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Karampuri A, Kundur S, Perugu S. Exploratory drug discovery in breast cancer patients: A multimodal deep learning approach to identify novel drug candidates targeting RTK signaling. Comput Biol Med 2024; 174:108433. [PMID: 38642491 DOI: 10.1016/j.compbiomed.2024.108433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 04/04/2024] [Accepted: 04/07/2024] [Indexed: 04/22/2024]
Abstract
Breast cancer, a highly formidable and diverse malignancy predominantly affecting women globally, poses a significant threat due to its intricate genetic variability, rendering it challenging to diagnose accurately. Various therapies such as immunotherapy, radiotherapy, and diverse chemotherapy approaches like drug repurposing and combination therapy are widely used depending on cancer subtype and metastasis severity. Our study revolves around an innovative drug discovery strategy targeting potential drug candidates specific to RTK signalling, a prominently targeted receptor class in cancer. To accomplish this, we have developed a multimodal deep neural network (MM-DNN) based QSAR model integrating omics datasets to elucidate genomic, proteomic expression data, and drug responses, validated rigorously. The results showcase an R2 value of 0.917 and an RMSE value of 0.312, affirming the model's commendable predictive capabilities. Structural analogs of drug molecules specific to RTK signalling were sourced from the PubChem database, followed by meticulous screening to eliminate dissimilar compounds. Leveraging the MM-DNN-based QSAR model, we predicted the biological activity of these molecules, subsequently clustering them into three distinct groups. Feature importance analysis was performed. Consequently, we successfully identified prime drug candidates tailored for each potential downstream regulatory protein within the RTK signalling pathway. This method makes the early stages of drug development faster by removing inactive compounds, providing a hopeful path in combating breast cancer.
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Affiliation(s)
- Anush Karampuri
- Department of Biotechnology, National Institute of Technology, Warangal, 500604, India
| | - Sunitha Kundur
- Department of Biotechnology, National Institute of Technology, Warangal, 500604, India
| | - Shyam Perugu
- Department of Biotechnology, National Institute of Technology, Warangal, 500604, India.
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Karampuri A, Perugu S. A breast cancer-specific combinational QSAR model development using machine learning and deep learning approaches. FRONTIERS IN BIOINFORMATICS 2024; 3:1328262. [PMID: 38288043 PMCID: PMC10822965 DOI: 10.3389/fbinf.2023.1328262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 12/21/2023] [Indexed: 01/31/2024] Open
Abstract
Breast cancer is the most prevalent and heterogeneous form of cancer affecting women worldwide. Various therapeutic strategies are in practice based on the extent of disease spread, such as surgery, chemotherapy, radiotherapy, and immunotherapy. Combinational therapy is another strategy that has proven to be effective in controlling cancer progression. Administration of Anchor drug, a well-established primary therapeutic agent with known efficacy for specific targets, with Library drug, a supplementary drug to enhance the efficacy of anchor drugs and broaden the therapeutic approach. Our work focused on harnessing regression-based Machine learning (ML) and deep learning (DL) algorithms to develop a structure-activity relationship between the molecular descriptors of drug pairs and their combined biological activity through a QSAR (Quantitative structure-activity relationship) model. 11 popularly known machine learning and deep learning algorithms were used to develop QSAR models. A total of 52 breast cancer cell lines, 25 anchor drugs, and 51 library drugs were considered in developing the QSAR model. It was observed that Deep Neural Networks (DNNs) achieved an impressive R2 (Coefficient of Determination) of 0.94, with an RMSE (Root Mean Square Error) value of 0.255, making it the most effective algorithm for developing a structure-activity relationship with strong generalization capabilities. In conclusion, applying combinational therapy alongside ML and DL techniques represents a promising approach to combating breast cancer.
