Targeting Cytotoxin-Associated Antigen A, a Virulent Factor of <i>Helicobacter pylori</i>-Associated Gastric Cancer: Structure-Based In Silico Screening of Natural Compounds
Shan He,
Abdulraheem Ali Almalki,
Misbahuddin M. Rafeeq,
Ziaullah M. Sain,
Amany I. Alqosaibi,
Mashael M. Alnamshan,
Ibtesam S. Al-Dhuayan,
Abdul Rahaman,
Yang Zhang,
Hamsa Jameel Banjer,
Farah Anjum,
Haitham Ali M. Alzghaibi,
Ali H. Alharbi,
Qazi Mohammad Sajid Jamal
Affiliations
Shan He
School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou 510006, China
Abdulraheem Ali Almalki
Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
Misbahuddin M. Rafeeq
Department of Pharmacology, Faculty of Medicine, King Abduaziz University, Jeddah 21589, Saudi Arabia
Ziaullah M. Sain
Department of Microbiology, Faculty of Medicine, King Abduaziz University, Jeddah 21589, Saudi Arabia
Amany I. Alqosaibi
Department of Biology, College of Science, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam 31441, Saudi Arabia
Mashael M. Alnamshan
Department of Biology, College of Science, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam 31441, Saudi Arabia
Ibtesam S. Al-Dhuayan
Department of Biology, College of Science, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam 31441, Saudi Arabia
Abdul Rahaman
School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China
Yang Zhang
School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou 510006, China
Hamsa Jameel Banjer
Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
Farah Anjum
Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
Haitham Ali M. Alzghaibi
Department of Health Informatics, College of Public Health and Health Informatics, Qassim University, Al Bukayriyah 52741, Saudi Arabia
Ali H. Alharbi
Department of Health Informatics, College of Public Health and Health Informatics, Qassim University, Al Bukayriyah 52741, Saudi Arabia
Qazi Mohammad Sajid Jamal
Department of Health Informatics, College of Public Health and Health Informatics, Qassim University, Al Bukayriyah 52741, Saudi Arabia
Gastric cancer is the fifth most frequent cancer and the third major cause of mortality worldwide. Helicobacter pylori, a bacterial infection linked with GC, injects the cytotoxin-associated antigen A (CagA; an oncoprotein) into host cells. When the phosphorylated CagA protein enters the cell, it attaches to other cellular components, interfering with normal cellular signaling pathways. CagA plays an important role in the progression of GC by interacting with phosphatidylserine of the host cell membrane. Therefore, disrupting the CagA–phosphatidylserine connection using small molecules appears to be a promising therapeutic approach. In this report, we screened the natural compounds from ZINC database against the CagA protein using the bioinformatics tools. Hits were initially chosen based on their physicochemical, absorption, distribution, metabolism, excretion, and toxicity (ADMET) characteristics, as well as other drug-like characteristics. To locate safe and effective hits, the PAINS filter, binding affinities estimation, and interaction analysis were used. Three compounds with high binding affinity and specificity for the CagA binding pocket were discovered. The final hits, ZINC153731, ZINC69482055, and ZINC164387, were found to bind strongly with CagA protein, with binding energies of −11.53, −10.67, and −9.21 kcal/mol, respectively, which were higher than that of the control compound (−7.25 kcal/mol). Further, based on binding affinity and interaction pattern, two leads (ZINC153731, ZINC69482055) were chosen for molecular dynamics (MD) simulation analysis. MD results showed that they displayed stability in their vicinity at 100 ns. This study suggested that these compounds could be used as possible inhibitors of CagA protein in the fight against GC. However, additional benchwork tests are required to validate them as CagA protein inhibitors.
