Chemistry and Biotechnology Institute, Federal University of Alagoas, Campus A.C. Simões, Lourival Melo Mota Avenue, Maceió 57072-970, Brazil; Laboratory of Organic and Medicinal Synthesis, Federal University of Alagoas, Campus Arapiraca, Manoel Severino Barbosa Avenue, Arapiraca 57309-005, Brazil.
Laboratory of Organic and Medicinal Synthesis, Federal University of Alagoas, Campus Arapiraca, Manoel Severino Barbosa Avenue, Arapiraca 57309-005, Brazil.
Bioorg Med Chem. 2021 Jul 1;41:116213. doi: 10.1016/j.bmc.2021.116213. Epub 2021 May 11.
Chagas disease and Human African Trypanosomiasis (HAT) are caused by Trypanosoma cruzi and T. brucei parasites, respectively. Cruzain (CRZ) and Rhodesain (RhD) are cysteine proteases that share 70% of identity and play vital functions in these parasites. These macromolecules represent promising targets for designing new inhibitors. In this context, 26 CRZ and 5 RhD 3D-structures were evaluated by molecular redocking to identify the most accurate one to be utilized as a target. Posteriorly, a virtual screening of a library containing 120 small natural and nature-based compounds was performed on both of them. In total, 14 naphthoquinone-based analogs were identified, synthesized, and biologically evaluated. In total, five compounds were active against RhD, being three of them also active on CRZ. A derivative of 1,4-naphthoquinonepyridin-2-ylsulfonamide was found to be the most active molecule, exhibiting IC values of 6.3 and 1.8 µM for CRZ and RhD, respectively. Dynamic simulations at 100 ns demonstrated good stability and do not alter the targets' structures. MM-PBSA calculations revealed that it presents a higher affinity for RhD (-25.3 Kcal mol) than CRZ, in which van der Waals interactions were more relevant. A mechanistic hypothesis (via C3-Michael-addition reaction) involving a covalent mode of inhibition for this compound towards RhD was investigated by covalent molecular docking and DFT B3LYP/6-31 + G* calculations, exhibiting a low activation energy (ΔG) and providing a stable product (ΔG), with values of 7.78 and - 39.72 Kcal mol, respectively; similar to data found in the literature. Nevertheless, a reversibility assay by dilution revealed that JN-11 is a time-dependent and reversible inhibitor. Finally, this study applies modern computer-aided techniques to identify promising inhibitors from a well-known chemical class of natural products. Then, this work could inspire other future studies in the field, being useful for designing potent naphthoquinones as RhD inhibitors.
恰加斯病和人类非洲锥虫病（HAT）分别由克氏锥虫和布氏锥虫寄生虫引起。克鲁嗪（CRZ）和罗得西亚锥虫（RhD）是半胱氨酸蛋白酶，它们具有 70%的同源性，在这些寄生虫中发挥着重要作用。这些大分子代表了设计新抑制剂的有前途的靶标。在这种情况下，通过分子重新对接评估了 26 个 CRZ 和 5 个 RhD 的 3D 结构，以确定最准确的结构作为靶标。随后，对包含 120 种天然和基于天然的小化合物库对两者进行了虚拟筛选。总共鉴定出 14 种萘醌类似物，对它们进行了合成和生物评估。总共发现了 5 种化合物对 RhD 有活性，其中 3 种对 CRZ 也有活性。发现 1,4-萘醌嘧啶-2-基磺酰胺的衍生物是最活跃的分子，对 CRZ 和 RhD 的 IC 值分别为 6.3 和 1.8µM。100ns 的动态模拟表明其稳定性良好，且不会改变靶标结构。MM-PBSA 计算表明，与 CRZ 相比，它对 RhD 具有更高的亲和力（-25.3 Kcal mol），其中范德华相互作用更为重要。通过共价分子对接和 DFT B3LYP/6-31+G*计算研究了该化合物对 RhD 的机制假说（通过 C3-Michael-加成反应），涉及这种化合物对 RhD 的共价抑制模式，表现出较低的活化能（ΔG）并提供稳定的产物（ΔG），其值分别为 7.78 和-39.72 Kcal mol，与文献中的数据相似。然而，通过稀释进行的可逆性测定表明，JN-11 是一种时间依赖性和可逆抑制剂。最后，本研究应用现代计算机辅助技术从天然产物这一广为人知的化学类群中鉴定出有前途的抑制剂。然后，这项工作可以为其他未来的研究提供灵感，对于设计有效的萘醌类化合物作为 RhD 抑制剂很有用。