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Affiliation(s)
| | - Shyam Perugu
- Department of Biotechnology, National Institute of Technology, Warangal, India
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3
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Kim T, Chung KC, Park H. Derivation of Highly Predictive 3D-QSAR Models for hERG Channel Blockers Based on the Quantum Artificial Neural Network Algorithm. Pharmaceuticals (Basel) 2023; 16:1509. [PMID: 38004375 PMCID: PMC10675541 DOI: 10.3390/ph16111509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 10/14/2023] [Accepted: 10/20/2023] [Indexed: 11/26/2023] Open
Abstract
The hERG potassium channel serves as an annexed target for drug discovery because the associated off-target inhibitory activity may cause serious cardiotoxicity. Quantitative structure-activity relationship (QSAR) models were developed to predict inhibitory activities against the hERG potassium channel, utilizing the three-dimensional (3D) distribution of quantum mechanical electrostatic potential (ESP) as the molecular descriptor. To prepare the optimal atomic coordinates of dataset molecules, pairwise 3D structural alignments were carried out in order for the quantum mechanical cross correlation between the template and other molecules to be maximized. This alignment method stands out from the common atom-by-atom matching technique, as it can handle structurally diverse molecules as effectively as chemical derivatives that share an identical scaffold. The alignment problem prevalent in 3D-QSAR methods was ameliorated substantially by dividing the dataset molecules into seven subsets, each of which contained molecules with similar molecular weights. Using an artificial neural network algorithm to find the functional relationship between the quantum mechanical ESP descriptors and the experimental hERG inhibitory activities, highly predictive 3D-QSAR models were derived for all seven molecular subsets to the extent that the squared correlation coefficients exceeded 0.79. Given their simplicity in model development and strong predictability, the 3D-QSAR models developed in this study are expected to function as an effective virtual screening tool for assessing the potential cardiotoxicity of drug candidate molecules.
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Affiliation(s)
| | - Kee-Choo Chung
- Department of Bioscience and Biotechnology, Sejong University, 209 Neungdong-ro, Kwangjin-gu, Seoul 05006, Republic of Korea;
| | - Hwangseo Park
- Department of Bioscience and Biotechnology, Sejong University, 209 Neungdong-ro, Kwangjin-gu, Seoul 05006, Republic of Korea;
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Balaji S. Metabophore-mediated retro-metabolic ('MeMeReMe') approach in drug design. Drug Discov Today 2023; 28:103736. [PMID: 37586644 DOI: 10.1016/j.drudis.2023.103736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 06/13/2023] [Accepted: 08/09/2023] [Indexed: 08/18/2023]
Abstract
Preclinical toxicity assessments of new drugs require the use of in silico prediction techniques as ethics, cost, time, and complexity limit in vitro and in vivo methods. This review discusses the fundamental concepts of biophores especially toxicophores and their detection methodologies, tools and techniques, as well as ongoing challenges, and methods for overcoming them. This will guide the design community in manipulating lead compounds via a pre-determined pathway based on the MeMeReMe approach. The ideas discussed will be useful both for predicting toxicity and for de-risking leads through optimization.
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Affiliation(s)
- Seetharaman Balaji
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, Karnataka 57614, India.
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Le Questel JY. Conformations and Physicochemical Properties of Biological Ligands in Various Environments. Int J Mol Sci 2023; 24:ijms24119630. [PMID: 37298581 DOI: 10.3390/ijms24119630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 05/23/2023] [Indexed: 06/12/2023] Open
Abstract
An accurate description of the conformational behavior of drug-like molecules is often a prerequisite for a comprehensive understanding of their behavior, in particular in the targeted receptor surroundings [...].
