Abstract

Exploring promiscuous catalytic activity of enzymes to stereoselective transformations uncovers ecofriendly asymmetric catalysts and provides scope to execute new-to-nature chemistry. Biocatalytic promiscuous diastereoselective Henry reaction (DHR) is restricted to a few hydroxynitrile lyases (HNLs), often engineered, with narrow synthetic scope and anti-selectivity. Here, we report a single native enzyme exhibiting complementary diastereoselectivity in an asymmetric Henry reaction. Baliospermum montanum HNL (BmHNL)-catalyzed DHR enabled the production of thirty-two anti-(1S,2R)-β-nitroalcohols with up to >99% conversion, >99% ee, and >99% de using longer nitroalkanes. It afforded syn diastereomers, i.e., (1S,2S)-β-nitroalcohols as thermodynamically controlled products by manipulating the reaction conditions. Reuse of BmHNL in DHR for 20 cycles has empowered the synthesis of (1S,2R)-2-nitro-1-phenylpropan-1-ol (NPP), where it retained 82% of its initial activity, maintained >99% ee on each cycle, and provided total turnover number >3.7 × 104, which is 140-fold higher compared to the only existing biocatalytic DHR. Our study demonstrates a gram-scale synthesis of (1S,2R)-NPP and a preparative-scale synthesis of (1S,2S)-NPP, a precursor to d-norpseudoephedrine used for the treatment of obesity. The origin of the inverse diastereoselectivity was probed using isotope labeling studies. Molecular modeling of the reaction using density functional theory methods reveals the underlying mechanism of the diastereoselectivity and the competing kinetic vs thermodynamic nature of the reaction. Despite a promiscuous catalytic activity, the outstanding catalytic efficiency, broad synthetic scope, and complementary diastereoselectivity of the native enzyme of BmHNL on DHR are remarkable, which illustrates it as a specialized biocatalyst for greener technology and stereocontrolled production of diverse β-nitroalcohols.

Abstract

AuCu nanoclusters have widespread application in reactions like activation of CO2, selective oxidation, and cross-coupling reactions. In this study, we investigate the stepwise doping of copper atoms in a pure 13-atom gold cluster, denoted as AumCun (m+n = 13). The genetic algorithm based on the artificial bee colony algorithm has been utilized to model various isomers of each composition. The potential energy landscape of these clusters was analyzed by means of the density functional theory method with pure Perdew−Burke−Ernzerhof (PBE) functional. We identify the minimum energy isomer for each cluster composition to evaluate molecular properties like HOMO–LUMO gap, binding energy/atom, second order difference in energy, vertical ionization energy, and vertical electron affinity. Notably, the introduction of copper atoms in these clusters enhances their stability and reactivity. Distinct odd–even oscillations due to close shell electronic configurations are absent, as all cluster compositions have an overall open shell configuration. To assess the catalytic activity of the clusters, we study the adsorption energies of small molecules like O 2 and C 2 H 4 on all available sites on the cluster. This study thereby comprehensively explores the range of copper-doped 13-atom gold cluster compositions and their implications on their structure–property relationships vital for catalysis and nanomaterial applications.

Abstract

Chemical reaction prediction, encompassing forward synthesis and retrosynthesis, stands as a fundamental challenge in organic synthesis. A widely adopted computational approach frames synthesis prediction as a sequence-to-sequence translation task, using the commonly used SMILES representation for molecules. The current evaluation of machine learning methods for retrosynthesis assumes perfect training data, overlooking imperfections in reaction equations in popular datasets, such as missing reactants, products, other physical and practical constraints such as temperature and cost, primarily due to a focus on the target molecule. This limitation leads to an incomplete representation of viable synthetic routes, especially when multiple sets of reactants can yield a given desired product. In response to these shortcomings, this study examines the prevailing evaluation methods and introduces comprehensive metrics designed to address imperfections in the dataset. Our novel metrics not only assess absolute accuracy by comparing predicted outputs with ground truth but also introduce a nuanced evaluation approach. We provide scores for partial correctness and compute adjusted accuracy through graph matching, acknowledging the inherent complexities of retrosynthetic pathways. Additionally, we explore the impact of small molecular augmentations while preserving chemical properties and employ similarity matching to enhance the assessment of prediction quality. We introduce SynFormer, a sequence-to-sequence model tailored for SMILES representation. It incorporates architectural enhancements to the original transformer, effectively tackling the challenges of chemical reaction prediction. SynFormer achieves a Top-1 accuracy of 53.2% on the USPTO-50k dataset, matching the performance of widely accepted models like Chemformer, but with greater efficiency by eliminating the need for pre-training.

