Targeting Key Signalling Pathways in Leukemia: A Docking-Based Approach for Drug Discovery

Fadilullahi Opeyemi Ibiyemi*; Ismail Kolawole Odetayo

1Department of Chemistry & Industrial Chemistry, Osun State Water Regulatory Commission, Ministry of Water Resources , Osun State, Nigeria

2Department of Biochemistry & Chemistry Fountain University, P.M.B. 4491 Osogbo Osun State, Nigeria

*Correspondence: ibiyemi.ademola97@gmail.com

DOI: https://doi.org/10.71431/IJRPAS.2025.4806   

INTRODUCTION

Understanding the causes, chance components, and treatment choices for cancer is basic in organize to successfully coordinate and anticipate the ailment, {31}. Cancer may be a complex and multifaceted sickness that impacts millions of individuals around the world. It is basic to educate oneself nearly the different sorts of cancer and their influence on the people, {44}. This data will enable individuals to create taught choices with regard to their healthcare and conceivably reduce the rate and mortality of cancer. Besides, remaining updated on the foremost later headways in cancer ask almost and treatment can give trust for individuals overseeing with a cancer assurance, {8}. Cancer may be a disease that requires a comprehensive and multidisciplinary approach to conclusion and treatment. This consolidates early area through standard screenings, understanding the diverse treatment choices open such as surgery, chemotherapy, radiation treatment, centered on medications, immunotherapy, and palliative care, and giving back for patients' physical, psychosocial, and otherworldly well-being. Additionally, it is basic to recognize the aberrations in cancer treatment availability between unmistakable countries and work towards moving forward get to to comprehensive care for all individuals, regardless of their wage level. By understanding the causes, chance components, and treatment choices for cancer, individuals can suitably manage and expect the ailment, {32}. Cancer could be a complex and differing malady that can influence different organs and tissues within the body. One particular sort of cancer that warrants dialog is leukemia, which is characterized by the abnormal production of white blood cells, {42}. Leukemia may be a shape of blood cancer that basically impacts the bone marrow and blood. It is classified into a couple of subtypes, checking seriously lymphoblastic leukemia, seriously myeloid leukemia, consistent lymphocytic leukemia, and incessant myeloid leukemia. These subtypes of leukemia contrast in terms of their movement, treatment alternatives, and guess. Leukemia could be an exceedingly heterogeneous illness, with different hereditary changes contributing to its advancement and movement, {16}. Understanding the atomic and hereditary premise of leukemia has significantly extended in later a long time. Looking at sedate advancement and customized helpful mediations for leukemia sufferers, the examination has been ingested with data. Through the presentation of genomic approaches, basic information enveloping the beginning of leukemia has been collected. Within the dominance of leukemia, the enactment of the FLT3 pathway and the JAK-STAT signaling are basic {27}, embroiling that they are promising targets that can be practicable. There are recommendations that the availability and handiness of medicines can change from country to country, unexpected on certain levels of wage. Whereas comprehensive treatment is allegedly accessible in more than 90% of high-income nations, less than 15% of low-income nations have get to to such. In conclusion, information and understanding are key within the fight against cancer. By remaining educated almost the causes, chance variables, and treatment choices for cancer, people can make way better choices almost their healthcare and possibly decrease the frequency and mortality of the malady. Understanding cancer, active ongoing investment in cancer research {15}, not just of the kind going into experimental methods and theories, the basics and descriptive aspects of cancer research, contributes greatly into better comprehending this dreadful illness and coming up with possibly new breakthrough remedies. In a nutshell, aiming for a comprehensive concept of cancer matters the most when it comes to proper managing at all the stages, trying to stop effectively its spread or implementation of curative measures. Briefly - could be equivalent - trying to fully explore the cancer process, a key in numerous critical aspects involving cancer care enforcement.

