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      Analogues of Dihydroflavonol and Flavone as Protein Tyrosine Phosphatase 1B Inhibitors from the Leaves of Artocarpus elasticus

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          Abstract

          Protein tyrosine phosphatase 1B (PTP1B) is one of the target enzymes whose disruption leads to obesity and diabetes. A series of PTP1B inhibitors were isolated from the leaves of Artocarpus elasticus , used in traditional medicines for diabetes. The isolated inhibitors ( 1–13), including two new compounds ( 1 and 2), consisted of dihydroflavonols and flavones. The structural requirements for the PTP1B inhibitory mode and potency were revealed in both skeletons. The two highest PTP1B inhibitory properties were dihydroflavonol 1 and flavone 6 analogs with IC 50 values of 0.17 and 0.79 μM, respectively. The stereochemistry also affected inhibitory potencies: trans isomer 1 (IC 50= 0.17 μM) vs cis isomer 2 (IC 50= 2.24 μM). Surprisingly, the dihydroflavonol and flavone glycosides ( 11 and 13) displayed potent inhibition with IC 50s of 2.39 and 0.22 μM, respectively. Furthermore, competitive inhibitor 1 was applied to time-dependence experiments as a simple slow-binding inhibitor with parameters of K i app = 0.064103 μM, k 3 = 0.2262 μM –1 min –1, and k 4 = 0.0145 min –1. The binding affinities by using the fluorescence quenching experiment were highly correlated with inhibitory potencies: 1 (IC 50= 0.17 μM, K SV = 0.4375 × 10 5 L·mol –1) vs 3 (IC 50= 17.79 μM, K SV = 0.0006 × 10 5 L·mol –1). The specific binding interactions were estimated at active and allosteric sites according to the inhibitory mode by molecular docking.

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          Improved protein-ligand docking using GOLD.

          The Chemscore function was implemented as a scoring function for the protein-ligand docking program GOLD, and its performance compared to the original Goldscore function and two consensus docking protocols, "Goldscore-CS" and "Chemscore-GS," in terms of docking accuracy, prediction of binding affinities, and speed. In the "Goldscore-CS" protocol, dockings produced with the Goldscore function are scored and ranked with the Chemscore function; in the "Chemscore-GS" protocol, dockings produced with the Chemscore function are scored and ranked with the Goldscore function. Comparisons were made for a "clean" set of 224 protein-ligand complexes, and for two subsets of this set, one for which the ligands are "drug-like," the other for which they are "fragment-like." For "drug-like" and "fragment-like" ligands, the docking accuracies obtained with Chemscore and Goldscore functions are similar. For larger ligands, Goldscore gives superior results. Docking with the Chemscore function is up to three times faster than docking with the Goldscore function. Both combined docking protocols give significant improvements in docking accuracy over the use of the Goldscore or Chemscore function alone. "Goldscore-CS" gives success rates of up to 81% (top-ranked GOLD solution within 2.0 A of the experimental binding mode) for the "clean list," but at the cost of long search times. For most virtual screening applications, "Chemscore-GS" seems optimal; search settings that give docking speeds of around 0.25-1.3 min/compound have success rates of about 78% for "drug-like" compounds and 85% for "fragment-like" compounds. In terms of producing binding energy estimates, the Goldscore function appears to perform better than the Chemscore function and the two consensus protocols, particularly for faster search settings. Even at docking speeds of around 1-2 min/compound, the Goldscore function predicts binding energies with a standard deviation of approximately 10.5 kJ/mol. Copyright 2003 Wiley-Liss, Inc.
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            Molecular Docking: A Powerful Approach for Structure-Based Drug Discovery

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              Allosteric inhibition of protein tyrosine phosphatase 1B.

              Obesity and type II diabetes are closely linked metabolic syndromes that afflict >100 million people worldwide. Although protein tyrosine phosphatase 1B (PTP1B) has emerged as a promising target for the treatment of both syndromes, the discovery of pharmaceutically acceptable inhibitors that bind at the active site remains a substantial challenge. Here we describe the discovery of an allosteric site in PTP1B. Crystal structures of PTP1B in complex with allosteric inhibitors reveal a novel site located approximately 20 A from the catalytic site. We show that allosteric inhibitors prevent formation of the active form of the enzyme by blocking mobility of the catalytic loop, thereby exploiting a general mechanism used by tyrosine phosphatases. Notably, these inhibitors exhibit selectivity for PTP1B and enhance insulin signaling in cells. Allosteric inhibition is a promising strategy for targeting PTP1B and constitutes a mechanism that may be applicable to other tyrosine phosphatases.
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                Author and article information

                Journal
                ACS Omega
                ACS Omega
                ao
                acsodf
                ACS Omega
                American Chemical Society
                2470-1343
                14 February 2024
                27 February 2024
                : 9
                : 8
                : 9053-9062
                Affiliations
                []Division of Applied Life Science (BK21 Four), IALS, Gyeongsang National University , Jinju 52828, Republic of Korea
                []Division of Applied Life Science (BK21 Four), ABC-RLRC, PMBBRC, Gyeongsang National University , Jinju 52828, Korea
                Author notes
                [* ]E-mail: khpark@ 123456gnu.ac.kr . Tel: +82-55-772-1965. Fax: +82-55-772-1969.
                Author information
                https://orcid.org/0000-0002-2918-7556
                https://orcid.org/0000-0003-4467-2709
                Article
                10.1021/acsomega.3c07471
                10905692
                38434867
                559b389d-29d4-42ca-82c5-23aea548ad09
                © 2024 The Authors. Published by American Chemical Society

                Permits non-commercial access and re-use, provided that author attribution and integrity are maintained; but does not permit creation of adaptations or other derivative works ( https://creativecommons.org/licenses/by-nc-nd/4.0/).

                History
                : 03 October 2023
                : 01 February 2024
                : 18 December 2023
                Funding
                Funded by: Ministry of Education, doi 10.13039/501100002701;
                Award ID: NA
                Funded by: National Research Foundation of Korea, doi 10.13039/501100003725;
                Award ID: NRF-2022R1A2C1091270
                Funded by: National Research Foundation of Korea, doi 10.13039/501100003725;
                Award ID: NRF-2015R1A6A1A03031413
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                ao3c07471

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