Theoretical NMR correlations based Structure Discussion

The constitutional assignment of natural products by NMR spectroscopy is usually based on 2D NMR experiments like COSY, HSQC, and HMBC. The actual difficulty of the structure elucidation problem depends more on the type of the investigated molecule than on its size. The moment HMBC data is involved in the process or a large number of heteroatoms is present, a possibility of multiple solutions fitting the same data set exists. A structure elucidation software can be used to find such alternative constitutional assignments and help in the discussion in order to find the correct solution. But this is rarely done. This article describes the use of theoretical NMR correlation data in the structure elucidation process with WEBCOCON, not for the initial constitutional assignments, but to define how well a suggested molecule could have been described by NMR correlation data. The results of this analysis can be used to decide on further steps needed to assure the correctness of the structural assignment. As first step the analysis of the deviation of carbon chemical shifts is performed, comparing chemical shifts predicted for each possible solution with the experimental data. The application of this technique to three well known compounds is shown. Using NMR correlation data alone for the description of the constitutions is not always enough, even when including 13C chemical shift prediction

Report on characterisation of New Psychoactive Substances (NPS)

The emergence of designer drugs as abused substances has seen a dramatic increase over the past few years. About 70 new psychoactive substances were discovered in 2012 and more than 80 in 2013. Customs and forensic laboratories are faced with a challenge in identifying the chemical structure of these new compounds. Their analytical controls based on infrared spectroscopy and gas chromatography-mass spectrometry allow the recognition of known substances already recorded in spectroscopic libraries. However the identification of new derivatives as well as new chemical structures requires highly sophisticated analytical techniques such as Nuclear Magnetic Resonance (NMR) and High Resolution Mass Spectrometry (HR-MS). The report introduces an analytical strategy allowing the characterisation of unknown compounds based on the experience of the JRC in the use of these techniques. These approaches have been tested in the laboratory of the Joint Research Centre (JRC) and the efficiency of the proposed approach has been successfully demonstrated on several study cases. The report gives an overview of the analytical strategies and modern laboratory techniques needed to perform a fast unambiguous identification and characterisation of unknown organic chemical substances such as New Psychoactive Substances (NPS).JRC.I.1-Chemical Assessment and Testin

Aplisulfamines, New Sulfoxide-Containing Metabolites from an Aplidium Tunicate: Absolute Stereochemistry at Chiral Sulfur and Carbon Atoms Assigned Through an Original Combination of Spectroscopic and Computational Methods

Two new sulfoxide-containing metabolites, aplisulfamines A (1) and B (2), have been isolated from an Aplidium sp. collected in the Bay of Naples. Their planar structure and geometry of a double bond were readily determined by using standard methods, mainly NMR spectroscopy. An original approach was used to assign the absolute configuration at the three contiguous chiral centers present in the structures of both aplisulfamines, two at carbon and one at sulfur. This involved Electronic Circular Dichroism (ECD) studies, J-based configuration analysis and Density Functional Theory (DFT) calculations and represents an interesting integration of modern techniques in stereoanalysis, which could contribute to the enhancement of theoretical protocols recently applied to solve stereochemical aspects in structure elucidation

MOLECULAR DOCKING STUDIES OF ISOLATED COMPOUNDS ANDROGRAPHOLIDE AND BETULIN FROM METHANOLIC LEAVES EXTRACT OF ANDROGRAPHIS ECHIOIDES AS ALPHA-AMYLASE AND ALPHA-GLUCOSIDASE ACTIVATORS