Leukemia is a type of cancer that affects the white blood cells, and it has been associated with dysregulation of key signaling pathways {4}. These pathways play a crucial role in the development and progression of leukemia, making them attractive targets for therapeutic intervention. In this study, we employed a docking-based approach to identify potential drug candidates that can effectively target these key signaling pathways in leukemia. By utilizing molecular docking techniques, we aimed to predict the binding interactions between a library of compounds and the key molecules involved in leukemia signaling pathways. Through this approach, we aimed to prioritize compounds that have a high binding affinity and favorable in silico ADME properties, {26}. By targeting these key signaling pathways, we hope to discover novel drug candidates that can effectively inhibit leukemia cell growth and improve patient outcomes. Furthermore, this approach may provide insights into the underlying mechanisms of leukemia pathogenesis and aid in the development of personalized therapeutic strategies for patients with different subtypes of leukemia. Through the utilization of a docking-based approach, this study aims to identify potential drug candidates that can effectively target key signaling pathways in leukemia,  {25}. By understanding and targeting these signaling pathways, we hope to improve treatment outcomes for patients with leukemia and potentially develop more personalized therapeutic approaches. Utilizing a docking-based approach, this study aims to identify potential drug candidates that can effectively target key signaling pathways in leukemia, {33}. By understanding and targeting these signaling pathways, the study aims to improve treatment outcomes for patients with leukemia and potentially develop more personalized therapeutic approaches. The utilization of a docking-based approach in this study aims to identify potential drug candidates that can effectively target key signaling pathways in leukemia, {11}. By understanding and targeting these pathways, the study aims to improve treatment outcomes for patients with leukemia and potentially develop more personalized therapeutic approaches, {24}. The FLT3 quality, moreover known as FMS-like tyrosine kinase 3, may be a protein-coding quality that plays a significant part in hematopoiesis, the arrangement of blood cells within the bone marrow, {21}. It is located on chromosome 13q12 and encodes a receptor tyrosine kinase included within the control of cell survival, multiplication, and separation. The molecular structure of the FLT3 gene consists of several important components, {37}. The FLT3 gene contains 24 exons that are transcribed into a primary mRNA transcript. The primary mRNA transcript undergoes several post-transcriptional modifications, including splicing, to remove introns and generate a mature mRNA molecule, {17}. The mature mRNA molecule is then translated into the FLT3 protein, which consists of an extracellular domain, a transmembrane domain, and an intracellular domain. The extracellular domain of the FLT3 protein is responsible for binding to its ligand, known as FL, and initiating the signaling cascade, {30}. Upon ligand binding, the intracellular domain of FLT3 undergoes autophosphorylation at specific tyrosine residues, driving to actuation of downstream signaling pathways included in cell multiplication and survival. This activation of downstream signaling pathways is critical for normal hematopoiesis. Understanding the molecular structure of the FLT3 gene is important for comprehending its function in hematopoiesis and its potential role in diseases, such as acute myeloid leukemia, {13}. Discussions about the FLT3 gene's molecular structure typically involve its role in hematopoiesis, its location on chromosome 13q12, and the components of the gene, including its exons, mRNA transcript, and protein structure. In expansion, it is worth noticing that changes within the FLT3 quality have been recognized in a noteworthy number of patients with intense myeloid leukemia, which can lead to constitutive activation of its signaling pathways and contribute to disease progression, {15}. The FLT3 gene, also known as FMS-like tyrosine kinase 3, is an essential gene involved in hematopoiesis. Its molecular structure consists of 24 exons that are transcribed into a primary mRNA transcript. The primary mRNA transcript undergoes post-transcriptional modifications, including splicing, to generate a mature mRNA molecule, {34}. This mature mRNA molecule is translated into the FLT3 protein, which comprises of an extracellular space, a transmembrane space, and an intracellular space. The extracellular space of the FLT3 protein is capable for authoritative to its ligand, FL, and starting signaling pathways included in cell multiplication and survival In outline, the FLT3 quality plays a pivotal part in hematopoiesis and its atomic structure comprises of 24 exons, {23}. . The FLT3 gene is involved in hematopoiesis and its molecular structure includes 24 exons that are transcribed into a primary mRNA transcript.

ROLE of FLT3 GENE

The main functions and roles of FLT3 include:

Delving into the therapeutic domain closely associated with cancer, particularly acute myeloid leukemia (AML), we encounter FLT3. Explored as a target for treatment, FLT3 inhibitors have emerged, akin to tyrosine kinase inhibitors. These inhibitors endeavor to impede aberrant signaling emanating from the abnormal FLT3 signaling uniformly present within cancerous cells. We discover that such investigations and advancements originated from prior knowledge of FLT3's correlation with the genesis and exacerbation of cancer cells. As affirmed by {35}, diverse trials and attenuations have been attempted for FLT3 throughout these years by various entities. Uncertain as to the precise outcomes of these initiatives, we confront a dubious conception of definitive findings.

