RASA: a rapid retrosynthesis-based scoring method for the assessment of synthetic accessibility of drug-like molecules

In this account, a rapid retrosynthesis-based scoring method for the assessment of synthetic accessibility of drug-like molecules, called RASA (Retrosynthesis-based Assessment of Synthetic Accessibility) is devised. RASA first constructs a synthesis tree for the target molecule based on retrosynthetic analysis; in this process a series of strategies are suggested for limiting combinatorial explosion of the synthesis tree. A scoring function (RASA-score) for the assessment of synthetic accessibility is then proposed based on the optional effective synthetic routes, the complexity of reaction, and the difficulty of separation/purification associated with the most favorable synthetic route. The contributions of individual components are calibrated by linear regression analysis based on the synthetic accessibility estimates of a training set (100 compounds) given by a group of medicinal chemists (G1). Two external test sets (TS1 and TS2), whose synthetic accessibility estimates were given by the group G1 medicinal chemists and another group (G2) of medicinal chemists (from literature), respectively, were adopted for the evaluation of RASA. The correlation coefficient between the calculated RASA-score values and the estimated scores by medicinal chemists for TS1 is 0.807 and that for TS2 is 0.792, which demonstrate the validity and reliability of RASA. The validity and reliability as well as the high speed of RASA and its capability of suggesting synthetic routes enable it a useful tool in drug discovery.     

The meaning and definition of “charge” in molecules

Atomic charges have been calculated by a simple model involving partition of total molecular bonding energy into “ionic” and “covalent” components. These charges agree well with those obtained by Politzer's electron-count method of assigning charge but not with charges obtained by populational analysis. It is argued that Politzer's definition of charge is closer to the intuitive use of the word “charge” by chemists than is that based on populational analysis. Further examples of the importance of consideration of valence state electronegativities and charge capacities are discussed.     

Building a three-dimensional model of CYP2C9 inhibition using the Autocorrelator: an autonomous model generator

In modern day drug discovery campaigns, computational chemists have to be concerned not only about improving the potency of molecules but also reducing any off-target ADMET activity. There are a plethora of antitargets that computational chemists may have to consider. Fortunately many antitargets have crystal structures deposited in the PDB. These structures are immediately useful to our Autocorrelator: an automated model generator that optimizes variables for building computational models. This paper describes the use of the Autocorrelator to construct high quality docking models for cytochrome P450 2C9 (CYP2C9) from two publicly available crystal structures. Both models result in strong correlation coefficients (R2 > 0.66) between the predicted and experimental determined log(IC??) values. Results from the two models overlap well with each other, converging on the same scoring function, deprotonated charge state, and predicted the binding orientation for our collection of molecules.     

Novel, customizable scoring functions, parameterized using N-PLS, for structure-based drug discovery

The ability to accurately predict biological affinity on the basis of in silico docking to a protein target remains a challenging goal in the CADD arena. Typically, "standard" scoring functions have been employed that use the calculated docking result and a set of empirical parameters to calculate a predicted binding affinity. To improve on this, we are exploring novel strategies for rapidly developing and tuning "customized" scoring functions tailored to a specific need. In the present work, three such customized scoring functions were developed using a set of 129 high-resolution protein-ligand crystal structures with measured Ki values. The functions were parametrized using N-PLS (N-way partial least squares), a multivariate technique well-known in the 3D quantitative structure-activity relationship field. A modest correlation between observed and calculated pKi values using a standard scoring function (r2 = 0.5) could be improved to 0.8 when a customized scoring function was applied. To mimic a more realistic scenario, a second scoring function was developed, not based on crystal structures but exclusively on several binding poses generated with the Flo+ docking program. Finally, a validation study was conducted by generating a third scoring function with 99 randomly selected complexes from the 129 as a training set and predicting pKi values for a test set that comprised the remaining 30 complexes. Training and test set r2 values were 0.77 and 0.78, respectively. These results indicate that, even without direct structural information, predictive customized scoring functions can be developed using N-PLS, and this approach holds significant potential as a general procedure for predicting binding affinity on the basis of in silico docking.     

