Search results for "DOCKING"
showing 10 items of 299 documents
Docking of indolo- and pyrrolo-pyrimidines to DNA. New DNA-interactive polycycles from amino-indoles/pyrroles and BMMA
2004
New indolo- and pyrrolo-pyrimidines of type 1-4 were studied for their ability to form stable complexes with DNA fragments. The calculated free energies of binding were found in the range -8.39 ÷ -16.72 Kcal/mol. The docking studies revealed a common binding mode with the chromophore intercalated between GC base pairs whereas the side chain lies along the minor groove.
Discovery of benzimidazole-based Leishmania mexicana cysteine protease CPB2.8ΔCTE inhibitors as potential therapeutics for leishmaniasis
2018
Abstract: Chemotherapy is currently the only effective approach to treat all forms of leishmaniasis. However, its effectiveness is severely limited due to high toxicity, long treatment length, drug resistance, or inadequate mode of administration. As a consequence, there is a need to identify new molecular scaffolds and targets as potential therapeutics for the treatment of this disease. We report a small series of 1,2‐substituted‐1H‐benzo[d]imidazole derivatives (9ad) showing affinity in the submicromolar range (Ki = 0.150.69 μM) toward Leishmania mexicanaCPB2.8ΔCTE, one of the more promising targets for antileishmanial drug design. The compounds confirmed activity in vitro against intrace…
Synthesis, structure, properties and antimicrobial activity of para trifluoromethyl phenylboronic derivatives
2021
The [2-formyl-4-(trifluoromethyl)phenyl]boronic acid as well as its benzoxaborole and bis(benzoxaborole) derivatives were obtained and their properties studied. The 2-formyl compound displays an unusual structure in the crystalline state, with a significant twist of the boronic group, whereas in DMSO solution it tautomerizes with formation of a cyclic isomer. All the studied compounds exhibit relatively high acidity as well as a reasonable antimicrobial activity. Docking studies showed interactions of all the investigated compounds with the binding pocket of Candida albicans LeuRS. High activity against Bacillus cereus was determined for the 2-formyl compound as well as for the novel bis(be…
A Practical Perspective: The Effect of Ligand Conformers on the Negative Image-Based Screening.
2019
Negative image-based (NIB) screening is a rigid molecular docking methodology that can also be employed in docking rescoring. During the NIB screening, a negative image is generated based on the target protein’s ligand-binding cavity by inverting its shape and electrostatics. The resulting NIB model is a drug-like entity or pseudo-ligand that is compared directly against ligand 3D conformers, as is done with a template compound in the ligand-based screening. This cavity-based rigid docking has been demonstrated to work with genuine drug targets in both benchmark testing and drug candidate/lead discovery. Firstly, the study explores in-depth the applicability of different ligand 3D conformer…
De novo design of protein kinase inhibitors by in silico identification of hinge region-binding fragments.
2013
Protein kinases constitute an attractive family of enzyme targets with high relevance to cell and disease biology. Small molecule inhibitors are powerful tools to dissect and elucidate the function of kinases in chemical biology research and to serve as potential starting points for drug discovery. However, the discovery and development of novel inhibitors remains challenging. Here, we describe a structure-based de novo design approach that generates novel, hinge-binding fragments that are synthetically feasible and can be elaborated to small molecule libraries. Starting from commercially available compounds, core fragments were extracted, filtered for pharmacophoric properties compatible w…
Development of peptidomimetic boronates as proteasome inhibitors.
2013
Abstract Proteasome inhibition has emerged over the past decade as an effective therapeutic approach for the treatment of hematologic malignancies. It is a multicatalytic complex, whose proteolytic activity relies in three types of subunits: chymotrypsin-like (β5), trypsin-like (β2) and caspase-like (β1). Most important for the development of effective antitumor agents is the inhibition of the β5 subunits. In this context, the dipeptide boronate bortezomib (Velcade ® ) represents the first proteasome inhibitor approved by the FDA and the lead compound in drug discovery. This paper describes the synthesis and biological evaluation of a series of conformationally constrained pseudopeptide bor…
A Definitive Pharmacophore Modelling Study on CDK2 ATP Pocket Binders: Tracing the Path of New Virtual High-Throughput Screenings
2020
Cyclin Dependent Kinases-2 (CDK2) are members of serine/threonine protein kinases family. They play an important role in the regulation events of the eukaryotic cell division cycle, especially during the G1 to S phase transition. Experimental evidence indicate that excessive expression of CDK2s should cause abnormal cell cycle regulation. Therefore, since a long time, CDK2s have been considered potential therapeutic targets for cancer therapy. In this work, onehundred and forty-nine complexes of inhibitors bound in the CDK2-ATP pocket were submitted to short MD simulations (10ns) and free energy calculation. Comparison with experimental data (K<sub>i</sub>, K<sub>d</su…
Comparing molecular dynamics-derived pharmacophore models with docking: A study on CDK-2 inhibitors
2020
Abstract We compared the performance of molecular dynamics (MD)-derived pharmacophore modeling approaches, Common Hit Approach (CHA), and the Molecular dYnamics SHAred PharmacophorE (MYSHAPE) approach, with semi-flexible constrained/unconstrained docking. The aim of this work is to enrich the hit-list of a virtual screening on CDK-2 known inhibitors as a case study. Cyclin-dependent kinases (CDKs) deregulation is associated with cancer growth. CDKs are an attractive target for anticancer agents. MD-derived pharmacophore models have been obtained with LigandScout 4.2.1. Docking analysis has been performed through Glide 7.6. The results highlighted the MYSHAPE approach has a better performanc…
Studio del ruolo delle mutazioni “gatekeeper” V654A e T670I di c-kit kinase nell’interazione con inibitori attraverso un approccio misto Dinamica Mol…
2012
La sovraespressione del proto-oncogene c-kit è stata riscontrata nelle cellule ematopoietiche, nel cancro a piccole cellule del polmone e nei tumori stromali gastrointestinali1-3. L’importanza clinica dell’espressione di c-kit nei tumori ha indirizzato la ricerca verso inibitori di questa tirosina chinasi. Imatinib (Gleevec®) (in figura) è stato il primo farmaco utilizzato in terapia, ma la comparsa di mutazioni su c-kit ha portato ad una riduzione dell’efficacia o a completa resistenza a questo trattamento. In alternativa, altri composti si sono mostrati attivi anche nei confronti dei mutanti come ad esempio Sunitinib (Sutent®)4, ma la necessità di nuovi e più efficaci inibitori contro i m…
Spectroscopic, crystal structural, theoretical and biological studies of phenylacetohydrazide Schiff base derivatives and their copper complexes
2020
Two phenylacetohydrazide Schiff base derivatives: N’-(1-(2-hydroxyphenyl)ethylidene)-2-phenylacetohydrazide, HL1, and N’-((1-hydroxynaphthalen-2-yl)methylene)-2-phenylacetohydrazide, HL2, were synthesized. HL1 dimerizes in presence of HCl, probably via radical mechanism to give (2,2’-((1E)-hydrazine-1,2-diylidenebis(ethan-1-yl-1-ylidene))diphenol (DIM). Thermal reactions of Cu(II) ions with the two Schiff base ligands resulted in formation of the binuclear complexes [(CuL1)2] and [(CuL2)2]. The stoichiometry and structures of the reported compounds were investigated by several spectroscopic and analytical techniques. The structure of the HL1 ligand and its complex [(CuL1)2] as well as the D…