Application progress of deep generative models in de novo drug design.

The deep molecular generative model has recently become a research hotspot in pharmacy. This paper analyzes a large number of recent reports and reviews these models. In the central part of this paper, four compound databases and two molecular representation methods are compared. Five model architectures and applications for deep molecular generative models are emphatically introduced. Three evaluation metrics for model evaluation are listed. Finally, the limitations and challenges in this field are discussed to provide a reference and basis for developing and researching new models published in future.

Olefin Metathesis at the Dawn of Implementation in Pharmaceutical and Specialty-Chemicals Manufacturing.

The recent uptake of molecular metathesis catalysts in specialty-chemicals and pharmaceutical manufacturing is reviewed.

On QSAR modeling with novel degree-based indices and thermodynamics properties of eye infection therapeutics.

Topological descriptors are numerical results generated from the structure of a chemical graph that are useful in identifying the physicochemical characteristics of a wide range of drugs. The introduction of molecular descriptors advances quantitative structure-property relationship research. This article focuses on the nine degree-based topological indices and the linear regression model of the eye infection drugs. We introduced two new indices, namely, the "first revised Randic index" and the "second revised Randic index, for the analysis of eye infection drugs. Topological indices are calculated by using edge partitioning, vertex degree counting, and vertex degree labeling. This analysis is done with a scientific calculator and then authenticated with Matlab, a potent tool for examining data. The experimental data and results of the topological indices serve as inputs for the statistical computations and provide the values of intercepts, slopes, and correlation coefficients. All the correlations for the eye-infection drugs are positive, indicating a direct relationship between the experimental and estimated results of the drugs. There are significant results of the p-test for all of the characteristics of eye infection, such as molecular weight, boiling point, enthalpy, flash point, molar refraction, and molar volume, that validate the accuracy of the computations. A significant link was determined in this study between the defined indices with two properties: molar weight and molar refraction. The molar weight and molar refraction have a correlation coefficient ranging from 0.9. These results demonstrate a strong association between the indices and the properties under investigation. The linear regression approach is a valuable tool for chemists and pharmacists to obtain data about different medicines quickly and cost-effectively.

30th Annual GP2A Medicinal Chemistry Conference.

The Group for the Promotion of Pharmaceutical Chemistry in Academia (GP2A) held their 30th annual conference in August 2022 in Trinity College Dublin, Ireland. There were 9 keynote presentations, 10 early career researcher presentations and 41 poster presentations.

Medicinal Chemistry for Sustainable Development.

Pharmaceutical chemistry has many industrial processes that must be studied and adapted to a new reality where the environment must be the focus of all production chains. Thus, new technologies that are cleaner and use renewable sources of raw materials still need to be developed and applied to materials that go to the market, and they need to reach a level that is less harmful to the environment. This applies especially in areas related to the pharmaceutical industries since chemical products are used in the production of medicines and used in many other areas of everyday life and are included in the Sustainable Development Goals proposed by the United Nations. This article intends to provide insight into some relevant topics that can stimulate researchers toward medicinal chemistry that can contribute to a sustainable future of the biosphere. This article is structured around four interconnected themes that influence how green chemistry can be important for a future where science, technology and innovation are key to mitigating climate change and increasing global sustainability.

Platform headspace gas chromatography method for high-throughput determination of residual solvents in pharmaceutical materials.

Static headspace capillary gas chromatography (HSGC) has been employed to monitor the level of residual solvents in the pharmaceutical materials. Most of the HSGC methods, however, consume significant amounts of diluents and require considerable amount of sample preparation time. Accordingly, a HSGC method featured with fast turnaround time, and minimal amount of solvent use has been developed for the quantitative analysis of 27 residual solvents frequently used in the development and manufacturing processes of pharmaceutical industry. This HSGC-FID method employs a commercially available fused silica capillary column, a split injection (40:1), and a programmed temperature ramp. It was qualified for specificity, accuracy, repeatability/precision, linearity, LOQ, solution stability, and robustness using two representative sample matrices. The standards, samples and spiked samples were demonstrated to be stable for at least 10 days at room temperature in sealed headspace vials with a recovery of ≥ 93%. The method was also shown to be robust, and its performance was not affected by small changes of carrier gas flow rate, initial oven temperature or the headspace oven temperature. In this new approach, the analytical sample was prepared by dissolving the sample into 1 mL of the diluent and the standard solution was prepared by diluting 1 mL of the custom-made stock into 9 mL of the diluent whereas the traditional approach requires liters of the diluent, making the new approach environmentally friendly, sustainable, economical, agile, error-proofing and thus appropriate for a variety of pharmaceutical applications.