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Barchi JJ, Strain CN. The effect of a methyl group on structure and function: Serine vs. threonine glycosylation and phosphorylation. Front Mol Biosci 2023; 10:1117850. [PMID: 36845552 PMCID: PMC9950641 DOI: 10.3389/fmolb.2023.1117850] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 01/30/2023] [Indexed: 02/12/2023] Open
Abstract
A variety of glycan structures cover the surface of all cells and are involved in myriad biological processes, including but not limited to, cell adhesion and communication, protein quality control, signal transduction and metabolism, while also being intimately involved in innate and adaptive immune functions. Immune surveillance and responses to foreign carbohydrate antigens, such as capsular polysaccharides on bacteria and surface protein glycosylation of viruses, are the basis of microbial clearance, and most antimicrobial vaccines target these structures. In addition, aberrant glycans on tumors called Tumor-Associated Carbohydrate Antigens (TACAs) elicit immune responses to cancer, and TACAs have been used in the design of many antitumor vaccine constructs. A majority of mammalian TACAs are derived from what are referred to as mucin-type O-linked glycans on cell-surface proteins and are linked to the protein backbone through the hydroxyl group of either serine or threonine residues. A small group of structural studies that have compared mono- and oligosaccharides attached to each of these residues have shown that there are distinct differences in conformational preferences assumed by glycans attached to either "unmethylated" serine or ß-methylated threonine. This suggests that the linkage point of antigenic glycans will affect their presentation to the immune system as well as to various carbohydrate binding molecules (e.g., lectins). This short review, followed by our hypothesis, will examine this possibility and extend the concept to the presentation of glycans on surfaces and in assay systems where recognition of glycans by proteins and other binding partners can be defined by different attachment points that allow for a range of conformational presentations.
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Affiliation(s)
| | - Caitlin N. Strain
- Center for Cancer Research, Chemical Biology Laboratory, National Cancer Institute at Frederick, Frederick, MD, United States
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Hricovíni M, Owens RJ, Bak A, Kozik V, Musiał W, Pierattelli R, Májeková M, Rodríguez Y, Musioł R, Slodek A, Štarha P, Piętak K, Słota D, Florkiewicz W, Sobczak-Kupiec A, Jampílek J. Chemistry towards Biology-Instruct: Snapshot. Int J Mol Sci 2022; 23:14815. [PMID: 36499140 PMCID: PMC9739621 DOI: 10.3390/ijms232314815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/15/2022] [Accepted: 11/23/2022] [Indexed: 12/05/2022] Open
Abstract
The knowledge of interactions between different molecules is undoubtedly the driving force of all contemporary biomedical and biological sciences. Chemical biology/biological chemistry has become an important multidisciplinary bridge connecting the perspectives of chemistry and biology to the study of small molecules/peptidomimetics and their interactions in biological systems. Advances in structural biology research, in particular linking atomic structure to molecular properties and cellular context, are essential for the sophisticated design of new medicines that exhibit a high degree of druggability and very importantly, druglikeness. The authors of this contribution are outstanding scientists in the field who provided a brief overview of their work, which is arranged from in silico investigation through the characterization of interactions of compounds with biomolecules to bioactive materials.
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Affiliation(s)
- Miloš Hricovíni
- Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, 845 38 Bratislava, Slovakia
| | - Raymond J. Owens
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus, UK, University of Oxford, Oxford OX11 0QS, UK
- Division of Structural Biology, The Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Andrzej Bak
- Institute of Chemistry, University of Silesia, Szkolna 9, 40 007 Katowice, Poland