Objective: The purpose of this study is to isolate and characterize the andrographolide and betulin from methanolic leaves extract of Andrographis echioides and also used to evaluate the alpha-amylase and alpha-glucosidase inhibitory activity of isolated compounds using in silico docking studies. Methods: The isolation was done using column chromatography using gradient mobile phase. Structural elucidation was carried out on the basis of spectral analysis. In this view, andrographolide and betulin were prepared for the docking evaluation. In silico docking studies were carried out using a recent version of Auto Dock 4.2, which has the basic principle of Lamarckian genetic algorithm. Results: On the basis of the spectral data, the compounds have been established as andrographolide and betulin are being reported from this plant for the first time. The result showed that the andrographolide showed a binding affinity for amylase: (-7.9 kcal/mol) and for glucosidase (-7.2 kcal/mol) while betulin showed (-8.6 kcal/mol) and (-5.2 kcal/mol), respectively. Conclusion: Therefore, it is suggested that isolated compounds andrographolide and betulin contributed excellent α-amylase and α-glucosidase inhibitory activity because of its structural parameters. Thus, these isolated compounds can be effectively used as drugs for treating diabetes which is predicted on the basis of docking scores

Sherlock—A Free and Open-Source System for the Computer-Assisted Structure Elucidation of Organic Compounds from NMR Data

The structure elucidation of small organic molecules (<1500 Dalton) through 1D and 2D nuclear magnetic resonance (NMR) data analysis is a potentially challenging, combinatorial problem. This publication presents Sherlock, a free and open-source Computer-Assisted Structure Elucidation (CASE) software where the user controls the chain of elementary operations through a versatile graphical user interface, including spectral peak picking, addition of automatically or user-defined structure constraints, structure generation, ranking and display of the solutions. A set of forty-five compounds was selected in order to illustrate the new possibilities offered to organic chemists by Sherlock for improving the reliability and traceability of structure elucidation results

Seven Golden Rules for heuristic filtering of molecular formulas obtained by accurate mass spectrometry

BACKGROUND: Structure elucidation of unknown small molecules by mass spectrometry is a challenge despite advances in instrumentation. The first crucial step is to obtain correct elemental compositions. In order to automatically constrain the thousands of possible candidate structures, rules need to be developed to select the most likely and chemically correct molecular formulas. RESULTS: An algorithm for filtering molecular formulas is derived from seven heuristic rules: (1) restrictions for the number of elements, (2) LEWIS and SENIOR chemical rules, (3) isotopic patterns, (4) hydrogen/carbon ratios, (5) element ratio of nitrogen, oxygen, phosphor, and sulphur versus carbon, (6) element ratio probabilities and (7) presence of trimethylsilylated compounds. Formulas are ranked according to their isotopic patterns and subsequently constrained by presence in public chemical databases. The seven rules were developed on 68,237 existing molecular formulas and were validated in four experiments. First, 432,968 formulas covering five million PubChem database entries were checked for consistency. Only 0.6% of these compounds did not pass all rules. Next, the rules were shown to effectively reducing the complement all eight billion theoretically possible C, H, N, S, O, P-formulas up to 2000 Da to only 623 million most probable elemental compositions. Thirdly 6,000 pharmaceutical, toxic and natural compounds were selected from DrugBank, TSCA and DNP databases. The correct formulas were retrieved as top hit at 80–99% probability when assuming data acquisition with complete resolution of unique compounds and 5% absolute isotope ratio deviation and 3 ppm mass accuracy. Last, some exemplary compounds were analyzed by Fourier transform ion cyclotron resonance mass spectrometry and by gas chromatography-time of flight mass spectrometry. In each case, the correct formula was ranked as top hit when combining the seven rules with database queries. CONCLUSION: The seven rules enable an automatic exclusion of molecular formulas which are either wrong or which contain unlikely high or low number of elements. The correct molecular formula is assigned with a probability of 98% if the formula exists in a compound database. For truly novel compounds that are not present in databases, the correct formula is found in the first three hits with a probability of 65–81%. Corresponding software and supplemental data are available for downloads from the authors' website

