Computational Methodologies in the Discovery of Natural multi-target Drugs in Cancer Treatment
Mohammad Chand Jamali1*, Sameh Elsonbaty1, Amina Toumi1, Ali Jaber M Alqahtani1,
Mohammed Abdalhamied M. Abushohada2, Ahmed Atef Ibrahim Belal3
Hanan Mesfer Alyami4, Maxime Merheb5
Shashi Kumar6, Rakesh Kumar Singh7, Adham Elsonbaty8
1College of Medical and Health Sciences, Liwa University, Abu Dhabi, United Arab Emirates.
2Thumbay College of Management and AI in Healthcare, Gulf Medical University, Ajman,
United Arab Emirates.
3Department of Health Research Methods, Evidence and Impact, McMaster University, Hamilton, Canada.
4Department of Medical and Surgical Nursing, College of Nursing, Princess Nourah Bint Abdulrahman University, Riyadh 13412, Saudi Arabia.
5College of Health Sciences, Dubai Medical University, Dubai, United Arab Emirates.
6Director and HOD Nephrology, Paras HMRI, Patna, India.
7Head, Centre for Nanoscience and Nanotechnology, Aryabhatta Knowledge University Patna, India.
8Medical Student, College of Medicine October 6 University, Egypt.
*Corresponding Author E-mail: mjamali68@gmail.com, sameh.elsonbaty@lu.ac.ae, amina.eltomi@lu.ac.ae, ali.alqahtani@lu.ac.ae, dr.abdalhamied@gmu.ac.ae, belala@mcmaster.ca, malyami@pnu.edu.sa, maxime.merheb@dmu.ae, shashigmc@yahoo.co.in, rakeshsinghpu@gmail.com, adham.elsonbaty@gmail.com
ABSTRACT:
Introduction: A new era in drug discovery must start. Almost all pharmaceutical development methods use computer-based data and findings. This article highlights advanced simulation techniques for drug development. By 2040, the worldwide cancer burden will reach 30 million new cases, with the highest growth in lowand middle-income nations. By 2040, cancer diagnoses are predicted to grow by 55 percent, reaching 6.23 million in the Americas. Kinetic profiles of ligand binding mechanisms and drug-target affinities must be investigated. Methodology: A systematic literature review was conducted using multiple academic and scientific databases, including ResearchGate, ScienceDirect, CORE Library, Google, Web of Science, Google Scholar, and Scientific Digital Library Online (SciELO). The search covered publications from August 2009 to August 2024 to ensure the inclusion of foundational and recent studies. Result and Discussion: Plant-derived drugs include methyl transferase inhibitors, DNA damage inhibitors, HDAC inhibitors, and mitotic disruptorsthe compounds' anticancer effectiveness and clinical trial development. MTAs are currently used in cancer detection since they target specific driver genes or diagnostics. This method is constrained by the high gene alterations in multiple driving genes in each tumor. Digital drug assignment (DDA) method that prioritizes potential.
KEYWORDS: Computational drug discovery, Multi-target drug development, Cancer treatment, Natural compounds in drug discovery, Ligand binding kinetics, Computer-aided drug design (CADD).
INTRODUCTION:
Cancer can occur in practically any organ or tissue in the body when aberrant cells proliferate unchecked, cross their boundaries, and spread to other parts of the body and to other organs.1 Patients who have cancer are more likely to die if the disease spreads. Metastasizing is the term for this. Two more words for cancer are neoplasm and malignant tumor. Cancer claimed the lives of 9.6 million people around the world in 2018, or one in every six people. Most common cancers in men include lung, prostrate, colon, stomach, and liver. There are people worldwide whose health, mental health, and financial well-being are being adversely affected by the rising incidence of cancer2. Many cancer patients worldwide are unable to receive timely and appropriate medical care because of underdeveloped health systems in low and middle-income countries. In 2019, predicted that the year 2000 would see 20 incidences of breast cancer and 10 million deaths from cancer. World Health Organization In the next two decades, the burden of cancer is expected to rise by nearly 60 percent, putting significant strain on health systems, individuals, and communities3.There will be an estimated 30 million additional cancer cases worldwide by 2040. The most considerable growth will be seen among developing countries, particularly in low and medium-income countries. If no other measures are taken to prevent and control cancer, the number of cancer diagnoses in the Americas will rise by 55% to 6.23 million by 2040. Common cancers are also one of the most hazardous because they can go undetected at various stages of the disease. Early detection of tumors is expected to improve patient survival rates due to this new technology. True positives are generated in great numbers by this method. In 2020, Low-dose CT radiation exposure may also raise a patient's cancer risk4,5.