Synthesis of a theranostic platform based on fibrous silica nanoparticles for the enhanced treatment of triple-negative breast cancer promoted by a combination of chemotherapeutic agents.

A new series of theranostic silica materials based on fibrous silica particles acting as nanocarriers of two different cytotoxic agents, namely, chlorambucil and an organotin metallodrug have been prepared and structurally characterized. Besides the combined therapeutic activity, these platforms have been decorated with a targeting molecule (folic acid, to selectively target triple negative breast cancer) and a molecular imaging agent (Alexa Fluor 647, to enable their tracking both in vitro and in vivo). The in vitro behaviour of the multifunctional silica systems showed a synergistic activity of the two chemotherapeutic agents in the form of an enhanced cytotoxicity against MDA-MB-231 cells (triple negative breast cancer) as well as by a higher cell migration inhibition. Subsequently, the in vivo applicability of the siliceous nanotheranostics was successfully assessed by observing with in vivo optical imaging techniques a selective tumour accumulation (targeting ability), a marked inhibition of tumour growth paired to a marked antiangiogenic ability after 13 days of systemic administration, thus, confirming the enhanced theranostic activity. The systemic nanotoxicity was also evaluated by analyzing specific biochemical markers. The results showed a positive effect in form of reduced cytotoxicity when both chemotherapeutics are administered in combination thanks to the fibrous silica nanoparticles. Overall, our results confirm the promising applicability of these novel silica-based nanoplatforms as advanced drug-delivery systems for the synergistic theranosis of triple negative breast cancer.

Magnetic polymeric core-shell as a carrier for gradual release in-vitro test drug delivery.

At first functionalized graphene oxide was selected as a basic substrate obtained through process of functionalization of graphene oxide with diethylenetriamine as substrates. Then magnetic nanoparticle sediments were formed and coated on the functionalized graphene oxide as the core center. The core nanoparticle was added to a gel containing poly (lactic-co-glycolic acid), polyethylene glycol, and polyvinylpyrrolidone and nilotinib drug for forming a shell on the core. After separation and freeze-drying, single core-shell particles were obtained. The second shell was coated by dispersing first core-shell in a new gel containing polylactic acid, polyvinyl alcohol, polyethylene glycol, and nilotinib. The third layer was laminated on core-dual shell particle by entering in sodium alginate, polyethylene glycol, poly (lactic-co-glycolic acid), polylactic acid and nilotinib gel according to the same method used above. In order to determine the gradual release, the core-single, dual and triple shell nanoparticles dispersed in phosphate buffer saline at the several pHs (3, 5.4, 7.4) and as well as monitoring the released concentration of nilotinib by UV-Vis spectrophotometer technique. Core-triple shell particle had gradual release at three different rates over the long time. Finally, the average release rate for 400 mg of drug, in single layer, double-layer and three layers were reported to be equal to 15.8, 10.4 and 6.6 mg/h at intervals of 24, 37 and 60 h, respectively. The release rate of the drug reduced by increasing the pH value. All products were characterized using several techniques.

Development and implementation of an enterprise-wide predictive model for early absorption, distribution, metabolism and excretion properties.

Background: Accurate prediction of absorption, distribution, metabolism and excretion (ADME) properties can facilitate the identification of promising drug candidates. Methodology & Results: The authors present the Janssen generic Target Product Profile (gTPP) model, which predicts 18 early ADME properties, employs a graph convolutional neural network algorithm and was trained on between 1000-10,000 internal data points per predicted parameter. gTPP demonstrated stronger predictive power than pretrained commercial ADME models and automatic model builders. Through a novel logging method, the authors report gTPP usage for more than 200 Janssen drug discovery scientists. Conclusion: The investigators successfully enabled the rapid and systematic implementation of predictive ML tools across a drug discovery pipeline in all therapeutic areas. This experience provides useful guidance for other large-scale AI/ML deployment efforts.

29th Annual GP2A Medicinal Chemistry Conference.

