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      Um paradigma da química medicinal: a flexibilidade dos ligantes e receptores Translated title: A medicinal chemistry paradigm: ligands and receptor flexibility

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          Translated abstract

          In general, molecular modeling techniques applied in medicinal chemistry have been static and drug based. However the active site geometry and the intrinsic flexibility of both receptor and ligand are fundamental properties for molecular recognition and drug action. As a consequence, the use of dynamic models to describe the ligand-receptor complex is becoming a more common procedure. In this work we discuss the relevance of considering the receptor structure in medicinal chemistry studies as well as the flexibility of the ligand-receptor complex.

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          Most cited references121

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          Photos — a universal Monte Carlo for QED radiative corrections in decays

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            Structural basis for the beta lactam resistance of PBP2a from methicillin-resistant Staphylococcus aureus.

            The multiple antibiotic resistance of methicillin-resistant strains of Staphylococcus aureus (MRSA) has become a major clinical problem worldwide. The key determinant of the broad-spectrum beta-lactam resistance in MRSA strains is the penicillin-binding protein 2a (PBP2a). Because of its low affinity for beta-lactams, PBP2a provides transpeptidase activity to allow cell wall synthesis at beta-lactam concentrations that inhibit the beta-lactam-sensitive PBPs normally produced by S. aureus. The crystal structure of a soluble derivative of PBP2a has been determined to 1.8 A resolution and provides the highest resolution structure for a high molecular mass PBP. Additionally, structures of the acyl-PBP complexes of PBP2a with nitrocefin, penicillin G and methicillin allow, for the first time, a comparison of an apo and acylated resistant PBP. An analysis of the PBP2a active site in these forms reveals the structural basis of its resistance and identifies features in newly developed beta-lactams that are likely important for high affinity binding.
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              Predicting absolute ligand binding free energies to a simple model site.

              A central challenge in structure-based ligand design is the accurate prediction of binding free energies. Here we apply alchemical free energy calculations in explicit solvent to predict ligand binding in a model cavity in T4 lysozyme. Even in this simple site, there are challenges. We made systematic improvements, beginning with single poses from docking, then including multiple poses, additional protein conformational changes, and using an improved charge model. Computed absolute binding free energies had an RMS error of 1.9 kcal/mol relative to previously determined experimental values. In blind prospective tests, the methods correctly discriminated between several true ligands and decoys in a set of putative binders identified by docking. In these prospective tests, the RMS error in predicted binding free energies relative to those subsequently determined experimentally was only 0.6 kcal/mol. X-ray crystal structures of the new ligands bound in the cavity corresponded closely to predictions from the free energy calculations, but sometimes differed from those predicted by docking. Finally, we examined the impact of holding the protein rigid, as in docking, with a view to learning how approximations made in docking affect accuracy and how they may be improved.
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                Author and article information

                Contributors
                Role: ND
                Role: ND
                Journal
                qn
                Química Nova
                Quím. Nova
                Sociedade Brasileira de Química (São Paulo )
                1678-7064
                February 2005
                : 28
                : 1
                : 95-102
                Affiliations
                [1 ] Universidade Federal do Rio Grande do Sul Brazil
                [2 ] Universidade Federal do Rio de Janeiro Brazil
                Article
                S0100-40422005000100018
                10.1590/S0100-40422005000100018
                40cf336e-d781-43ea-8327-5d9e00f55b71

                http://creativecommons.org/licenses/by/4.0/

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                SciELO Brazil

                Self URI (journal page): http://www.scielo.br/scielo.php?script=sci_serial&pid=0100-4042&lng=en
                Categories
                CHEMISTRY, MULTIDISCIPLINARY

                General chemistry
                lock and key model,induced fit,molecular dynamics
                General chemistry
                lock and key model, induced fit, molecular dynamics

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