Repurposing of approved drugs for targeting CDK4/6 and aromatase protein using molecular docking and molecular dynamics studies

PLOS ONE RESEARCH ARTICLE Repurposing of approved drugs for targeting CDK4/6 and aromatase protein using molecular docking and molecular dynamics studies Fatima A. yousif1, Abdulrahim A. Alzain1, Alhafez M. Alraih2, Walaa Ibraheem ID1* a1111111111 a1111111111 a1111111111 a1111111111 a1111111111 1 Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Wad Madani, Sudan, 2 Department of Chemistry, College of Science and Arts, Mohail Aseer, King Khalid University, Abha, Kingdom of Saudi Arabia * Abstract OPEN ACCESS Citation: yousif FA, Alzain AA, Alraih AM, Ibraheem W (2023) Repurposing of approved drugs for targeting CDK4/6 and aromatase protein using molecular docking and molecular dynamics studies. PLoS ONE 18(9): e0291256. https://doi. org/10.1371/journal.pone.0291256 Editor: Ahmed A. Al-Karmalawy, Ahram Canadian University, EGYPT Received: June 19, 2023 Accepted: August 25, 2023 Published: September 8, 2023 Copyright: © 2023 yousif et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Data Availability Statement: All relevant data are within the paper. and Structures and files for the ligand protein complexes resulting from MD simulations have been deposited in GitHub (GitHub - https://github.com/abdulrahim1990/MD_ MMGBSA_results). Funding: AMA RGP2/197/44 the Deanship of Scientific Research at King Khalid University https://www.kku.edu.sa/en/taxonomy/term/3226 he sponsors helped inpreparation of the manuscript Breast cancer is a leading cause of cancer-related morbidity and mortality worldwide, with the highest incidence among women. Among the various subtypes of breast cancer, estrogen-receptor positive (ER+) is the most diagnosed. Estrogen upregulates cyclin D1, which in turn promotes the activity of CDK4/6 and facilitates cell cycle progression. To address this, the first-line treatment for ER+ breast cancer focuses on inhibiting estrogen production by targeting aromatase, the enzyme responsible for the rate-limiting step in estrogen synthesis. Thus, combining CDK4/6 inhibitors with aromatase inhibitors has emerged as a crucial treatment strategy for this type of breast cancer. This approach effectively suppresses estrogen biosynthesis and controls uncontrolled cell proliferation, significantly improving overall survival rates and delayed disease progression. This study aimed to identify compounds that are likely to inhibit CDK4/6 and aromatase simultaneously by using a structurebased drug design strategy. 12,432 approved and investigational drugs were prepared and docked into the active site of CDK6 using HTVS and XP docking modes of Glide resulting in 277 compounds with docking scores � -7 kcal/mol. These compounds were docked into aromatase enzyme using XP mode to give seven drugs with docking scores� -6.001 kcal/ mol. Furthermore, the shortlisted drugs were docked against CDK4 showing docking scores ranging from -3.254 to -8.254 kcal/mol. Moreover, MM-GBSA for the top seven drugs was calculated. Four drugs, namely ellagic acid, carazolol, dantron, and apomorphine, demonstrated good binding affinity to all three protein targets CDK4/6 and aromatase. Specifically, they exhibited favourable binding free energy with CDK6, with values of -51.92, -53.90, -50.22, and -60.97 kcal/mol, respectively. Among these drugs, apomorphine displayed the most favourable binding free energy with all three protein targets. To further evaluate the stability of the interaction, apomorphine was subjected to a 100 ns molecular dynamics simulation with CDK6. The results indicated the formation of a stable ligand-protein complex. While the results obtained from the MM-GBSA calculation of the binding free energies of the MD conformations of apomorphine showed less favourable binding free energy compared PLOS ONE | https://doi.org/10.1371/journal.pone.0291256 September 8, 2023 1 / 17 PLOS ONE Competing interests: he authors have declared that no competing interests exist. Repurposing of Approved Drugs for targeting CDK4/6 and Aromatase protein to that obtained post-docking. All these computational findings will provide better structural insight for the development of CDK4/6 and aromatase multi-target inhibitors. 1. Introduction Breast cancer is the most commonly diagnosed cancer among women worldwide [1], with the estrogen receptor-positive (ER+) subtype being the most prevalent [2]. Estrogen plays a critical role in the development of breast cancer in both pre-and postmenopausal women [3]. Consequently, targeting the estrogen signalling pathway has proven to be a successful strategy in treating this type of breast cancer [4]. The initial drug used to counter this pathway is tamoxifen, a selective estrogen receptor modulator (SERM). However, tamoxifen has undesirable side effects and provides incomplete blockade of estrogen, leading to the development of aromatase enzyme inhibitors (AIs) [5]. These inhibitors are effective and well-tolerated compared to tamoxifen [3]. AIs are categorized as steroidal and non-steroidal, with exemestane, anastrozole, and letrozole being the most commonly used AIs to treat estrogen receptor-positive breast cancer in postmenopausal women [6, 7]. Uncontrolled cell proliferation and the development of cancer are consequences of accelerated cell cycle progression. The cell cycle consists of four sequential phases: G1 (pre-DNA synthesis), S (DNA synthesis), G2 (pre-division), and M (cell division). The transition through these phases is regulated by different series of kinase activities [8]. Cyclin-dependent kinases (CDKs), a family of serine-threonine kinases, along with their protein partners called cyclins, are responsible for the regulation of the cell cycle. CDK4 and CDK6 are initiators of the transition from the G1 phase to the S phase [9]. Dysregulation of the cyclin D1-CDK4/6-Rb signalling cascade has been observed in breast cancer and other malignancies and is associated with poor prognosis and increased metastasis. Estrogen signalling induces cyclin D1, which enhances CDK4/6 activity and contributes to cancer progression [10]. The multi-targeting of CDK4/6 and aromatase inhibit estrogen biosynthesis and uncontrolled cell proliferation. Thus, has become the cornerstone of treatment for hormone receptor (HR)-positive, human epidermal growth factor receptor-2 (HER2)-negative metastatic breast cancer [11]. This combined approach has significantly delayed disease progression and improved overall survival rates [12]. Identification of new targets for older drugs is less likely to fail in future clinical trials due to their established clinical safety and known toxic properties, which are the primary causes of drug failures [13]. Drug repurposing refers to the process of discovering new therapeutic indications for existing drugs to (...truncated)