Abstract

Drug-Drug Interactions (DDI) can trigger unexpected pharmacological consequences, including adverse drug events (ADE). The rise in polypharmacy underscores the importance of understanding how different drug molecules influence each other’s pharmacological activities and necessitates the investigation of potential interactions between newly developed drugs and existing medications. Traditional laboratory methods for DDI detection are time-consuming, making the development of computational prediction methods crucial. This study introduces GraphDDI, a machine learning method utilizing Graph Neural Networks (GNN) to predict DDI accurately. The proposed methodology, trained end-to-end, comprises three stages. (1) Featurization stage: A GNN extracts atomic features from two drugs separately. (2) Interaction stage: an interaction map is calculated between all atom pairs of the drugs. (3) Prediction stage: the model combines the interaction map and drug features to create a unified representation of the drug molecules. Subsequently, the model concatenates these representations and employs a feed-forward neural network to predict the DDI. We demonstrate the efficacy of our proposed model in predicting both the presence of DDI and the specific types of interactions (DDI events). Comparative analysis reveals that our framework surpasses existing models, achieving an F1 score of 0.98 in predicting the existence of drug-drug interactions and 0.90 in categorizing DDI event types. The code is available in our GitHub repository (https://github.com/devalab/GraphDDI).

Abstract

In recent years, the rapid advancement of generative artificial intelligence (GenAI) has revolutionized the landscape of drug design, offering innovative solutions to potentially expedite the discovery of novel therapeutics. GenAI encompasses algorithms and models that autonomously create new data, including text, images, and molecules, often mirroring characteristics of existing datasets. This comprehensive review delves into the realm of GenAI for drug design, emphasizing recent advancements and methodologies that have propelled the field forward. Specifically, we focus on three prominent paradigms: transformers, diffusion models, and reinforcement learning algorithms, which have been exceptionally impactful in the last few years. By synthesizing insights from a myriad of studies and developments, we elucidate the potential of these approaches in accelerating the drug discovery process. Through a detailed analysis, we explore the current state and future directions of GenAI in the context of drug design, highlighting its transformative impact on pharmaceutical research and development.

Abstract

Chemical reaction prediction, encompassing forward synthesis and retrosynthesis, stands as a fundamental challenge in organic synthesis. A widely adopted computational approach frames synthesis prediction as a sequence-to-sequence translation task, using the common SMILES representation for molecules. Current evaluation of machine learning methods for retrosynthesis assume perfect training data, overlooking imperfections in reaction equations in popular datasets, such as missing reactants, products, other physical and practical constraints such as temperature and cost, primarily driven by a focus on the target molecule. This limitation leads to an incomplete representation of viable synthetic routes, especially when multiple sets of reactants can yield a given desired product. In response to these shortcomings, this study examines the prevailing evaluation methods and introduces comprehensive metrics designed to address imperfections in the dataset. Our novel metrics not only assess absolute accuracy by comparing predicted outputs with ground truth but also introduce a nuanced evaluation approach. We provide scores for partial correctness and compute adjusted accuracy through graph matching, acknowledging the inherent complexities of retrosynthetic pathways. Additionally, we explore the impact of small molecular augmentations while preserving chemical properties and employ similarity matching to enhance the assessment of prediction quality. We introduce SynFormer, a sequence-to-sequence model tailored for SMILES representation. It incorporates architectural enhancements to the original transformer, effectively tackling the challenges of chemical reaction prediction. SynFormer achieves a top-1 accuracy of 53.2% on the USPTO-50k dataset, demonstrating an improvement over previous state-of-the-art language models while being more efficient and eliminating the need for pre-training.