Due to the enormous population that needs to be screened, a new, less invasive screening method is needed. To ensure that such a broad spectrum of healthcare professionals can operate the technology effectively, as of Sensors and microelectronics can be used in various industries to reduce the size of complex equipment5. Medical technology has led to the development of diagnostic sensors over time. Sensor development in this field focuses on precisely identifying biomarkers and volatile metabolites associated with lung cancer. Their approaches to discovering cancer-related chemicals differed substantially as a result5. It is necessary to have sensors that can identify specific molecules.
METHODOLOGY:
Researchers searched literature from August 2011 to August 2021 using methods utilized in prior study initiatives abroad. Each database was searched. E-research archives contain data from peer-reviewed articles, books, research papers, patent filings, and other anticancer plant studies. These records date back to August 2021. The most common cancers that affect both men and women include prostate and breast cancer, as well as Kaposi sarcoma and Burkitt's lymphoma.
RESULT AND DISCUSSION:
Evaluation of Cancer Target Medication:
Proteins are ideal for cancer treatment because they are natural and readily available. Incorporating protein into a patient's regular diet is simple due to its high absorption rate. Compared to synthetic substances, proteins are less toxic to human cells and are more tolerated by the body6. Some exceptions include cyanogenetic glycosides and lignans, and some taxanes. Clinical trials may be possible for plant-derived medicines if the study is selective, nontoxic to regular cell lines, and cytotoxic to cancer cells. A few years ago, Inhibitors of histone deacetylase (HDA), methyltransferase (MT), or mitotic disruption (MD) were all examples of plant-derived medicines7. As seen in Figure 1, the numerous substances under review include their origin, anticancer activity, and development toward clinical trials in 1997.
Figure 1: Natural bioactive components discovery from 18th to 19th Century.
Sulforaphane, isothiocyanates, isoflavones, and pomiferin are all HDAC inhibitors. They block carcinogenic proteins from causing cancer8. Sulforaphane, for example, blocks critical targets in breast cancer development. Sulforaphane reduced ER, EGFR, and HER-2 expression in breast cancer cell lines. Apoptotic cells can enter apoptosis when HDAC inhibitors reactivate epigenetically suppressed acetylation-dependent genes (apoptosis)8. Plant-derived HDAC inhibitors can cure human malignancies more successfully. Vinca alkaloid derivatives include vincristine, vinblastine, vinorelbine, vindesine, and vinflunine target microtubule dynamics by binding to tubulin. Taxanes like these, including Paclitaxel and docetaxel, destroy microtubules. These chemicals hinder metaphase-anaphase transition, causing growth arrest and death. Paclitaxel works by stabilizing or polymerizing microtubules within cancer cells. Paclitaxel changed cancer treatment, and vincristine and vinblastine, two of its variants, were identified first. Plant extracts combining vinca alkaloids, Urtica membranaceous, Taxus diterpenes, Podophyllum lignans, and Camptotheca alkaloids may have improved anticancer effects9. The study indicated that anticancer plant extracts might destroy cancer cells without affecting normal human lymphocytes and fibroblasts. Using plant extracts instead of chemical ones minimizes the chance of hazardous side effects. The plant extracts improved the number of G1 cells with decreased DNA content and chromatin condensation.
Traditional Concept for cancer management:
Although the public has spent billions on cancer research, no medications have been shown to lessen the mortality rate from the disease10. Doctors often assume that only synthetic treatments like chemotherapy or surgery can cure the disease. In contrast, these drugs encourage the growth of cancer cells. In contrast, ancient metaphysics and systems had a firm grasp of balance, harmony, and life concepts. In the fight against cancer, modern medicine has fallen short due to its failure to recognize the role of immunity. In 2012, traditional healers were aware of it, but contemporary science was unaware of it at the time. Cancer-induced imbalances have not been addressed by existing treatment, according to experts. Smoking and drinking are the two things that can stabilize your body and lower your risk of cancer. Modern drugs and medicines can become carcinogens when used for an extended period because of their ability to generate mutations11. Re-energizing the cells requires a sattvic diet rich in green and rainbow foods. One of the most popular myths about veganism is that it can heal and prevent cancer. Cancer cells are said to be energized and balanced by several modalities, including yoga, acupuncture, and crystal treatment. Controlling or regulating one's anger, emotions, and desires can be beneficial. It is possible to achieve inner peace and harmony via compassionate life12.
