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1.
Sci Rep ; 13(1): 21069, 2023 11 29.
Artigo em Inglês | MEDLINE | ID: mdl-38030689

RESUMO

The discovery of potential therapeutic agents for life-threatening diseases has become a significant problem. There is a requirement for fast and accurate methods to identify drug-like molecules that can be used as potential candidates for novel targets. Existing techniques like high-throughput screening and virtual screening are time-consuming and inefficient. Traditional molecule generation pipelines are more efficient than virtual screening but use time-consuming docking software. Such docking functions can be emulated using Machine Learning models with comparable accuracy and faster execution times. However, we find that when pre-trained machine learning models are employed in generative pipelines as oracles, they suffer from model degradation in areas where data is scarce. In this study, we propose an active learning-based model that can be added as a supplement to enhanced molecule generation architectures. The proposed method uses uncertainty sampling on the molecules created by the generator model and dynamically learns as the generator samples molecules from different regions of the chemical space. The proposed framework can generate molecules with high binding affinity with [Formula: see text]a 70% improvement in runtime compared to the baseline model by labeling only [Formula: see text]30% of molecules compared to the baseline oracle.


Assuntos
Ensaios de Triagem em Larga Escala , Software
2.
Front Med (Lausanne) ; 9: 916481, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-36213671

RESUMO

The pursuit of potential inhibitors for novel targets has become a very important problem especially over the last 2 years with the world in the midst of the COVID-19 pandemic. This entails performing high throughput screening exercises on drug libraries to identify potential "hits". These hits are identified using analysis of their physical properties like binding affinity to the target receptor, octanol-water partition coefficient (LogP) and more. However, drug libraries can be extremely large and it is infeasible to calculate and analyze the physical properties for each of those molecules within acceptable time and moreover, each molecule must possess a multitude of properties apart from just the binding affinity. To address this problem, in this study, we propose an extension to the Machine learning framework for Enhanced MolEcular Screening (MEMES) framework for multi-objective Bayesian optimization. This approach is capable of identifying over 90% of the most desirable molecules with respect to all required properties while explicitly calculating the values of each of those properties on only 6% of the entire drug library. This framework would provide an immense boost in identifying potential hits that possess all properties required for a drug molecules.

3.
Chem Commun (Camb) ; 58(35): 5316-5331, 2022 Apr 28.
Artigo em Inglês | MEDLINE | ID: mdl-35416193

RESUMO

The discovery of new molecules and materials helps expand the horizons of novel and innovative real-life applications. In pursuit of finding molecules with desired properties, chemists have traditionally relied on experimentation and recently on combinatorial methods to generate new substances often complimented by computational methods. The sheer size of the chemical space makes it infeasible to search through all possible molecules exhaustively. This calls for fast and efficient methods to navigate the chemical space to find substances with desired properties. This class of problems is referred to as inverse design problems. There are a variety of inverse problems in chemistry encompassing various subfields like drug discovery, retrosynthesis, structure identification, etc. Recent developments in modern machine learning (ML) methods have shown great promise in tackling problems of this kind. This has helped in making major strides in all key phases of molecule discovery ranging from in silico candidate generation to their synthesis with a focus on small organic molecules. Optimization techniques like Bayesian optimization, reinforcement learning, attention-based transformers, deep generative models like variational autoencoders and generative adversarial networks form a robust arsenal of methods. This highlight summarizes the development of deep learning to tackle a wide variety of inverse design problems in chemistry towards the quest for synthesizing small organic compounds with a purpose.


Assuntos
Aprendizado Profundo , Teorema de Bayes , Desenho de Fármacos , Descoberta de Drogas/métodos , Aprendizado de Máquina
4.
J Chem Inf Model ; 61(12): 5815-5826, 2021 12 27.
Artigo em Inglês | MEDLINE | ID: mdl-34866384

RESUMO

The design of new inhibitors for novel targets is a very important problem especially in the current scenario with the world being plagued by COVID-19. Conventional approaches such as high-throughput virtual screening require extensive combing through existing data sets in the hope of finding possible matches. In this study, we propose a computational strategy for de novo generation of molecules with high binding affinities to the specified target and other desirable properties for druglike molecules using reinforcement learning. A deep generative model built using a stack-augmented recurrent neural network initially trained to generate druglike molecules is optimized using reinforcement learning to start generating molecules with desirable properties like LogP, quantitative estimate of drug likeliness, topological polar surface area, and hydration free energy along with the binding affinity. For multiobjective optimization, we have devised a novel strategy in which the property being used to calculate the reward is changed periodically. In comparison to the conventional approach of taking a weighted sum of all rewards, this strategy shows an enhanced ability to generate a significantly higher number of molecules with desirable properties.


Assuntos
COVID-19 , Desenho de Fármacos , Humanos , Redes Neurais de Computação , Recompensa , SARS-CoV-2
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