1.      Hematopoiesis Regulation: Differentiation and proliferation of hematopoietic stem regulation involves FLT3. Quite vital in different blood cell lineages development- red blood, white blood and platelets role is played by it cells of postorative kinds hematopoiesis and differentiation into a part of proliferation onymous is also FLT3.

2.      Immune System Function: FLT3 is particularly important for the development and maturation of dendritic cells, which are crucial for the initiation of immune responses, {38}. Dendritic cells process and present antigens to T cells, initiating the adaptive immune response.

3. Cell Survival and Apoptosis: FLT3 signaling contributes to cell survival by activating pathways that prevent apoptosis (programmed cell death). This is important for the maintenance and expansion of hematopoietic stem and progenitor cells.

4.      Oncogenesis in Acute Myeloid Leukemia (AML): Alterations in the FLT3 gene manifest frequently in acute myeloid leukemia (AML), a neoplasm of the blood. These mutations encompass internal tandem duplications and point mutations in the tyrosine kinase domain. These mutations induce constitutive activation of FLT3 signaling, engendering uncontrolled cell proliferation and persistence. Targeting these FLT3 mutations has evolved into a consequential therapeutic maneuver in AML, {22}.

5.      Target for Therapy: Due to its involvement in cancer, particularly in AML, FLT3 has been identified as a therapeutic target. Various FLT3 inhibitors, such as tyrosine kinase inhibitors, have been developed and tested for their ability to block aberrant FLT3 signaling in cancer cells, {35}.

LITERATURE REVIEW

(Natarajan et al., 2019) displayed a worldview move within the treatment of incessant myelogenous leukemia (CML) with focused on treatment utilizing exceedingly particular tyrosine kinase inhibitors (TKIs). In spite of this advance, sedate resistance caused by changes within the kinase space presents a challenge to helpful adequacy. This think about points to address this issue by examining elective restorative targets other than the BCR-ABL oncoprotein. In specific, the center in BCR-ABL is on blocking the interaction between development factor-binding protein-2 (Grb-2) and phosphorylated tyrosine (Y177), which is an vital step within the enactment of Ras and PI3K/AKT signaling pathway (Audrito et al., 2011). Utilizing computer based methods involving drug design researchers identified compounds of inhibiting the binding of Grb 2, to Y177 by targeting the binding site of the BCR domain (Xu et al., 2016). Examination of gene expressions in the GEO dataset revealed associations with processes such as hematopoietic cell line, NK cell mediated cytotoxicity, NF κB and chemokine signaling, cytokine cytokine receptor interaction, histidine metabolism and transcriptional dysregulation in cancer (Bajbouj et al., 2018). The BCR domain structure was simulated using the SPARKS X tool resulting in a Z score of 8.21. By analyzing gene expression profiles docked to BCR, a list of drugs was generated. Through Schrodinger XP docking studies compounds like diphosphopyridine nucleotide, hesperidin, butyrosine, ovoflavin and nor dihydroguaretic acid were identified for their interaction near the active binding site containing Y177 (Barrett et al. 2007). Validation was carried out using iGEMDOCK along, with Parallelized Open Babel and AutoDock suit Pipeline (POAP). This study not as it were growing the run of drugs for unused signs, but too offers the plausibility of combination treatment with standard drugs utilized within the treatment of CML. Be that as it may, the adequacy of these reusable drugs requires assist considers with considers in vitro and in vivo.