Abstract

RNA molecules play a significant role in many biological pathways and have diverse functional roles, which is a result of their structural flexibility to fold into diverse conformations. This structural flexibility makes it challenging to obtain the structures of RNAs experimentally. Deep learning can be used to predict the secondary structures of RNA and other properties such as the backbone torsion angles, to be used as restraints for the computational optimization of the tertiary structures of RNA. TorRNA is a transformer encoder-decoder model, that takes an input RNA sequence and predicts the (pseudo)torsion angles of each nucleotide with a pre-trained RNA-FM model as the encoder. TorRNA is able to achieve a performance boost of 2% − 16% over the previous (pseudo)torsion angle prediction method for RNAs. We also demonstrate that TorRNA can used as a tool for model quality assessment of candidate RNA structures

Abstract

Computing binding affinities is of great importance in drug discovery pipeline and its prediction using advanced machine learning methods still remains a major challenge as the existing datasets and models do not consider the dynamic features of protein-ligand interactions. To this end, we have developed PLAS-20k dataset, an extension of previously developed PLAS-5k, with 97,500 independent simulations on a total of 19,500 different protein-ligand complexes. Our results show good correlation with the available experimental values, performing better than docking scores. This holds true even for a subset of ligands that follows Lipinski’s rule, and for diverse clusters of complex structures, thereby highlighting the importance of PLAS-20k dataset in developing new ML models. Along with this, our dataset is also beneficial in classifying strong and weak binders compared to docking. Further, OnionNet model has been retrained on PLAS-20k dataset and is provided as a baseline for the prediction of binding affinities. We believe that large-scale MD-based datasets along with trajectories will form new synergy, paving the way for accelerating drug discovery.

Abstract

Molecular spectroscopy studies the interaction of molecules with electromagnetic radiation, and interpreting the resultant spectra is invaluable for deducing the molecular structures. However, predicting the molecular structure from spectroscopic data is a strenuous task that requires highly specific domain knowledge. DeepSPInN is a deep reinforcement learning method that predicts the molecular structure when given Infrared and 13C Nuclear magnetic resonance spectra by formulating the molecular structure prediction problem as a Markov decision process (MDP) and employs Monte-Carlo tree search to explore and choose the actions in the formulated MDP. On the QM9 dataset, DeepSPInN is able to predict the correct molecular structure for 91.5% of the input spectra in an average time of 77 seconds for molecules with less than 10 heavy atoms. This study is the first of its kind that uses only infrared and 13C nuclear magnetic resonance spectra for molecular structure prediction without referring to any pre-existing spectral databases or molecular fragment knowledge bases, and is a leap forward in automated molecular spectral analysis.

Abstract

Computational drug discovery is intrinsically interdisciplinary and has to deal with the multifarious factors which are often dependent on the type of disease. Molecular Property Diagnostic Suite (MPDS) is a Galaxy based web portal which was conceived and developed as a disease specific web portal, originally developed for tuberculosis (MPDSTB). As specific computational tools are often required for a given disease, developing a disease specific web portal is highly desirable. This paper emphasises on the development of the customised web portal for COVID-19 infection and is referred to as MPDSCOVID-19. Expectedly, the MPDS suites of programs have modules which are essentially independent of a given disease, whereas some modules are specific to a particular disease. In the MPDSCOVID-19 portal, there are modules which are specific to COVID-19, and these are clubbed in SARS-COV-2 disease library. Further, the new additions and/or significant improvements were made to the disease independent modules, besides the addition of tools from galaxy toolshed. This manuscript provides a latest update on the disease independent modules of MPDS after almost 6 years, as well as provide the contemporary information and tool-shed necessary to engage in the drug discovery research of COVID-19. The disease independent modules include file format converter and descriptor calculation under the data processing module; QSAR, pharmacophore, scaffold analysis, active site analysis, docking, screening, drug repurposing tool, virtual screening, visualisation, sequence alignment, phylogenetic analysis under the data analysis module; and various machine learning packages, algorithms and in-house developed machine learning antiviral prediction model are available. The MPDS suite of programs are expected to bring a paradigm shift in computational drug discovery, especially in the academic community, guided through a transparent and open innovation approach. The MPDSCOVID-19 can be accessed at http://mpds.neist.res.in:8085.