtle conformational factors play an important role determining relationship between chemical composition GAGs and their activity. Therefore, a thorough understanding structural flexibility is needed, which addressed this work by means all-atom molecular dynamics (MD) simulations. Four major with different...
HIV1 integrase is an important target for the antiviral therapy. Guanine-rich quadruplex, such as 93del, have been shown to be potent inhibitors of this enzyme and thus representing a new class agents. Although X-ray NMR structures 93del reported, there no structural information complex mechanism inhibition still remains unexplored. A number computational methods including automated protein-DNA docking molecular dynamics simulation in explicit solvent were used model binding integrase....