| | - Violetta Kozik
- Institute of Chemistry, University of Silesia, Szkolna 9, 40 007 Katowice, Poland
| | - Witold Musiał
- Department of Physical Chemistry and Biophysics, Pharmaceutical Faculty, Wroclaw Medical University, Borowska 211A, 50 556 Wrocław, Poland
| | - Roberta Pierattelli
- Magnetic Resonance Center and Department of Chemistry “Ugo Schiff”, University of Florence, 50019 Sesto Fiorentino, Italy
| | - Magdaléna Májeková
- Center of Experimental Medicine SAS and Department of Biochemical Pharmacology, Institute of Experimental Pharmacology and Toxicology, Slovak Academy of Sciences, Dubravska cesta 9, 841 04 Bratislava, Slovakia
| | - Yoel Rodríguez
- Department of Natural Sciences, Eugenio María de Hostos Community College, City University of New York, 500 Grand Concourse, Bronx, NY 10451, USA
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Robert Musioł
- Institute of Chemistry, University of Silesia, Szkolna 9, 40 007 Katowice, Poland
| | - Aneta Slodek
- Institute of Chemistry, University of Silesia, Szkolna 9, 40 007 Katowice, Poland
| | - Pavel Štarha
- Department of Inorganic Chemistry, Faculty of Science, Palacký University Olomouc, 17. listopadu 1192/12, 771 46 Olomouc, Czech Republic
| | - Karina Piętak
- Department of Materials Science, Faculty of Materials Engineering and Physics, Cracow University of Technology, 37 Jana Pawła II Av., 31 864 Krakow, Poland
| | - Dagmara Słota
- Department of Materials Science, Faculty of Materials Engineering and Physics, Cracow University of Technology, 37 Jana Pawła II Av., 31 864 Krakow, Poland
| | - Wioletta Florkiewicz
- Department of Materials Science, Faculty of Materials Engineering and Physics, Cracow University of Technology, 37 Jana Pawła II Av., 31 864 Krakow, Poland
| | - Agnieszka Sobczak-Kupiec
- Department of Materials Science, Faculty of Materials Engineering and Physics, Cracow University of Technology, 37 Jana Pawła II Av., 31 864 Krakow, Poland
| | - Josef Jampílek
- Department of Analytical Chemistry, Faculty of Natural Sciences, Comenius University, Ilkovičova 6, 842 15 Bratislava, Slovakia
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Gervasoni S, Malloci G, Bosin A, Vargiu AV, Zgurskaya HI, Ruggerone P. AB-DB: Force-Field parameters, MD trajectories, QM-based data, and Descriptors of Antimicrobials. Sci Data 2022; 9:148. [PMID: 35365662 PMCID: PMC8976083 DOI: 10.1038/s41597-022-01261-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 03/11/2022] [Indexed: 12/13/2022] Open
Abstract
Antibiotic resistance is a major threat to public health. The development of chemo-informatic tools to guide medicinal chemistry campaigns in the efficint design of antibacterial libraries is urgently needed. We present AB-DB, an open database of all-atom force-field parameters, molecular dynamics trajectories, quantum-mechanical properties, and curated physico-chemical descriptors of antimicrobial compounds. We considered more than 300 molecules belonging to 25 families that include the most relevant antibiotic classes in clinical use, such as β-lactams and (fluoro)quinolones, as well as inhibitors of key bacterial proteins. We provide traditional descriptors together with properties obtained with Density Functional Theory calculations. Noteworthy, AB-DB contains less conventional descriptors extracted from μs-long molecular dynamics simulations in explicit solvent. In addition, for each compound we make available force-field parameters for the major micro-species at physiological pH. With the rise of multi-drug-resistant pathogens and the consequent need for novel antibiotics, inhibitors, and drug re-purposing strategies, curated databases containing reliable and not straightforward properties facilitate the integration of data mining and statistics into the discovery of new antimicrobials. Measurement(s) | molecular physical property analysis objective | Technology Type(s) | Computer Modeling |
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Affiliation(s)
- Silvia Gervasoni
- University of Cagliari, Department of Physics, I-09042, Monserrato (Cagliari), Italy
| | - Giuliano Malloci
- University of Cagliari, Department of Physics, I-09042, Monserrato (Cagliari), Italy.
