Bridging Machine Learning and Thermodynamics for Accurate p Prediction.

Integrating scientific principles into machine learning models to enhance their predictive performance and generalizability is a central challenge in the development of AI for Science. Herein, we introduce Uni-p , a novel framework that successfully incorporates thermodynamic principles into machine learning modeling, achieving high-precision predictions of acid dissociation constants (p ), a crucial task in the rational design of drugs and catalysts, as well as a modeling challenge in computational physical chemistry for small organic molecules. Uni-p utilizes a comprehensive free energy model to represent molecular protonation equilibria accurately.

Uni-Dock: GPU-Accelerated Docking Enables Ultralarge Virtual Screening.

Molecular docking, a structure-based virtual screening method, is a reliable tool to enrich potential bioactive molecules from molecular databases. With the rapid expansion of compound library sizes, the speed of existing molecular docking programs becomes less than adequate to meet the demand for screening ultralarge libraries containing tens of millions or billions of molecules. Here, we propose Uni-Dock, a GPU-accelerated molecular docking program that supports various scoring functions including vina, vinardo, and ad4.

A retro-inverso modified peptide alleviated ovalbumin-induced asthma model by affecting glycerophospholipid and purine metabolism of immune cells.

Allergic asthma is a heterogeneous disease involving a variety of inflammatory cells. Immune imbalance or changes in the immune microenvironment are the essential causes that promote inflammation in allergic asthma. Tetraspanin CD81 can be used as a platform for receptor clustering and signal transmission owing to its special transmembrane structure and is known to participate in the physiological processes of cell proliferation, differentiation, adhesion, and migration.

Chemo- and Site-Selective Lysine Modification of Peptides and Proteins under Native Conditions Using the Water-Soluble Zolinium.

Site-selective lysine modification of peptides and proteins in aqueous solutions or in living cells is still a big challenge today. Here, we report a novel strategy to selectively quinolylate lysine residues of peptides and proteins under native conditions without any catalysts using our newly developed water-soluble zoliniums. The zoliniums could site-selectively quinolylate K350 of bovine serum albumin and inactivate SARS-CoV-2 3CL covalently modifying two highly conserved lysine residues (K5 and K61).

Simulation and Machine Learning Methods for Ion-Channel Structure Determination, Mechanistic Studies and Drug Design.

Ion channels are expressed in almost all living cells, controlling the in-and-out communications, making them ideal drug targets, especially for central nervous system diseases. However, owing to their dynamic nature and the presence of a membrane environment, ion channels remain difficult targets for the past decades. Recent advancement in cryo-electron microscopy and computational methods has shed light on this issue.

Halogen Bonds Exist between Noncovalent Ligands and Natural Nucleic Acids.

Because of their strong electron-rich properties, nucleic acids (NAs) can theoretically serve as halogen bond (XB) acceptors. From a PDB database survey, Kolář found that no XBs are formed between noncovalent ligands and NAs. Through statistical database analysis, quantum-mechanics/molecular-mechanics (QM/MM) optimizations, and energy calculations, we find that XBs formed between natural NAs and noncovalent ligands are primarily underestimated and that NAs can serve as XB acceptors to interact with noncovalent halogen ligands.

Site-specific protein modification by 3-n-butylphthalide in primary hepatocytes: Covalent protein adducts diminished by glutathione and N-acetylcysteine.

Aims: 3-n-Butylphthalide (NBP) is widely used for the treatment of cerebral ischaemic stroke but can causeliver injury in clinical practice. This study aims to elucidate the underlying mechanisms and propose potential preventive strategies.

Main Methods: NBP and its four major metabolites, 3-hydroxy-NBP (3-OH-NBP), 10-hydroxy-NBP, 10-keto-NBP and NBP-11-oic acid, were synthesized and evaluated in primary human or rat hepatocytes (PHHs, PRHs).

Discovery of chiral N-2'-aryletheryl-1'-alkoxy-ethyl substituted arylisoquinolones with anti-inflammatory activity from the nucleophilic addition reactions of the thiophenols and oxazolinium.

Herein we disclosed the novel nucleophilic addition reactions of the thiophenols and oxazolinium (DCZ0358) to produce N-2'-aryletheryl-1'-alkoxy-ethyl substituted arylisoquinolones. After evaluating the anti-inflammatory activity in vitro, 2d was found having significant anti-TNFα activity. Through the amplified synthesis of 2d, four monomers (3a-b and 4a-d) were obtained by chiral separation of the product.

Ligand-based approach for predicting drug targets and for virtual screening against COVID-19.