상백피로부터 새로운 플라바논 분리와 Network pharmacology에서 Molecular networking 응용법 연구

학위논문(석사) -- 서울대학교대학원 : 약학대학 약학과, 2023. 2. 진영원.Morus alba L. (Moraceae) also well known as White mulberry, is herb that is widely distributed among different parts of Asia including Korea, Japan, China, Thailand and Cambodia. Traditionally, extract of root bark of Morus alba has been used as for treatment of cardio-protection, analgesic, antioxidant, and hyperlipidemia. Research for compounds with cholesterol-lowering effect is promising due to increasing medical burden caused by cardiovascular disease worldwide, which contributed to highest death toll in 2019. One of renowned causes for cardiovascular diseases (CVD) is high serum level of low density lipoprotein cholesterol (LDL-C) which is controlled by low density lipoprotein receptor (LDLR), the receptor that is degraded by PCSK9. Hence, to overcome CVD, it is crucial to identify chemical constituents with PCSK9-inhibiting effects. The first part covers structural determination of twenty compounds isolated from PCSK9-lowering fractions including six newly discovered flavanones. Various column chromatography methods have been applied to methanol extract of M. alba root barks to isolate the twenty compounds. A wide range of physicochemical and spectroscopic methods such as 1D and 2D NMR spectroscopy and HRESIMS were enforced to confirm chemical structures of all twenty compounds with past research papers actively used as reference for partial fragments of the compounds. The second part evaluates the addition of molecular networking to network pharmacology to predict both cholesterol-related diseases and active fraction with optimal skeleton. Identification of compounds by molecular mass was aided by molecular network process supported with GNPS, while compound-target-disease network was built based on various Network pharmacology-related databases.Morus alba L. (Moraceae)는 상백피로도 잘 알려져 있는 식물이며, 대한민국, 일본, 중국, 태국, 캄보디아 등 아시아 대륙에 걸쳐 분포한다. 전통적으로 상백피 뿌리 추출물은 심장보호, 진통제, 항산화, 고지혈증 등으로도 쓰였다. 최근에 심혈관 질병이 갈수록 늘어나고 있고 2019년 기준 전 세계적으로 높은 사망 원인 중 하나로 심혈관 질병이 지목된 바, 콜레스테롤을 낮춰주는 화합물 발견은 미래 전망이 밝다고 볼 수 있다. 잘 알려진 심혈관 질병의 이유로는 혈청 속 높은 저밀도 지단백질 콜레스테롤 (LDL-C)이 꼽히며, 이는 PCSK9으로 인해 분해되는 저밀도 지단백질 수용체 LDLR을 조정한다. 따라서, 심혈관 질병을 이겨내기 위해선 PCSK9 억제 효과를 나타내는 화합물 발견이 중요하다. 첫 번째 파트에서는 PCSK9 억제 효과를 보인 분획에서 분리된 20종의 화합물 구조를 동정하였고, 이는 천연물에서 새롭게 발견된 6종의 플라바논을 포함한다. M. alba의 뿌리 껍질 부위의 메탄올 추출물을 다양한 column chromatography 방법을 동원해 분리하였다. 분리된 20종의 화합물은 1D 및 2D NMR spectroscopy와 HRESIMS 등을 포함한 여러가지 이화학적 및 분광학적 방법을 통해 화학구조를 결정하였고, 여러 참조 문헌들도 부분구조 확인을 위해 적극적으로 참고하였다. 두 번째 파트에선 네트워크 약리학에 Molecular networking을 활용함으로서 콜레스테롤 관련 질병들 유추하는 것과 확인된 화합물 골격 구조를 통해 활성화된 분획을 예측하는 것에 대해 탐구하였다. 다양한 구조 예측은 GNPS를 동원한 molecular network를 통해 이루어졌고, 화합물-수용체-질환 연결고리는 다양한 네트워크 약리학 관련 데이터베이스들을 통해 완성되었다.Part 1. Isolation of twenty compounds from Morus alba including six new flavanones 1 Chapter 1. Introduction 1 1.1. Study background 1 1.1.1. Relationship between cholesterol and CVD 1 1.1.2. PCSK9 inhibitory effect of root bark of Morus alba 2 1.2. Purpose of research 3 Chapter 2. Experimental section 4 2.1. Materials 4 2.1.1. Plant material 4 2.1.2. Reagents and apparatus 4 2.1.3. Heavy equipment 5 2.1.4. Software 6 2.2. Methods 7 2.2.1. Extraction, separation and purification 7 2.2.2. Chemical and spectral properties of isolated chemical compound 14 Chapter 3. Results 29 3.1. Structural elucidation of isolated compounds 29 3.1.1. Compound 1 29 3.1.2. Compound 2 34 3.1.3. Compound 3 38 3.1.4. Compound 4 42 3.1.5. Compound 5 46 3.1.6. Compound 6 51 3.1.7. Compound 7 56 3.1.8. Compound 8 59 3.1.9. Compound 9 62 3.1.10. Compound 10 64 3.1.11. Compound 11 66 3.1.12. Compound 12 68 3.1.13. Compound 13 70 3.1.14. Compound 14 72 3.1.15. Compound 15 74 3.1.16. Compound 16 76 3.1.17. Compound 17 79 3.1.18. Compound 18 82 3.1.19. Compound 19 84 3.1.20. Compound 20 86 Chapter 4. Conclusion 88 Part 2. Application of molecular networking to network pharmacology 89 Chapter 1. Introduction 89 1.1. Study background 89 1.1.1. Classic drug discovery process and its limitations 89 1.1.2. Network pharmacology and molecular networking 90 1.2. Purpose of research 91 Chapter 2. Experimental section 92 2.1. Molecular networking 92 2.2. Network pharmacology 93 2.2.1. Extraction of nodes 93 2.2.2. Visualization of the network 94 Chapter 3. Results 97 3.1. Prediction of plant-related diseases 97 3.2. Prediction of active fraction based on key skeleton 106 Chapter 4. Conclusion 110 BIBLIOGRAPHY 111 Abstract in Korean (국문 초록) 119석