Methods for identifying cancer drivers based on gene mutations.:
A gene known as a "driver" must be changed in order for a tumor to grow. Cell division, checkpoints, and other genomic alterations accumulate in cancer cells as a result of driver mutations, which are somatic mutations that contribute to abnormal cell proliferation and carcinogenesis (Figure 2). Mutations that have no effect on the cells may be possible13. In 2007, due to clonal proliferation, all final cancer cells will have attendant mutations, making them just as important as driving mutations14.
Figure 2: Mutations in the driver genes in the genome induce tumorigenicity in the cell.
Proto-oncogenes and tumor suppressor genes are two cancer-causing genes. Oncogene genes like BRAF, KRAS, or MYC must have a gain of function mutation to become cancerous. Two copies of the tumor suppressor gene must be inactivated for the tumor to form. This includes TP53, PTEN, and CDKN2A. Finding driver genes can be done by looking for DNA sequences that affect a particular protein location15. These genes can be used to classify mutations that cause disease. Those genes that have changed more frequently than expected are known as driver genes. In multi-cancer patients, driver changes are more common.
In 2009, mutational processes have caused an overstock of mutations relative to the projected base rate, leading to a new class of approaches for finding areas of DNA. It has been discovered that 568 genes are responsible for 28,000 tumors and 66 malignancies. Only 2% of driver mutations in proteins are accountable for the more than 20 different malignancies caused16. Knowledge of driver genes and their tumorigenic potential is necessary for cancer patients' antibody or other inhibitor treatment. There are still many unanswered questions about driving genes. In contrast to rare genes, those that often occur in the human population are discovered. A rare genetic mutation drives less than 1% of all malignancies17.
Figure 3: Classification of drive gene.
To understand why particular driver mutations are so rare, researchers used a theoretical framework. The protein is activated by tissue-specific driver mutations with high or low frequency, according to the explanation. Because just a few driver mutations happen, the protein activation is insufficient, according to the theory of this study. Even while clinically unusual drivers may be found, computational18,19 software may not, which creates an entirely different set of complications18. It is becoming more and more common knowledge that non-coding genes contribute to the occurrence of driving mutations, but their total number in the human genome is still very small. From a study stated that These components generate extraordinarily lengthy sequences, notwithstanding our discovery20.
Nano-medication for cancer drug development:
Nanoparticles have unique physical and chemical properties because of their small size and high surface-to-volume ratio. In the 2017, Tinkle S nanoparticles, made of biocompatible materials, are used in cancer therapy to solve issues such as limited specificity and bioavailability21. Increased solubility/biocompatibility, stability in physiological fluids, and retention duration in tumor vasculature benefit nanoparticle encapsulation. As an alternative, nanoparticles can be designed to release medications in reaction to specific triggers. A study stated that when the temperature changes, ThermoDox releases doxorubicin from the liposomes. Gold nanoparticles are attractive because of their optical, electrical, and toxicological properties. They are used in X-ray, CT, photoacoustic, and photodynamic therapy as contrast agents. The FDA approved AuroShell (Nanospectra) in 2012 to treat breast cancer with photodynamic therapy21. Drugs can deliver by using organic nanoparticles. There are two types of phospholipids: micelles and liposomes, both of which have the same structure. Similar to cell membranes, liposomes are spheres that contain at least one layer of lipid. Hydrophobic drugs can also be incorporated into the bilayer or chemically attached particles. The hydrophobic core of micelles allows them to encapsulate medications. Doxorubicin-loaded PEGylated liposomes were licensed by the FDA in 1995 for use in the treatment of AIDS-associated Kaposi's sarcoma22. There are fewer adverse effects associated with Doxorubicin use. Many liposomal cancer medicines, such as Myocet and DaunoXome, have been approved by the FDA since that time. They are highly flexible since their architecture can easily manipulated. Poly-L-lysine dendrimers loaded with doxorubicin have been shown to decrease angiogenesis in a tumor model23.