Discovering efficient drugs and identifying target proteins are still an unmet but urgent need for curing coronavirus disease 2019 (COVID-19). Protein structure-based docking is a widely applied approach for discovering active compounds against drug targets and for predicting potential targets of active compounds. However, this approach has its inherent deficiency caused by e.

Computational Insights into the Conformational Accessibility and Binding Strength of SARS-CoV-2 Spike Protein to Human Angiotensin-Converting Enzyme 2.

The spike protein of SARS-CoV-2 (CoV-2-S) mediates the virus entry into human cells. Experimental studies have shown the stronger binding affinity of the RBD (receptor binding domain) of CoV-2-S to angiotensin-converting enzyme 2 (ACE2) as compared to that of SARS-CoV spike (CoV-S). However, a similar or weaker binding affinity of CoV-2-S compared to that of CoV-S is observed if entire spikes are used in the bioassay.

Substitution Effect of the Trifluoromethyl Group on the Bioactivity in Medicinal Chemistry: Statistical Analysis and Energy Calculations.

The substitution of methyl (Me or -CH) by trifluoromethyl (TFM or -CF) is frequently used in medicinal chemistry. However, the exact effect of -CH/-CF substitution on bioactivity is still controversial. We compiled a data set containing 28 003 pairs of compounds with the only difference that -CH is substituted by -CF, and the statistical results showed that the replacement of -CH with -CF does not improve bioactivity on average.

Computational study of the substituent effect of halogenated fused-ring heteroaromatics on halogen bonding.

Halogen bonding (XB) has been applied in many fields from crystal engineering to medicinal chemistry. Compared with the well-studied XB of simple halogenated aromatics, little research has been done on the XB of halogenated fused-ring heteroaromatics, a prevalent substructure in organic compounds. With 1H-pyrrolo[3,2-b]pyridines (PPs) as examples of novel fused-ring heteroaromatics with hydrogen bond donor and acceptor and XB donor, the XB formed by the halogenated heteroaromatics was explored in this study.

Interaction Nature and Computational Methods for Halogen Bonding: A Perspective.

Halogen bonds are noncovalent interactions that have been widely used in many fields, including drug design, crystal engineering, and material sciences. A clear understanding of the nature of halogen bonding as well as the proper theoretical bonding description, especially the development of efficient and accurate computational chemical methods and their application in complex systems, is of great significance to promote the development of related fields. In this perspective, we reviewed the investigations of the nature of halogen bonding in recent years and discussed the development of quantum mechanical, molecular mechanical, and empirical scoring function methods in properly describing halogen-bonding interactions, as well as their achievements in corresponding areas.

D3Targets-2019-nCoV: a webserver for predicting drug targets and for multi-target and multi-site based virtual screening against COVID-19.

A highly effective medicine is urgently required to cure coronavirus disease 2019 (COVID-19). For the purpose, we developed a molecular docking based webserver, namely D3Targets-2019-nCoV, with two functions, one is for predicting drug targets for drugs or active compounds observed from clinic or / studies, the other is for identifying lead compounds against potential drug targets docking. This server has its unique features, (1) the potential target proteins and their different conformations involving in the whole process from virus infection to replication and release were included as many as possible; (2) all the potential ligand-binding sites with volume larger than 200 Å on a protein structure were identified for docking; (3) correlation information among some conformations or binding sites was annotated; (4) it is easy to be updated, and is accessible freely to public (https://www.

SAMPL6 host-guest binding affinities and binding poses from spherical-coordinates-biased simulations.

Host-guest binding is a challenging problem in computer simulation. The prediction of binding affinities between hosts and guests is an important part of the statistical assessment of the modeling of proteins and ligands (SAMPL) challenges. In this work, the volume-based variant of well-tempered metadynamics is employed to calculate the binding affinities of the host-guest systems in the SAMPL6 challenge.

Pnictogen, chalcogen, and halogen bonds in catalytic systems: theoretical study and detailed comparison.

Although halogen bond (XB), a typical σ-hole noncovalent interaction, has been widely exploited in organocatalysis within the last two decades, only very recently has its sister σ-hole interactions, such as chalcogen bond (ChB) and pnictogen bond (PnB), begun to be explored for potential applications in catalysis. Herein, a detailed comparison investigation of PnB, ChB, and XB interactions in catalytic systems was performed from a theoretical point of view. Owing to the excellent properties of the pentafluorophenyl moiety (CF) in catalysis, the complexes of (CF)Pn, (CF)Ch, and CFX with chloride ion were firstly studied.