Molecular modelling aided design and synthesis of photochromic dyes containing a permanent chromophore

Photochromic dyes are a very important and relatively novel class of dyes. The usual, though not exclusive, behaviour of these dyes is to show a reversible colour change from colourless to coloured when exposed to UV light. Among the photochromic dye classes, spirooxazines and naphthopyrans were selected for investigation. An attempt was made to construct molecules with a permanent chromophore (azo) in spirooxazines as well as naphthopyrans separately, with a view to providing a colour change from one colour to another. Three different isomers of dihydroxynaphthalene were used as one group of starting materials for the synthesis of spirooxazines with the introduction of the azo (hydrazone) chromophore by coupling. Other starting materials used were anthraquinones, naphthoquinones and pyrazolones. A range of molecular modelling techniques (molecular mechanics, MM2 and quantum mechanics, AM1) using the CAChe system, were applied to predict optimized geometrical conformations and energies of the ring-closed form and ringopened merocyanine forms of all the dyes. PPP-MO calculations were also carried out to predict the potential colour of the dyes. The dyes were characterized using DSC, FTIR, NMR, UV-Visible spectroscopy and elemental analysis. The photochromic properties of one of the azospirooxazines was subjected to a detailed study under different experimental conditions, and showed a unique slow colour change from orange to grey.Worshipful Company of Dyers (London

Statistical filtering for NMR based structure generation

The constitutional assignment of natural products by NMR spectroscopy is usually based on 2D NMR experiments like COSY, HSQC, and HMBC. The difficulty of a structure elucidation problem depends more on the type of the investigated molecule than on its size. Saturated compounds can usually be assigned unambiguously by hand using only COSY and 13C-HMBC data, whereas condensed heterocycles are problematic due to their lack of protons that could show interatomic connectivities. Different computer programs were developed to aid in the structural assignment process, one of them COCON. In the case of unsaturated and substituted molecules structure generators frequently will generate a very large number of possible solutions. This article presents a "statistical filter" for the reduction of the number of results. The filter works by generating 3D conformations using smi23d, a simple MD approach. All molecules for which the generation of constitutional restraints failed were eliminated from the result set. Some structural elements removed by the statistical filter were analyzed and checked against Beilstein. The automatic removal of molecules for which no MD parameter set could be created was included into WEBCOCON. The effect of this filter varies in dependence of the NMR data set used, but in no case the correct constitution was removed from the resulting set