Prediction of Compound Synthesis Accessibility Based on Reaction Knowledge Graph

With the increasing application of deep-learning-based generative models for de novo molecule design, the quantitative estimation of molecular synthetic accessibility (SA) has become a crucial factor for prioritizing the structures generated from generative models. It is also useful for helping in the prioritization of hit/lead compounds and guiding retrosynthesis analysis. In this study, based on the USPTO and Pistachio reaction datasets, a chemical reaction network was constructed for the identification of the shortest reaction paths (SRP) needed to synthesize compounds, and different SRP cut-offs were then used as the threshold to distinguish a organic compound as either an easy-to-synthesize (ES) or hard-to-synthesize (HS) class. Two synthesis accessibility models (DNN-ECFP model and graph-based CMPNN model) were built using deep learning/machine learning algorithms. Compared to other existing synthesis accessibility scoring schemes, such as SYBA, SCScore, and SAScore, our results show that CMPNN (ROC AUC: 0.791) performs better than SYBA (ROC AUC: 0.76), albeit marginally, and outperforms SAScore and SCScore. Our prediction models based on historical reaction knowledge could be a potential tool for estimating molecule SA.     

Mimicking/Extracting Structure and Functions of Natural Products: Synthetic Approaches that Address Unexplored Needs in Chemical Biology

Natural products are often attractive and challenging targets for synthetic chemists, and many have interesting biological activities. However, synthetic chemists need to be more than simply suppliers of compounds to biologists. Therefore, we have been seeking ways to actively apply organic synthetic methods to chemical biology studies of natural products and their activities. In this personal review, I would like to introduce our work on the development of new biologically active compounds inspired by, or extracted from, the structures of natural products, focusing on enhancement of functional activity and specificity and overcoming various drawbacks of the parent natural products.     

Drug efficiency indices for improvement of molecular docking scoring functions

A dataset of protein‐drug complexes with experimental binding energy and crystal structure were analyzed and the performance of different docking engines and scoring functions (as well as components of these) for predicting the free energy of binding and several ligand efficiency indices were compared. The aim was not to evaluate the best docking method, but to determine the effect of different efficiency indices on the experimental and predicted free energy. Some ligand efficiency indices, such as ΔG/W (Wiener index), ΔG/NoC (number of carbons), and ΔG/P (partition coefficient), improve the correlation between experimental and calculated values. This effect was shown to be valid across the different scoring functions and docking programs. It also removes the common bias of scoring functions in favor of larger ligands. For all scoring functions, the efficiency indices effectively normalize the free energy derived indices, to give values closer to experiment. Compound collection filtering can be done prior or after docking, using pharmacokinetic as well as pharmacodynamic profiles. Achieving these better correlations with experiment can improve the ability of docking scoring functions to predict active molecules in virtual screening. © 2009 Wiley Periodicals, Inc. J Comput Chem 2010     

单萜吲哚生物碱Uleine及其衍生物的合成进展

生物碱uleine及其衍生物从结构上看属于单萜吲哚生物碱,它们共同的结构特征是吲哚核与碱性氮原子之间只有一个碳相隔,而不像其它单萜吲哚生物碱有两个碳原子.由于其结构特异,天然含量少,因而其合成工作一直吸引着化学工作者.总结uleine生物碱及其衍生物的合成方法,根据构建环的种类不同,把合成方法分为五类.大部分方法都是以吲哚和吡啶衍生物为起始原料进行四环的合成,有几条合成路线简短易行.     

Prediction of proton NMR couplings in flexible ring systems: application to the stereochemical analysis of synthetic β‐substituted tryptophans

The stereochemical analysis of synthetic β‐substituted tryptohans was achieved through the study of their conformationally constrained 1,2,3,4‐tetrahydro‐β‐carboline derivatives. The relative configuration of the contiguous asymmetric centers of interest was determined by analysis of the vicinal proton–proton coupling constant values J. Two compounds presenting intermediate J values led to the assessment of both coupling and energy evaluation methods. Energy was found to be adequately calculated by the semi‐empirical AM1 method on a set of lowest energy conformations. The latter were generated by molecular dynamics, based on the empirical force field CFF91. Compounds that led to ambiguous J values were shown to undergo conformational exchange due to steric repulsions between bulky trans‐oriented substituents. Copyright © 2003 John Wiley & Sons, Ltd.     