(Yang et al., 2023) highlighted that transformations in FLT3‐ITD and FLT3‐TKD contribute to over 30–35% of AML cases, supporting the enactment of FLT3 protein and activating downstream signaling proteins included in cell expansion, separation, and survival. In spite of the accessibility of various inhibitors in clinical hone focusing on these changes, the by and large survival rate for AML patients beneath medicine remains at 5 years (Singh et al., 2017). To tackle this issue researchers conducted simulations and studies, on selected plant based compounds against the FLT3 protein receptor in search of medications for FLT3 induced AML (American Physiological Society, 2019). They used docking simulations with the human FLT3 protein target (PDB ID; 6JQR). Tested 313 plant-based compounds alongside standard anticancer drugs like Sorafenib and Gilteritinib (Choudhary et.al., 2020). The proteins structure was obtained from the Protein Data Bank. Prepared using Biovia Discovery Studio. The structures of the plant based compounds were sourced from the NCBI PubChem database. Prepared using Open Babel and VConf program. PyRx on Autodock Vina was used for docking and the ADMET properties of the promising compounds were assessed using SwissADME and pkCMS web servers. The findings revealed that compounds such as glabridin, ellipticine along with its derivatives (elliptinium and 9 methoxyellipticine) mezerein, ursolic acid, formononetin, cycloartocarpesin, hypericin, silymarin and indirubin exhibited binding affinities compared to sorafenib and gilteritinib. These performing compounds demonstrated binding properties as well as favorable ADMET profiles positioning them as potential starting points or candidates for new drug discovery, against FLT3 induced AML (Sweta et al., 2019).

(Islam et al., 2024) set up that roughly 30% of patients with intense myeloid leukemia (AML) harbor enacting transformations in Cat McDonough Sarcoma (FMS)-like tyrosine kinase 3 (FLT3), making it a promising restorative target for AML treatment. Given the wide range of tyrosine kinase inhibitors accessible, which have demonstrated compelling in obstructing different stages of cell multiplication in cancer, our ponder is centered on recognizing strong antileukemic specialists against the FLT3 gene. To accomplish this objective, we at first chosen well-known antileukemic medicate candidates to make a structure focused pharmacophore is used to analyze 217,77093 compounds from the Zinc database, for screening (Adelusi et al., 2022). The distinguished hit compounds experienced docking against the target protein, and the best four compounds were at that point subjected to ADMET examination. Utilizing thickness utilitarian hypothesis (DFT), the ponder conducted geometry optimization, the evaluation of the frontier orbitals (FMO) HOMO LUMO and global reactivity descriptors confirms a profile and reactivity ranking, for the selected candidates (Chattaraj and giri 2007). In comparison to control compounds, the docking comes about uncovered significant authoritative energies (-11.1 to −11.5 kcal/mol) for the four compounds with FLT3. The physicochemical and ADMET expectations adjusted with the bioactive and secure nature of these candidates. Atomic flow (MD) examination affirmed prevalent authoritative fondness and soundness compared to gilteritinib, showing the potential of these compounds as FLT3 inhibitors. This computational approach recognizes vigorous and secure antileukemic operators, justifying advance in-vivo and in-vitro examinations for comprehensive validation.

Within the 2022 think about, (Abohassan et al., 2022) centered on Intense Myeloid Leukemia (AML), a cancer stamped by disturbed cell signaling. They highlighted the significance of focusing on the PI3K/AKT pathway (Mirza & Karim, 2023) to stifle AML cell development successfully. To move forward treatment results and decrease side impacts (Greim et al., 2014), the analysts supported for customized drugs. They utilized a combined approach to distinguish double inhibitors for PI3K and AKT (Mirza & Karim, 2023), illustrating their viability in controling AML cell proliferation. The  investigate included progressed screening methods to find little atoms within the ChemBridge library that emphatically tie to particular targets inside the PI3K pathway. The group chosen compounds with negligible off-target impacts for encourage examination, (Woods and Vassiliou, 2014). Among the recognized compounds, one named C16 showed up basic guarantee. It shown strong enjoying for key proteins inside the PI3K pathway and outlined effective anti-cancer impacts in AML cells.

(Helmi et al., 2024) Intense myeloid leukemia (AML) could be a deadly shape of cancer, characterized by the visit upregulation of B cell lymphoma 2 (BCL2), a significant player within the survival of both AML cells and AML stem cells. This consider pointed to find novel plant-based compounds focusing on BCL2 and evaluate their pharmacokinetics and harmfulness through in-silico tools. The investigate strategy included in-silico screening of phytochemicals against the BCL2 dynamic location utilizing the PyRx 0. 8 AutoDock instrument. In this way, in silico pharmacokinetic and poisonous quality expectations were conducted, (usher et al., 2017). Protein-protein interaction examination utilizing the STRING database evaluated intelligent between BCL2 and its neighboring proteins, (sabe et al., 2021). nA add up to of 1106 terpenoids compounds experienced screening to assess their authoritative fondness towards BCL2, (Del Prado-Audelo et al., 2021). Among them, five common compounds displayed strong official to the BCL2 protein, outperforming the official energies of the positive control (venetoclax). These compounds were distinguished through careful screening, nitty gritty interaction examination, and visual assessments. Critically, they illustrated higher official energies and were found to tie to key BCL2 buildups, having favorable drug-like properties, (fan et al., 2023). In conclusion, these recognized phytochemicals talk to a essential starting step in cure disclosure for managing AML. In any case, exploratory endorsement is fundamental to optimize these phytochemicals as potential BCL2 inhibitors.