The 29th Annual GP2A (Group for the Promotion of Pharmaceutical chemistry in Academia) Conference was a virtual event this year due to the COVID-19 pandemic and spanned three days from Wednesday 25 to Friday 27 August 2021. The meeting brought together an international delegation of researchers with interests in medicinal chemistry and interfacing disciplines. Abstracts of keynote lectures given by the 10 invited speakers, along with those of the 8 young researcher talks and the 50 flash presentation posters, are included in this report. Like previous editions, the conference was a real success, with high-level scientific discussions on cutting-edge advances in the fields of pharmaceutical chemistry.

Biosynthesis, total synthesis, and biological profiles of Ergot alkaloids.

While the use of ergot alkaloids in folk medicine has been practiced for millennia, systematic investigations on their therapeutic potential began about 100 years ago. Subsequently, Albert Hofmann's discovery of lysergic acid diethylamide (LSD) and its intense psychedelic properties garnered worldwide attention and prompted further studies of this compound class. As a result, several natural ergot alkaloids were discovered and unnatural analogs were synthesized, and some were used to treat an array of maladies, including Alzheimer's and Parkinson's disease. While LSD was never commercially approved, recent clinical studies have found it can be an innovative and effective treatment option for several psychiatric disorders. Ongoing biosynthetic and total synthetic investigations aim to understand the natural origins of ergot alkaloids, help develop facile means to produce these natural products and enable their continued use as medicinal chemistry lead structures. This review recounts major developments over the past 20 years in biosynthetic, total synthetic, and pharmaceutical studies. Many ergot alkaloid biosynthetic pathways have been elucidated, with some of them subsequently applied toward "green" syntheses. New chemical methodologies have fostered a fast and efficient access to the ergoline scaffold, prompting some groups to investigate biological properties of natural product-like ergot alkaloids. Limited pharmaceutical applications have yet to completely bypass the undesirable side effects of ergotism, suggesting further studies of this drug class are likely needed and will potentially harness major therapeutic significance.

Assessing the biodegradability of common pharmaceutical products (PPs) on the Zambian market.

Biodegradation is the breakdown of complex organic compounds into simpler molecules like carbon dioxide and water by microorganisms like bacteria and fungi. Biodegradation studies of pharmaceuticals are initially done to assess which pharmaceuticals are persistent in the environment. Whole pharmaceuticals or their metabolites are excreted from the human body via urine or fecal matter after administration. These go into the Wastewater Treatment Plants (WWTP) and are later released into the environment with the treated wastewater. Recent studies have reported a number of pharmaceuticals in the ecosystem and the effects of these on non-target species has become an issue of environmental concern. The biodegradation studies of eight pharmaceuticals were carried out in this research. The choice of pharmaceuticals was based on the most commonly prescribed medications at the University of Zambia (UNZA) Clinic in seven therapeutic groups: anti-hypertensives, antibiotic, antimalarial drugs, anti-tuberculosis, antihelminthics, antifungals and antiretroviral drugs. The biodegradability tests were carried out using a modified carbon dioxide evolution method (modified Sturm test). The inoculum was derived from the secondary effluent of the UNZA WWTP plant and Dextrose monohydrate was used as a system control. Using this guideline, the system control, dextrose monohydrate biodegraded 77 ± 0.270% in seven days. All the pharmaceuticals except ciprofloxacin were found to be non-biodegradable: Atenolol degraded 6.8 ± 0.026%, ketoconazole degraded 1.0 ± 0.003%, isoniazid/rifampicin degraded 0.8 ± 0.003%, mebendazole degraded 13.0 ± 0.050%, nevirapine degraded 1.3 ± 0.005%, pen-v degraded 1.0 ± 0.004% and quinine sulfate degraded 1.8 ± 0.008%. Ciprofloxacin showed a negative carbon dioxide evolution and it was noted that bacteria were not viable as the drug proved to be very potent against bacterial strains in the inoculum used.

Phytocannabinoids Profile in Medicinal Cannabis Oils: The Impact of Plant Varieties and Preparation Methods.