| | - Andrea Bosin
- University of Cagliari, Department of Physics, I-09042, Monserrato (Cagliari), Italy
| | - Attilio V Vargiu
- University of Cagliari, Department of Physics, I-09042, Monserrato (Cagliari), Italy
| | - Helen I Zgurskaya
- University of Oklahoma, Department of Chemistry and Biochemistry, Norman, OK, 73072, United States
| | - Paolo Ruggerone
- University of Cagliari, Department of Physics, I-09042, Monserrato (Cagliari), Italy
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Unsupervised Learning in Drug Design from Self-Organization to Deep Chemistry. Int J Mol Sci 2022; 23:ijms23052797. [PMID: 35269939 PMCID: PMC8910896 DOI: 10.3390/ijms23052797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 02/27/2022] [Accepted: 02/27/2022] [Indexed: 12/10/2022] Open
Abstract
The availability of computers has brought novel prospects in drug design. Neural networks (NN) were an early tool that cheminformatics tested for converting data into drugs. However, the initial interest faded for almost two decades. The recent success of Deep Learning (DL) has inspired a renaissance of neural networks for their potential application in deep chemistry. DL targets direct data analysis without any human intervention. Although back-propagation NN is the main algorithm in the DL that is currently being used, unsupervised learning can be even more efficient. We review self-organizing maps (SOM) in mapping molecular representations from the 1990s to the current deep chemistry. We discovered the enormous efficiency of SOM not only for features that could be expected by humans, but also for those that are not trivial to human chemists. We reviewed the DL projects in the current literature, especially unsupervised architectures. DL appears to be efficient in pattern recognition (Deep Face) or chess (Deep Blue). However, an efficient deep chemistry is still a matter for the future. This is because the availability of measured property data in chemistry is still limited.
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Matsuzaka Y, Uesawa Y. A Deep Learning-Based Quantitative Structure-Activity Relationship System Construct Prediction Model of Agonist and Antagonist with High Performance. Int J Mol Sci 2022; 23:ijms23042141. [PMID: 35216254 PMCID: PMC8877122 DOI: 10.3390/ijms23042141] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 02/12/2022] [Accepted: 02/14/2022] [Indexed: 01/27/2023] Open
Abstract
Molecular design and evaluation for drug development and chemical safety assessment have been advanced by quantitative structure–activity relationship (QSAR) using artificial intelligence techniques, such as deep learning (DL). Previously, we have reported the high performance of prediction models molecular initiation events (MIEs) on the adverse toxicological outcome using a DL-based QSAR method, called DeepSnap-DL. This method can extract feature values from images generated on a three-dimensional (3D)-chemical structure as a novel QSAR analytical system. However, there is room for improvement of this system’s time-consumption. Therefore, in this study, we constructed an improved DeepSnap-DL system by combining the processes of generating an image from a 3D-chemical structure, DL using the image as input data, and statistical calculation of prediction-performance. Consequently, we obtained that the three prediction models of agonists or antagonists of MIEs achieved high prediction-performance by optimizing the parameters of DeepSnap, such as the angle used in the depiction of the image of a 3D-chemical structure, data-split, and hyperparameters in DL. The improved DeepSnap-DL system will be a powerful tool for computer-aided molecular design as a novel QSAR system.
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Affiliation(s)
- Yasunari Matsuzaka
- Department of Medical Molecular Informatics, Meiji Pharmaceutical University, Kiyose 204-8588, Japan;
- Center for Gene and Cell Therapy, Division of Molecular and Medical Genetics, The Institute of Medical Science, University of Tokyo, Minato City 108-8639, Japan
| | - Yoshihiro Uesawa
- Department of Medical Molecular Informatics, Meiji Pharmaceutical University, Kiyose 204-8588, Japan;
- Correspondence: ; Tel.: +81-42-495-8983
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Mikhailov OV. The Physical Chemistry and Chemical Physics (PCCP) Section of the International Journal of Molecular Sciences in Its Publications: The First 300 Thematic Articles in the First 3 Years. Int J Mol Sci 2021; 23:ijms23010241. [PMID: 35008667 PMCID: PMC8745423 DOI: 10.3390/ijms23010241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 12/15/2021] [Indexed: 11/16/2022] Open
Abstract
The Physical Chemistry and Chemical Physics Section (PCCP Section) is one of the youngest among the sections of the International Journal of Molecular Sciences (IJMS)—the year 2021 will only mark three years since its inception [...]
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Affiliation(s)
- Oleg V Mikhailov
- Department of Analytical Chemistry, Certification and Quality Management, Kazan National Research Technological University, K. Marx Street 68, 420015 Kazan, Russia
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