Purification of Enantiomeric Mixtures in Enantioselective Synthesis: Overlooked Errors and Scientific Basis of Separation in Achiral Environment

The syntheses of optically active compounds (whether of pharmaceutical or synthetic importance, or as promising candidates as chiral ligands and auxiliaries in asymmetric syntheses) result in the formation of a mixture of products with one enantiomer predominating. Usually, the practice is to use standard open‐column chromatography for the first purification step in an enantioselective synthesis; the workup of the reaction product by crystallization or achiral chromatography would mask the real efficiency of the enantioselective methodology, since enantiomeric ratio (er) of the product may change by any of these methods. Most of the synthetic organic chemists are aware of the influence of crystallization on the er value. Majority of synthetic organic chemists are, however, not aware, while employing standard chromatography, that there may be an increase or decrease of er value. In other words, an undesired change in er goes unnoticed when such a mixture of enantiomers is isolated by chromatography on an achiral‐phase because of the prevalent concept of basic stereochemistry. Such unnoticed errors in enantioselective reactions may lead to misinterpretations of the enantioselective outcome of the synthesis. The scientific issue is, what is the difference between a racemic and nonracemic mixture in achiral environment (e.g., achiral‐phase chromatography) that leads to enantiomeric enrichment, amounting to separation of one particular enantiomer? There are sporadic reports on enantiomer separation of nonracemic mixtures in an achiral environment particularly from the scientists working in analytical chemistry. To cover/discuss all these reports is out of the scope of this article. The aim of the present report is to draw attention to the following points: i) How should the synthetic organic chemists and analytical chemists take care of the unexpected separation of enantiomers from nonracemic mixtures in a totally achiral environment? ii) What are the technical terms used in recent literature? iii) The requirement of revisiting definitions/terms (introduced in recent years, in particular) to describe such separations of enantiomers in light of prevalent scientific/chemical terminology used in the ‘language of chemistry’, the text book concept, and IUPAC background. iv) To propose logical scientific terminology or phrases for explaining the possible mechanism of separation under these conditions. v) To discuss briefly the concept/possibile phenomenon responsible for these enantioselective effects. It is also attempted to explain the effect of change of physical parameters influencing the separation from nonracemic mixture in achiral‐phase chromatography.     

What are the pKa values of C-H bonds in aromatic heterocyclic compounds in DMSO?

A first-principle method has been successfully developed for the prediction of pK_a values of aromatic heterocyclic compounds in DMSO solution with a precision of 1.1 pK_a units. Comparison of theoretical results and experimental data (where available) also shows excellent consistency. Armed with this useful approach, the pK_a values for a series of aromatic heterocycles were calculated in DMSO. Moreover, a discussion of the relationships between hydrogen acidities and molecular structures is conducted for the first time (determinants of C-H acidities, substituent effects, and some practical use of dehydrometalation). These statistics could be useful for synthetic chemists to design proper routes for introduction of aromatic heterocyclic moiety, especially when dehydrometalation reactions are used.     

Retrosynthetic accessibility score (RAscore) – rapid machine learned synthesizability classification from AI driven retrosynthetic planning

Computer aided synthesis planning (CASP) is part of a suite of artificial intelligence (AI) based tools that are able to propose synthesis routes to a wide range of compounds. However, at present they are too slow to be used to screen the synthetic feasibility of millions of generated or enumerated compounds before identification of potential bioactivity by virtual screening (VS) workflows. Herein we report a machine learning (ML) based method capable of classifying whether a synthetic route can be identified for a particular compound or not by the CASP tool AiZynthFinder. The resulting ML models return a retrosynthetic accessibility score (RAscore) of any molecule of interest, and computes at least 4500 times faster than retrosynthetic analysis performed by the underlying CASP tool. The RAscore should be useful for pre-screening millions of virtual molecules from enumerated databases or generative models for synthetic accessibility and produce higher quality databases for virtual screening of biological activity.

The retrosynthetic accessibility score (RAscore) is based on AI driven retrosynthetic planning, and is useful for rapid scoring of synthetic feasability and pre-screening of large datasets of virtual/generated molecules.     