Cannabis (Cannabis sativa L.) is a highly promising medicinal plant with well-documented effectiveness and growing use in the treatment of various medical conditions. Cannabis oils are mostly used in galenic preparations, due to their easy adjustment of the administration dose, together with the enhanced bioavailability of its active compounds. As stated by the Italian Law (9/11/2015, 279 Official Gazette), "to ensure the quality of the oil-based cannabis preparation, the titration of the active substance(s) should be carried out." This study aims to represent the Italian panorama of cannabis oils, which were analyzed (8,201) to determine their cannabinoids content from 2017 to 2019. After application of the exclusion criteria, 4,774 standardized cannabis oils were included, which belong to different medicinal cannabis varieties and prepared according to different extraction methods. The concentration of the principal cannabinoids was taken into account dividing samples on the basis of the main extraction procedures and cannabis varieties. According to this analysis, the most substantial variations should be attributed to different cannabis varieties rather than to their extraction protocols. This study may be the starting point of preparatory pharmacists to assess the correct implementation of the preparation procedures and the quality of the extracts.

The 12th AFMC International Medicinal Chemistry Symposium (AIMECS 2019) in Istanbul, Turkey.

AFMC-AIMECS meetings are internationally organized biannually by the Asian Federation for Medicinal Chemistry (AFMC) and are focused on recent studies in drug discovery and development both in academia and industry. Member organizations of the AFMC are the Pharmaceutical Society of Japan, the Chinese Pharmaceutical Association, the Royal Australian Chemical Institute, the Pharmaceutical Society of Korea, the Korean Chemical Society, the Chemical Society Located in Taipei, the Indonesian Society of Medicinal Chemistry, the Medicinal Chemistry Section of the Israel Chemical Society, and the Computer-Aided Drug Design & Development Society in Turkey. Each time, the symposium is organized within these member countries. The AIMECS 2019 symposium was held in Turkey this year, as Prof. Dr. Esin Aki-Yalcin is the current president of the AFMC (2018-2020); the next AIMECS meeting will be organized in 2021 in Tokyo, Japan. In this report, we discuss key topics at the 12th AFMC International Medicinal Chemistry Symposium - New Avenues for Design and Development of Translational Medicine (AIMECS 2019) held in Istanbul, September 8-11, 2019.

1,2,3-Triazole ß-lactam conjugates as antimicrobial agents.

A convenient and efficient synthesis of new triazole ß-lactam conjugates using click chemistry is described. ß-lactam 15 and 16 were prepared using cycloaddition strategy and propargylated at N-1 to afford compounds 17 and 18. Cu-catalyzed click reaction of these ß-lactams 17 and 18 with different aryl azides provided 1,2,3-triazole conjugates 6 and 7, respectively. The products were fully characterized spectroscopically and tested against Gram-(+) and Gram-(-) bacteria. Compound 7a and 7c were found to be most active.

Design and in silico screening of aryl allyl mercaptan analogs as potential histone deacetylases (HDAC) inhibitors.

The Zn+2 HDACIs show promising anticancer activity. Allyl mercaptan (AM), a metastabilzed monomeric form of diallyl disulphide (DADS) shows better HDACI activity. The present work screens a dataset of aryl AM derivatives 1(a-g) for potential HDACI action via in silico models. DFT calculations predicted the geometrical parameters and frontier orbital calculations suggested better chemical reactivity. Negative chemical potential and NBO hyper conjugative interactions predicted their chemical stability. ADME study confirmed favourable drug likeliness. Molecular docked models suggested the formation of coordinate bond between sulphur of allylmercaptan and Zn2+ cofactor of HDAC8. Besides, models also predicted the dominance of hydrophobic interactions. The aryl AM analogs docked perfectly with HDAC3 as well. The glide score and S-Zn distance of compounds 1a, 1f and 1g were found to be better than allylmercaptan. Therefore, the designed aryl AM analogs filtered as better HDACIs. These could be further used for design and synthesis of new improved HDACIs.

Enhancement of antioxidant activity of levan through the formation of nanoparticle systems with metal ions.