MATERIAL AND METHOD

MATERIAL:

Ø  Windows XP or Windows 7

Ø  Discovery Studio Visualizer

http://accelrys.com/products/discovery-studio/visualization-download.php

METHODOLOGY:

            Docking suits (Schrödinger Maestro, Windows-x64) employing a virtual screening workflow. This workflow utilized XP hits for each official location. The proteins was arranged by limited minimization utilizing drive field OPLS4e. The network sites were created using a Float receptor grid generator with a distance of 20 angstroms. The central points of the frameworks were identified through observations, on the target protein. Ligands were prepared using the force field OPLS4e. Potential states were generated within pH range of 7.0 ± 2.0. Docking scores are reported in kilocalories, per mole, where lower numbers indicate binding affinity.

PLAN OF WORK

•         In Silico Docking Studies

•         Ligand Preparation

•         Pharmacokinetics Analyses: ADME/ Toxicology Properties

•         Protein Preparation

•         Molecular Docking Using Schrödinger Maestro

PROTEIN USED:

Table 1: 1 ETE Protein and its identification number

SELECTED PHYTOCONSTITUENT USING LIPINKI’S RULE OF FIVE

With Lipinski's Rule of Five, the phyto-constituents were screened based on the following criteria: a molecular weight of less than 500 Daltons, a partition coefficient (log P) of less than 5, no more than 10 hydrogen bond acceptors, no more than 5 hydrogen bond donors, and a polar surface area not exceeding 140 Å.

Table 2: Selected phytoconstituent using lipkins rule of five

PREADMET FOR ADME AND TOXICOLOGY PREDICTION

The PreADMET is important in prediction of the toxicology profile and pharmacokinetic profile e.g Absorption, distribution Metabolism, Excretion, using parameters like, Human intestinal Absorption, CaCO-2 permeability, Blood brain  barrier penetration, plasma protein binding, and buffer solubility.

Table 3: PREADMET for ADME and toxicology prediction

RESULTS

This chapter meticulously examines and interprets the results obtained from the conducted experiments, aiming to elucidate the key findings and their significance within the context of the research objectives.

Figure 1: Gingerol binding with 1ete protein (442793)

Figure 2: Allicin binding with 1ETE (65036)

Figure 3: Guggulsterone binding with 1ETE (6450278)

Figure 4: Resveratrol binding with 1ETE (445154)

Figure 5: capsaicin binding with 1ETE (1548943)

Figure 6:  Berberine binding with 1ETE (2353)

Figure 7: Thymoquinone binding with 1ETE (10281)

Figure 8: Pterostilbene binding with 1ETE (5281727)

Figure 9: Artemisinin binding with 1ETE (68827)

BINDING INTERACTION OF RECEPTOR- LIGAND IN 2D FORMAT

Figure 10 : Artemisinin binding with 1ETE (68827)

Figure 11: Pterostilbene binding with 1ETE (5281727)

Figure 12: Thymoquinone binding with 1ETE (10281)

Figure 13:  Berberine  binding with 1ETE (2353)

Figure 14: capsaicin binding with 1ETE (1548943)

Figure 15: Resveratrol binding with 1ETE (445154)

Figure 16: Guggulsterone binding with 1ETE (6450278)

Figure 17: Allicin binding with 1ETE (65036)

Figure 18: Gingerol binding with 1ete protein (442793)

INFORMATION ON TARGET AND COMPONENTS FOR MOLECULAR DOCKING

This table presents the binding energies (docking scores) of the selected protein in interaction with the ligands.

Table 4: Overall binding result/ docking score