Estimation of the size of drug-like chemical space based on GDB-17 data

The goal of this paper is to estimate the number of realistic drug-like molecules which could ever be synthesized. Unlike previous studies based on exhaustive enumeration of molecular graphs or on combinatorial enumeration preselected fragments, we used results of constrained graphs enumeration by Reymond to establish a correlation between the number of generated structures (M) and the number of heavy atoms (N): logM = 0.584 × N × logN + 0.356. The number of atoms limiting drug-like chemical space of molecules which follow Lipinsky’s rules (N = 36) has been obtained from the analysis of the PubChem database. This results in M ≈ 10³³ which is in between the numbers estimated by Ertl (10²³) and by Bohacek (10⁶⁰).     

The most common chemical replacements in drug-like compounds

We have written a method that extracts one-to-one replacements of chemical groups in pairs of drug-like molecules with the same biological activity and counts the frequency of the replacements in a large collection of such molecules. There are two variations on the method that differ in their treatment of replacements in rings. This method is one possible approach to systematically identify candidate bioisosteres. Here we look at the MDDR database because it has a large diversity of drug-like compounds in a large number of therapeutic areas. The most frequent replacements in MDDR seem generally consistent with medicinal chemistry intuition about what chemical groups are equivalent or with groups that are easily converted by synthetic or metabolic pathways. This method can be applied to any set of molecules wherein the molecules can be paired by similar biological activity.     

Towards the comprehensive, rapid, and accurate prediction of the favorable tautomeric states of drug-like molecules in aqueous solution

Generating the appropriate protonation states of drug-like molecules in solution is important for success in both ligand- and structure-based virtual screening. Screening collections of millions of compounds requires a method for determining tautomers and their energies that is sufficiently rapid, accurate, and comprehensive. To maximise enrichment, the lowest energy tautomers must be determined from heterogeneous input, without over-enumerating unfavourable states. While computationally expensive, the density functional theory (DFT) method M06-2X/aug-cc-pVTZ(-f) [PB-SCRF] provides accurate energies for enumerated model tautomeric systems. The empirical Hammett–Taft methodology can very rapidly extrapolate substituent effects from model systems to drug-like molecules via the relationship between pK_T and pK_a. Combining the two complementary approaches transforms the tautomer problem from a scientific challenge to one of engineering scale-up, and avoids issues that arise due to the very limited number of measured pK_T values, especially for the complicated heterocycles often favoured by medicinal chemists for their novelty and versatility. Several hundreds of pre-calculated tautomer energies and substituent pK_a effects are tabulated in databases for use in structural adjustment by the program Epik, which treats tautomers as a subset of the larger problem of the protonation states in aqueous ensembles and their energy penalties. Accuracy and coverage is continually improved and expanded by parameterizing new systems of interest using DFT and experimental data. Recommendations are made for how to best incorporate tautomers in molecular design and virtual screening workflows.     

Water solubility of drug-like molecules with the cubic-plus-association equation of state

Although of extreme importance for evaluating the effective therapeutic action, aqueous solubility data involving drug-like molecules are scarce. Thermodynamic models can be used to estimate these solubilities, and different models, namely activity coefficient models, have been applied for that purpose. Still, these frequently cannot describe with accuracy broad temperature and pressure ranges, various solvent compositions or multifunctional molecules.     

Solubility of drug-like molecules in pure organic solvents with the CPA EoS

Solubility data in different solvents are an important issue for separation processes involving complex molecules such as natural products and pharmaceutical drugs. Nonetheless, solubility data are in general scarce and difficult to obtain, and so models are important tools to generate the necessary estimates.Different correlative, statistical and thermodynamic models have been proposed to evaluate solubilities. From these, the more theoretically sound thermodynamic models allow to generate estimates at broader temperature, pressure and composition conditions while using a smaller amount of experimental information. Among these, the cubic-plus-association equation of state that combines the simplicity and robustness of a cubic equation of state with the Wertheim's association contribution has been under attention. In this work, this EoS is for the first time proposed to model organic phase solubilities of drug-like molecules in a wide range of temperatures.Solubilities of acetanilide, acetylsalicylic acid, adipic acid, ascorbic acid, hydroquinone, ibuprofen, paracetamol and stearic acid were estimated in alcohols, ketones, alkanes, esters, acids, aromatics, chlorinated solvents, as well as in other common solvents. The hydrogen bonding behaviour was explicitly accounted for with each associating group being treated individually, as well as multiple group substitutions.Accurate correlations were obtained using a single binary interaction parameter (global AAD of 24.2%), while considering the complexity of the studied systems predictions were generally also satisfactory.     