Strategies for the Total Synthesis of Clavicipitic Acid

Clavicipitic acid is an ergot alkaloid, which was isolated from Claviceps strain and Claviceps fusiformis. Its unique tricyclic azepinoindole skeleton has attracted synthetic chemists, and various strategies have been developed for its total synthesis. These strategies can be generally categorized into two types based on the synthetic intermediates, namely, 4‐substituted gramine derivatives and 4‐substituted tryptophan derivatives. This Minireview summarizes the reported total syntheses from the point of these two key intermediates     

Application of Model of Ideal Solution of Interaction Products and Thermodynamic Modeling

The essence of the ideal solution of interaction products (ISIP) model for systems involving strong interactions of the components is described. With the help of this model and thermodynamic simulation methods, the activities of the components and partial and integral thermodynamic characteristics of Fe-Si solutions at 1873–2003 K in an initial Ar atmosphere and at a common pressure of 1 atm were calculated. The compositions and structures of Fe-Si solutions according to the ISIP model are determined as statistical mixtures of [Fe], [Si] and the clusters [FeSi], [FeSi₂], [Fe₃Si] and [Fe₅Si₃]. The calculated values of activities, thermodynamic characteristics, compositions and structures of Fe-Si solutions agree satisfactorily with reliable experimental data. The thermochemical and thermodynamic properties of the compounds FeSi, FeSi₂, Fe₃Si and Fe₅Si₃ were revised. The temperature dependences of the activities of the components, and also the influence of temperature elevation on the composition of Fe-Si melts are discussed.     

Reassignments and Corroborations of Oxo‐Bridged Natural Products Directed by OSE and DU8+ NMR Computation

Structural misassignments of natural products are prevalent in the literature. Developing methods and theoretical concepts to assist those undertaking structural elucidation is therefore of paramount importance, such that biologists and synthetic chemists avoid pursuing phantom chemical entities. Herein described is a strategy for predicting the isolabilities of oxygen‐substituted bridgehead natural products based on calculations of olefin strain energies, NMR chemical shifts and coupling constants (DU8+). This approach provides corroborating evidence for the structures of certain bridgehead alkene natural products while leading to the reassignment of several other structures.     

Ab initio and MNDO Calculations of Cyanuric Chloride,its 35Cl NQR Frequency and Asymmetry Parameter of the EFG at the 35Cl Nuclei

Ab initio molecular orbital calculations of the (CNCl)₃ (cyanuric chloride; 2,4,6-trichloro-1,3,5-triazine) molecule were performed at the RHF/6–31G* level. The ³⁵Cl NQR frequency and asymmetry parameter of the EFG at the ³⁵Cl nucleus were calculated from the total populations of the Cl atom valence p-orbitals and their components. The ³⁵Cl NQR frequency and asymmetry parameter which are determined for (CNCl)₃ based on these components agree well with the corresponding experimental values and demonstrate the importance of including the less diffuse components of the p-orbitals.     

金属次卟啉二甲酯对空气氧化环己烷的催化作用

在无任何外加溶剂及共还原剂的条件下, 将金属次卟啉二甲酯应用于催化空气氧化环己烷的氧化反应. 结果表明, 金属次卟啉二甲酯能够很好地催化环己烷的氧化反应, 与简单的金属四苯基卟啉相比, 金属次卟啉二甲酯催化剂具有更高的催化活性. 进而研究了络合金属对其催化性能的影响.     

Synthesis of an Orthogonal Topological Analogue of Helicene

The synthesis of an orthogonal topological pentamer analogue of helicene is presented. This analogue forms a tubular structure with its aromatic systems directed parallel to the axis of propagation, which creates a cavity with the potential to function as a host molecule. The synthetic strategy reported, based on a series of repeating Friedländer condensations that utilize pyrido[3,2‐d]pyrimidine moieties as protected amino aldehydes, allows for the facile access of higher generations of helical, tubular structures. As a result of the synthetic strategy, only a helical isomer of the pentamer is possible. The structure and absolute configuration of the pentamer were elucidated from a combination of NMR spectroscopic data, optical properties, X‐ray structures, and by comparison of an experimental electronic circular dichroism spectrum to a calculated spectrum.