2Ch-2N square and hexagon interactions: a combined crystallographic data analysis and computational study.

In recent years, chalcogen bonding (ChB), a typical σ-hole interaction, has shown great potential as a bottom-up design approach for specific applications. According to our survey of the Cambridge Structural Database (CSD), a large number of crystal structures containing 2Ch-2N square and hexagon interaction motifs were extracted. On the basis of the CSD search results, the 2Ch-2N square interactions in the dimers of 2,1,3-benzochalcogenadiazole 1 and 2,1,3-pyridochalcogenadiazole 2, together with 2Ch-2N hexagon interactions in the dimers of chalcogenazolo-pyridine 3 and triazolo-chalcogenadiazole 4, were firstly studied.

Halogen bonding in differently charged complexes: basic profile, essential interaction terms and intrinsic σ-hole.

Studies on halogen bonds (XB) between organohalogens and their acceptors in crystal structures revealed that the XB donor and acceptor could be differently charged, making it difficult to understand the nature of the interaction, especially the negatively charged donor's electrophilicity and positively charged acceptor's nucleophilicity. In this paper, 9 XB systems mimicking all possibly charged halogen bonding interactions were designed and explored computationally. The results revealed that all XBs could be stable, with binding energies after removing background interaction as strong as -1.

Description of noncovalent interactions involving π-system with high precision: An assessment of RPA, MP2, and DFT-D methods.

Efficient approaches with high precision are essential for understanding the formation and stability of noncovalent interaction complexes. Here, 21 noncovalent interaction complexes involving π-system are selected and grouped in three subsets according to ETS-NOCV method: dispersion-dominated, electrostatic-dominated, and mixed. We mainly focus on examining the performance of random-phase approximation (RPA) on these π systems.

Coxsackievirus A10 atomic structure facilitating the discovery of a broad-spectrum inhibitor against human enteroviruses.

Coxsackievirus A10 (CV-A10) belongs to the species A and is a causative agent of hand, foot, and mouth disease. Here we present cryo-EM structures of CV-A10 mature virion and native empty particle (NEP) at 2.84 and 3.

Flueggenoids A - E, new dinorditerpenoids from Flueggea virosa.

A phytochemical investigation on the twigs and leaves of Flueggea virosa (Euphorbiaceae) led to the isolation of flueggenoids A - E (1-5), five new 13-methyl-ent-podocarpanes, together with eleven known compounds (6-16). Their structures and absolute configurations were elucidated on the basis of extensive MS and NMR data analysis, and/or single-crystal X-ray diffraction, time-dependent density functional theory (TDDFT)-based electronic circular dichroism (ECD) calculations, and chemical transformation. All isolates were evaluated for anti-HCV activity, the results showed that terpenoids of F.

Cembrane-type diterpenoids from the South China Sea soft coral .

Eight cembrane-type diterpenoids, namely, (+)-(6)-6-hydroxyisosarcophytoxide (), (+)-(6)-6-acetoxyisosarcophytoxide (), (+)-17-hydroxyisosarcophytoxide (), sarcomililatins A-D (-), and sarcomililatol (), were isolated from the soft coral collected from Weizhou Island, Guangxi Autonomous Region, together with 2 known related analogues, (+)-isosarcophytoxide () and (+)-isosarcophine (). The structures of these compounds were elucidated by a combination of detailed spectroscopic analyses, chemical methods, and comparison with reported data. The absolute configuration of compound was established by the modified Mosher׳s method, while the absolute configurations of compounds and were assigned by electronic circular dichroism (ECD) spectroscopy and that of compound was established by time-dependent density functional theory electronic circular dichroism (TD-DFT ECD) calculation.

Theoretical Exploration of Halogen Bonding Interactions in the Complexes of Novel Nitroxide Radical Probes and Comparison with Hydrogen Bonds.

In this work, halogen bonding interactions in the complexes of two new nitroxide radicals, which contain both a halogen-bond-donor group and an electron-spin-resonance-active radical unit, were investigated using density functional theory calculations. For comparison, the corresponding hydrogen-bonded complexes were also examined. Halogen bonds in these systems are predicted to be linear and much stronger than hydrogen bonds.

Sarinfacetamides A and B, Nitrogenous Diterpenoids with Tricyclo[6.3.1.0]dodecane Scaffold from the South China Sea Soft Coral Sarcophyton infundibuliforme.

Two novel nitrogenous diterpenoids, sarinfacetamides A (1) and B (2), featuring an uncommon tricyclo[6.3.1.