Virtual Screening and Molecular docking of Cancer drugs:
By utilizing computer-aided drug design, you may save money, time, and effort to create new medications. In 2020, Chemotherapy has long targeted DNA replication because cancer cells expand unchecked compared to non-cancerous ones. DNA replication-licensing complex component MCM7 is a possible therapeutic target in some malignancies. We computationally tested 452 biogenic chemicals for their ability to bind to the MCM7 protein using the UEFS Natural Products dataset. According to three of them (UEFS99, UEFS137, and UEFS428) were shown to be very MCM7-specific (see below). Twelve active site amino acids in MCM7 are targeted by UEFS99 (Pro383, Gln384, Val 385, Ala386, Lys387, Ser388, Gln389, Asp445, Glu446, Lys449, Ala487, and Asn489). Van der Waals interactions between UEFS99 and MCM7 include Asp445, Gln389, and Lys449 of MCM7 (Figure 4).
Figure 4: UEFS99-binding residues in MCM7 Residual interactions are denoted by a variety of colors.
Digital drug assignment development for Artificial Intelligence:
Machine learning is commonly referred to as "artificial intelligence" (AI) (ML). When it comes to artificial intelligence (AI), computer science and the FDA's action plan use the term "intelligent computer programs24." In 2019, it is difficult to find good predictive algorithms for treatment decisions based on ML because of the various variables that influence MTA efficacy. An advanced then rule-based expert system was employed to build the DDA system based on the experimental data. Transparency, openness, and consistency are all hallmarks of rule-based expert systems. reduced the system's complexity. The Realtime Oncology Treatment CalculatorTM uses TMB, MSI, druggable targets, MTAs, and tumor type in its calculations25 (Figure 5). In addition, COSMIC was incorporated. A gene's molecular changes and druggable target genes and MTAs are all considered by the DDA algorithm during scoring26. In 2020, the MDAP will be implemented. Then, based on their link to all of the tumor's putative driver genes, it assigns each gene a score. Based on how many "driver genes" they have, how many "target genes," and their ratings, MTAs are ranked. A study by According to evidence, biological parameters in one tumor can be compared to those in other tumors to compute weights27.
Figure 5: Schematic representation of a digital medication assignment system (DDA). Druggable molecular targets (TARGET) and cancer-promoting genes (DRIVER) have been linked (MTA). A DDA score is produced for each driver gene present in the tumour, together with their targets and MTAs. In the AEL score computation for DRIVERS, TARGETS, and MTAs, the lines represent evidence-based functional associations, not physical correlations.
CONCLUSION:
Overexpression of MCM7, a DNA replication license complex component, is found in several types of human malignancies28-31. To discover MCM7 inhibitors, biogenic chemicals were screened against the MCM7 protein. DDA was used in this investigation to determine which MTAs should be prioritized for precision oncology. DDA is a sophisticated artificial intelligence (AI) system. Each case's unique algorithm, evidence database, and comprehensive explanations of reasoning and action procedure are all accessible to human quality assurance. Ifthen links and techniques abound in the expert system. These devices are included in the FDA's AI/ML Action Plan for Medical Devices32-36. The advantages of using an electronic nose versus a biosensor are numerous. In this way, the sensor can be utilized for multiple readings without any degradation in performance. Large-scale manufacture of these items is now possible. Modern science must first grasp and support traditional principles like harmony, healing, and compassion30. Balance, repair, and compassion can only be supported by modern science. Anticancer drugs produced from plants are becoming more popular because of their efficacy. Regulating these agents is necessary to accommodate demand and ensure their long-term viability. Sections of this report detail some of the leading players in the Cancer Cognitive Computing market at the end of the study37-40.' These companies include IBM; Microsoft; Google; Apple; Palantir; Alacris; and others. Financial information, product and service offerings, and recent developments are all included in this report41,42. Additionally, the big players in the industry are discussed both favorably and unfavorably in this part. As a result of this research, companies can use the data to develop business plans and identify new market opportunities in the cancer cognitive computing industry worldwide42.
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Received on 20.04.2025 Revised on 04.08.2025 Accepted on 16.10.2025 Published on 20.05.2026 Available online from May 25, 2026 Research J. Pharmacy and Technology. 2026;19(5):2343-2348. DOI: 10.52711/0974-360X.2026.00336 © RJPT All right reserved
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