ForceGen 3D structure and conformer generation: from small lead-like molecules to macrocyclic drugs

We introduce the ForceGen method for 3D structure generation and conformer elaboration of drug-like small molecules. ForceGen is novel, avoiding use of distance geometry, molecular templates, or simulation-oriented stochastic sampling. The method is primarily driven by the molecular force field, implemented using an extension of MMFF94s and a partial charge estimator based on electronegativity-equalization. The force field is coupled to algorithms for direct sampling of realistic physical movements made by small molecules. Results are presented on a standard benchmark from the Cambridge Crystallographic Database of 480 drug-like small molecules, including full structure generation from SMILES strings. Reproduction of protein-bound crystallographic ligand poses is demonstrated on four carefully curated data sets: the ConfGen Set (667 ligands), the PINC cross-docking benchmark (1062 ligands), a large set of macrocyclic ligands (182 total with typical ring sizes of 12–23 atoms), and a commonly used benchmark for evaluating macrocycle conformer generation (30 ligands total). Results compare favorably to alternative methods, and performance on macrocyclic compounds approaches that observed on non-macrocycles while yielding a roughly 100-fold speed improvement over alternative MD-based methods with comparable performance.     

Reversed-phase liquid chromatography-mass spectrometry of site-specific chemical modifications in intact immunoglobulin molecules and their fragments

The employment of a diphenyl column for the separation of intact monoclonal antibodies (mAbs) and their fragments by reversed-phase HPLC is discussed as a novel approach for the characterization of chemical modifications in a site-specific manner. Chromatographic separation of the intact mAb07 on the diphenyl support resulted in the separation of the cysteinylated from the non-cysteinylated mAb. A detected mass increase of 119 Da by mass spectrometric sequence analysis confirmed the cysteinylation. Furthermore, the diphenyl column resolved site-specific oxidation of five different methionine residues in the heavy chain (HC) of mAb03. Oxidized mAb03 HC eluted as five distinct peaks with shorter retention times than the corresponding peak representing unoxidized HC. Analysis of these peaks by in-line mass spectrometric analysis confirmed the site-specific oxidation of five different methionine residues. In another application, the diphenyl column was able to resolve free sulfhydryl groups containing Fc and Fab fragments, which were generated by limited proteolysis with endoproteinase Lys-C. The free sulfhydryl groups were responsible for a mass shift of approximately 2 Da. Their identity was further confirmed by N-ethylmaleimide labeling, which caused a shift in their chromatographic retention and led to a mass increase of 250 Da. This is the first report about chromatographic resolution on a reversed-phase column that results in site-specific separation of chemical modifications in intact mAb and mAb fragments.     

Transformation of aminoacyl tRNAs for the in vitro selection of "drug-like" molecules

Evolutionary approaches are regularly used to isolate single molecules with desired activities from large populations of nucleic acids (approximately 10(15)). Several methods have also been developed to generate libraries of mRNA-encoded peptides and proteins for the in vitro selection of functional polypeptides. In principal, such mRNA encoding systems could be used with libraries of nonbiological polymers if the ribosome can be directed to polymerize tRNAs carrying unnatural amino acids. The fundamental problem is that current chemical aminoacylation systems cannot easily produce sufficient amounts of the numerous misacylated tRNAs required to synthesize a complex library of encoded polymers. Here, we show that bulk-aminoacylated tRNA can be transformed into N-monomethylated aminoacyl tRNA and translated. Because poly-N-methyl peptide backbones are refractory to proteases and are membrane permeable, our method provides an uncomplicated means of evolving novel drug candidates.     

Synthesis of new penicillin derivatives as drug-like molecules for biological screening

Chemical modification of penicillin β-lactam ring was made.Six thiazolidine amides were produced through N4-C7 β-lactam ring opening of penicillin V methyl ester with various aliphatic,aromatic,and heterocyclic primary amines.Five 8-hydroxypenillic acid derivatives with side chains of methyl,propyl,benzyl,and diethylaminoethyl groups were yielded via β-lactam ring rearrangement from6-aminopenicillanic acid(6-APA).Parallel synthetic methods were used for the alkylation of8-hydroxypenillic acid and β-lactam ring opening of penicillin V methyl ester.The biological activities of the compounds were evaluated.     

Visualisation and subsets of the chemical universe database GDB-13 for virtual screening

Abstract  

The chemical universe database GDB-13, which enumerates 977 million organic molecules up to 13 atoms of C, N, O, S and Cl following simple chemical stability and synthetic feasibility rules, represents a vast reservoir for new fragments. GDB-13 was classified using the MQN-system discussed in the preceding paper for the analysis of PubChem fragments. Two hundred and fifty-five subsets of GDB-13 were generated by the combinatorial use of eight restrictive criteria, including fragment-like (“rule of three”) and scaffold-like (no acyclic carbon atoms) filters. Virtual screening for analogs of 15 commercial drugs of 13 non-hydrogen atoms or less shows that retrieving MQN-neighbors of a query molecule from GDB-13 or its subsets provides on average a 38-fold enrichment in structural analogs (Daylight-type substructure fingerprint Tanimoto T _SF > 0.7), and a 75-fold enrichment in shape-similar analogs (ROCS TanimotoCombo score > 1.4). An MQN-searchable version of GDB-13 is provided at .     

