Bisphenol-A (4,4'-dihydroxy-2,2-diphenylpropane, BPA, or BPA-A) and its derivatives, when exposed to humans, may affect functions of multiple organs by specific binding to the human estrogen-related receptor γ (ERRγ). We carried out atomistic molecular dynamics (MD) simulations of three ligand compounds including BPA-A, 4-α-cumylphenol (BPA-C), and 2,2-diphenylpropane (BPA-D) binding to the lig...

The search for new antibacterial agents that could decrease bacterial resistance is a subject in continuous development. Gram-negative and Gram-positive bacteria possess group of metalloproteins belonging to the MEROPS peptidase (M4) family, which main virulence factor these bacteria. In this work, we used previous results computational biochemistry protocol series ligands designed silico using...

Human immunodeficiency virus type 1 protease (HIV-1 PR) and renin are primary targets toward AIDS and hypertension therapies, respectively. Molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) free-energy calculations and inhibition assays for canagliflozin, an antidiabetic agent verified its effective binding to both proteins (ΔG(pred) = -9.1 kcal mol(-1) for canagliflozin-renin; K(i,e...

UNLABELLED Folding free energy is an important biophysical characteristic of proteins that reflects the overall stability of the 3D structure of macromolecules. Changes in the amino acid sequence, naturally occurring or made in vitro, may affect the stability of the corresponding protein and thus could be associated with disease. Several approaches that predict the changes of the folding free e...

The TATA-box binding protein (TBP) is required by eukaryotic RNA polymerases to bind to the TATA box, an eight-basepair DNA promoter element, to initiate transcription. Carcinogen adducts that bind to the TATA box can hamper this important process. Benzo[a]pyrene (BP) is a representative chemical carcinogen that can be metabolically converted to highly reactive benzo[a]pyrene diol epoxides (BPD...

Recently, the development of Src/Abl (c-Src/Bcr-Abl tyrosine kinases) dual inhibitors has attracted considerable attention from the research community for treatment of malignancies. In order to explore the different structural features impacting the Src and Abl inhibitory activities of N(9)-arenethenyl purines and to investigate the molecular mechanisms of ligand-receptor interactions, a molecu...

α-Isopropylmalate Synthase (α-IPMS) encoded by leuA in Mycobacterium tuberculosis (M.tb) is involved in the leucine biosynthesis pathway and is extremely critical for the synthesis of branched-chain amino acids (leucine, isoleucine and valine). α-IPMS activity is required not only for the proliferation of M.tb but is also indispensable for its survival during the latent phase of infection. It i...

The importance of computational chemistry in modern scientific research is well established. Continuous improvement in software and algorithms for the modeling of chemical interactions has transformed molecular modeling into a powerful tool for many current day research projects. From a medical perspective, one of the ultimate goals in computer-aided drug design (CADD) is the accurate predictio...

Virtanen, Salla Virtual screening: Development of a novel structure-based method Jyväskylä: University of Jyväskylä, 2013, 51 p. (Jyväskylä Studies in Biological and Environmental Science ISSN 1456-9701; 264) ISBN 978-951-39-5340-9 (nid.) ISBN 978-951-39-5341-6 (PDF) Yhteenveto: Virtuaaliseulonta; uuden rakennepohjaisen menetelmän kehitys Diss. Computational methods have become an integral part...