Saravanan Venkatesan, Chagaleti Bharath Kumar, Packiapalavesam Shakthi Devi, Kathiravan Muthukumaradoss
Department of Pharmaceutical Chemistry, SRM College of Pharmacy, SRM Institute of Science and Technology Kattankulathur Chengalpattu 603203 India.
Dr A. P. J. Abdul Kalam Research Lab, Department of Pharmaceutical Chemistry, SRM College of Pharmacy, SRM Institute of Science and Technology Kattankulathur, Chengalpattu Chennai 603 203 India
RSC Adv. 2024 Jan 22;14(5):3346-3358. doi: 10.1039/d3ra08618f. eCollection 2024 Jan 17.
Carbonic anhydrase IX is an important biomarker to fight hypoxic tumours in both initial and metastatic stages of many forms of cancer. Overexpression of hCA IX in the hypoxic environment, has an active role in pH maintenance and makes the hCA IX a better target for the inhibitors targeting specific types of cancer stages. Being a member of the carbonic anhydrase family and having sixteen isoforms, it is important to have a selective inhibition of hCA IX to limit the disruption in the biological and metabolic pathways where other isoforms of hCA are localised and to avoid the other toxicity and adverse effects we try to find selective hCA IX inhibitors from a natural derivative. In the process of finding selective hCA inhibitors we developed a pharmacophore model based on existing inhibitors with IC values of less than 50 nm, which is then validated with the external decoy set and used for database searching followed by virtual screening to identify the hits based on the pharmacophore fit score and RMSD. Molecular docking studies were performed to identify protein ligand interaction and molecular dynamics simulation studies to analyse the stability of the complex and DFT studies were carried out. The initial screening yielded 43 hits with the RMSD value less than 1, which when subjected to docking exhibited very good interaction with key residues ZN301, HIS94, HIS96 and HIS119. The top 4 compounds in the molecular dynamics simulation studies for 100 ns provided useful insights on the stability of the complex and the DFT studies confirmed the energy variation between HOMO and LUMO is within an acceptable range. An average binding score of -7.8 Kcal mol for the lead compounds and high stability margin in the dynamics study concludes that these lead compounds demonstrated outstanding potential for hCA IX inhibitory action theoretically and that further experimental studies for selective inhibition are inevitable.
碳酸酐酶IX是多种癌症在初始和转移阶段对抗缺氧肿瘤的重要生物标志物。在缺氧环境中hCA IX的过表达在维持pH值方面具有积极作用，这使得hCA IX成为针对特定癌症阶段的抑制剂的更好靶点。作为碳酸酐酶家族的一员且有16种同工型，选择性抑制hCA IX以限制hCA其他同工型所在的生物和代谢途径的破坏，并避免其他毒性和不良反应很重要，因此我们试图从天然衍生物中寻找选择性hCA IX抑制剂。在寻找选择性hCA抑制剂的过程中，我们基于IC值小于50 nm的现有抑制剂开发了一个药效团模型，然后用外部诱饵集进行验证，并用于数据库搜索，随后进行虚拟筛选以根据药效团拟合分数和均方根偏差（RMSD）识别命中物。进行了分子对接研究以确定蛋白质-配体相互作用，进行了分子动力学模拟研究以分析复合物的稳定性，并开展了密度泛函理论（DFT）研究。初步筛选产生了43个RMSD值小于1的命中物，这些命中物在对接时与关键残基ZN301、HIS94、HIS96和HIS119表现出非常好的相互作用。在100 ns的分子动力学模拟研究中排名前4的化合物为复合物的稳定性提供了有用的见解，DFT研究证实最高已占分子轨道（HOMO）和最低未占分子轨道（LUMO）之间的能量变化在可接受范围内。先导化合物的平均结合分数为-7.8千卡/摩尔，动力学研究中的高稳定性裕度表明这些先导化合物在理论上显示出对hCA IX抑制作用的杰出潜力，并且进一步的选择性抑制实验研究是不可避免的。