The molecule evoluator. An interactive evolutionary algorithm for the design of drug-like molecules

We developed a software tool to design drug-like molecules, the "Molecule Evoluator", which we introduce and describe here. An atom-based evolutionary approach was used allowing both several types of mutation and crossover to occur. The novelty, we claim, is the unprecedented interactive evolution, in which the user acts as a fitness function. This brings a human being's creativity, implicit knowledge, and imagination into the design process, next to the more standard chemical rules. Proof-of-concept was demonstrated in a number of ways, both computationally and in the lab. Thus, we synthesized a number of compounds designed with the aid of the Molecule Evoluator. One of these is described here, a new chemical entity with activity on alpha-adrenergic receptors.     

Exploring sets of molecules from patents and relationships to other active compounds in chemical space networks

Patents from medicinal chemistry represent a rich source of novel compounds and activity data that appear only infrequently in the scientific literature. Moreover, patent information provides a primary focal point for drug discovery. Accordingly, text mining and image extraction approaches have become hot topics in patent analysis and repositories of patent data are being established. In this work, we have generated network representations using alternative similarity measures to systematically compare molecules from patents with other bioactive compounds, visualize similarity relationships, explore the chemical neighbourhood of patent molecules, and identify closely related compounds with different activities. The design of network representations that combine patent molecules and other bioactive compounds and view patent information in the context of current bioactive chemical space aids in the analysis of patents and further extends the use of molecular networks to explore structure–activity relationships.     

Chemical fragments in real space: definitions, properties, and energetic decompositions

The physical and chemical meaning of real space molecular fragments resulting from arbitrary partitions of the density is reviewed under a common unifying formalism. Both fuzzy (interpenetrating) and non-fuzzy (exhaustive) decompositions are treated on an equal basis. Density decompositions are consistently generalized to compatible density matrix partitions by using Li and Parr's ideas (Li and Parr J Chem Phys 1986, 84, 1704), and these are carried onto an energy partition. It is argued that the merits of a given decomposition should be judged against both the charge and the energetic image it provides. Atomic partitions are used to show how the interacting quantum atoms approach (IQA) allows us to cope with the most important energy cancellations of quantum chemistry. Binding results from a trade-off between atomic (or fragment) energy deformations with respect to a reference and interatomic (interfragment) interactions. Deformation energies are divided into charge transfer and redistribution terms and their relative roles are analyzed. A number of systems are compared against the fuzziness of different density decompositions. The results consistently show that fuzzy partitions tend to give low atomic net charges and enhanced covalency, while exhaustive partitions generate larger net charges and smaller covalencies, across a wide range of bonding regimes.     

A distance function for retrieval of active molecules from complex chemical space representations

The concept of chemical space is of fundamental importance for chemoinformatics research. It is generally thought that high-dimensional space representations are too complex for the successful application of many compound classification or virtual screening methods. Here, we show that a simple "activity-centered" distance function is capable of accurately detecting molecular similarity relationships in "raw" chemical spaces of high dimensionality.     

Modification of poorly bioactive sinomenine into more potent immunosuppressive agents by embedding of drug-like fragments

Embedment of drug-like heterocyclic moieties was successfully employed in the novel modification of the readily available but poorly bioactive natural alkaloid sinomenine. Application of the newly proposed approach afforded a number of more potent sinomenine-like molecules with a significantly high hit rate. Among these new analogous, up to 500-fold increase of in vitro immunosuppressive activity was achieved. Further biological experiments of representative compound 4b indicated that it might inhibit NF-κB activation induced by TNF-α in a dose dependent way and showed remarkable in vivo treatment effects against the mouse experimental autoimmune uveoretinitis (EAU) disease models.     

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.     

Study of the geometric structure of the molecules of H2O,Li2O,and LiOH by the method of diatomic fragments in molecules

Conclusion The results of the present work indicate that the DFM method can be used successfully to determine the geometric parameters of the ground states of triatomic molecules. The additional possibilities provided by the method are associated with the variation of the parameters of the theory which are not single-valued, in particular the parameters of the mixing of states of the same symmetry of the diatomic fragments. It has also been shown that the correct choice of the model of the molecule is of considerable importance.Chemistry Department, M. V. Lomonosov Moscow State University. Translated from Zhurnal Strukturnoi Khimii, Vol. 19, No. 5, pp. 771–778, September–October, 1978.