Levan, a natural polymer, is widely used in biomedical applications, such as antioxidants, anti-inflammatory, and anti-tumor. The present study aimed to enhance the antioxidant activity of levan by combining it with various metal ions in the nanoparticle (NP) system. Levansucrase encoding gene from Bacillus licheniformis BK1 has been inserted into an expression vector and the obtained recombinant was labeled as Lsbl-bk1 (accession number MF774877.1). That enzyme was used for in vitro levan synthesis in 12% (w/v) sucrose as a substrate and about 4.28 mg/mL of levan was obtained. Levan-based metal ion NPs were synthesized using the coprecipitation method. In the production of NPs, levan acts as a reducing and stabilizing agent. Four types of levan-based metal ion NPs were synthesized, namely, levan-Fe2+ NPs, levan-Cu+ NPs, levan-Co2+ NPs, and levan-Zn2+ NPs. The transmission electron microscopy (TEM) technique was applied to visualize the size and shape of the synthesized levan-metal NPs. All levan-based metal ion NPs have a particle size of less than 100 nm, and even levan-Cu+ and levan-Zn2+ have particle sizes less than 50 nm. Levan-Fe2+ NPs and levan-Cu+ NPs exhibited prominent antioxidant activity with an inhibition level of up to 88% and 95%, respectively. And the inhibition level of two metal ion NPs had about 33%-40% higher antioxidant activity compared with the inhibition level of levan only. The two levan-metal ion NPs, therefore, have future prospects to be developed as the new formulation for the antioxidant drugs.

Degree-based topological indices on anticancer drugs with QSPR analysis.

From last two to three decades, the world is facing the threat of finding treatment for Cancer. This disease is striking almost ten million people every year throughout the world. Anticancer drugs are those which are used to cure malignant disease i.e. Cancer. These anticancer drugs are available in different forms including alkalyting agents, hormones and anti metabolites. Various examinations reveals that, there will be a adjacent relationship between the characteristics of alkanes and the anticancer drugs viz. Boiling point, melting point, enthalpy etc. with their chemical structures. In this proposed work, various topological indices are defined on some anticancer drugs to help the researchers to know the physical characteristics and chemical reaction associated with them. We also discuss the QSPR analysis of thirteen degree based topological indices. Further, we showcase that the characteristics have good correlation with physico-chemical characteristics of anticancer drugs.

Synthesis and evaluation of novel chromanone and quinolinone analogues of uniflorol as anti-leishmanial agents.

Within this work, we describe the design and synthesis of a range of novel chromanones and quinolinones, based on natural products reported to possess anti-leishmanial action. The core heterocycles were obtained either via classical or ionic liquid mediated Kabbe condensation in the case of chromanones, or aqueous Sonogashira based alkynylation followed by acid-catalysed cyclisation in the case of quinolinones. Upon testing in promastigotes, axenic amastigotes and Leishmania-infected macrophages, compound 13c was identified as displaying interesting activity, inhibiting axenic amastigotes and intracellular amastigotes with IC50s of 25.3 and 24.6µM respectively.

Quantum modelling and molecular docking evaluation of some selected quinoline derivatives as anti-tubercular agents.

Mycobacterium tuberculosis has instigated a serious challenge toward the effective treatment of tuberculosis. The reoccurrence of the resistant strains of the disease to accessible drugs/medications has mandate for the development of more effective anti-tubercular agents with efficient activities. Time expended and costs in discovering and synthesizing new hypothetical drugs with improved biological activity have been a major challenge toward the treatment of multi-drug resistance strain M. tuberculosis (TB). Meanwhile, to solve the problem stated, a new approach i.e. QSAR which establish connection between novel drugs with a better biological against M. tuberculosis is adopted. The anti-tubercular model established in this study to forecast the biological activities of some anti-tubercular compounds selected and to design new hypothetical drugs is subjective to the molecular descriptors; AATS7s, VE2_Dzi, SpMin7-Bhe and RDF110i. The significant of the model were observed with R2 of 0.8738, R2 adj of 0.8351 Q_cvˆ2 of 0.7127 which served as criteria to substantiate the QSAR model. More also, the model significant with the QSAR external validation criterial ''(R2test) of 0.7532. Ligand-receptor interactions between quinoline derivatives and the receptor (DNA gyrase) was carried out using molecular docking technique by employing the PyRx virtual screening software and discovery studio visualizer software. Furthermore, docking study indicates that compounds 10 of the derivatives with promising biological activity have the utmost binding energy of -18.8 kcal/mol. Meanwhile, the interaction of the standard drug; isoniazid with the target enzyme was observed with the binding energy -14.6 kcal/mol which was significantly lesser than the binding energy of the ligand (compound 10). This implies that ligand 10 could be used as a structural template to design better hypothetical anti-tubercular drugs with more efficient activities. The presumption of this research aid the medicinal chemists and pharmacist to design and synthesis a novel drug candidate against the tuberculosis. Moreover, in-vitro and in-vivo test could be carried out to validate the computational results.