Natural product-informed exploration of chemical space to enable bioactive molecular discovery

Diversity pattern and antibiotic activity of microbial communities inhabiting a karst cave from Costa Rica

The studies of cave bacterial communities worldwide have revealed their potential to produce antibiotic molecules. In Costa Rica, ~400 caves have been identified; however, their microbial diversity and biotechnological potential remain unexplored. In this work, we studied the chemical composition and microbial diversity of a Costa Rican cave (known as the Amblipigida cave) located in Puntarenas, Costa Rica. Additionally, through culture-dependent methods, we evaluated the potential of its microbiota to produce antibiotic molecules. Mineralogical and elemental analyses revealed that the Amblipigida cave is primarily composed of calcite. However, small variations in chemical composition were observed as a result of specific conditions, such as light flashes or the input of organic matter. The 16S rRNA gene metabarcoding revealed an extraordinarily high microbial diversity (with an average Shannon index of ~6.5), primarily comprising bacteria from the phyla Pseudomonadota, Actinomycetota, Firmicutes and Acidobacteriota, with the family Pseudomonadaceae being the most abundant. A total of 93 bacteria were isolated, of which 15% exhibited antibiotic activity against at least one Gram-positive or yeast strain and were classified within the genera Lysobacter, Streptomyces, Pseudomonas, Brevundimonas and Bacillus. These findings underscore the highly diverse nature of cave microbiota and their significant biotechnological potential, particularly in the production of antibiotic compounds.

A Comprehensive Review on Potential In Silico Screened Herbal Bioactive Compounds and Host Targets in the Cardiovascular Disease Therapy

Herbal medicines (HMs) have deciphered indispensable therapeutic effects against cardiovascular disease (CVD) (the predominant cause of death worldwide). The conventional CVD therapy approaches have not been efficient and need alternative medicines. The objective of this study was a review of herbal bioactive compound efficacy for CVD therapy based on computational and in silico studies. HM bioactive compounds with potential anti-CVD traits include campesterol, naringenin, quercetin, stigmasterol, tanshinaldehyde, Bryophyllin A, Bryophyllin B, beta-sitosterol, punicalagin, butein, eriodyctiol, butin, luteolin, and kaempferol discovered using computational studies. Some of the bioactive compounds have exhibited therapeutic effects, as followed by in vitro (tanshinaldehyde, punicalagin, butein, eriodyctiol, and butin), in vivo (gallogen, luteolin, chebulic acid, butein, eriodyctiol, and butin), and clinical trials (quercetin, campesterol, and naringenin). The main mechanisms of action of bioactive compounds for CVD healing include cell signaling and inhibition of inflammation and oxidative stress, decrease of lipid accumulation, and regulation of metabolism and immune cells. Further experimental studies are required to verify the anti-CVD effects of herbal bioactive compounds and their pharmacokinetic/pharmacodynamic features.

NIMO: A Natural Product-Inspired Molecular Generative Model Based on Conditional Transformer

Natural products (NPs) have diverse biological activity and significant medicinal value. The structural diversity of NPs is the mainstay of drug discovery. Expanding the chemical space of NPs is an urgent need. Inspired by the concept of fragment-assembled pseudo-natural products, we developed a computational tool called NIMO, which is based on the transformer neural network model. NIMO employs two tailor-made motif extraction methods to map a molecular graph into a semantic motif sequence. All these generated motif sequences are used to train our molecular generative models. Various NIMO models were trained under different task scenarios by recognizing syntactic patterns and structure-property relationships. We further explored the performance of NIMO in structure-guided, activity-oriented, and pocket-based molecule generation tasks. Our results show that NIMO had excellent performance for molecule generation from scratch and structure optimization from a scaffold.

Bicyclo[m.n.k]alkane Building Blocks as Promising Benzene and Cycloalkane Isosteres: Multigram Synthesis, Physicochemical and Structural Characterization

Electrophilic double bond functionalization - intramolecular enolate alkylation sequence was used to obtain a series of bridged and fused bicyclo[m.n.k]alkane derivatives (i. e., bicyclo[4.1.1]octanes, bicyclo[2.2.1]heptanes, bicyclo[3.2.1]octanes, bicyclo[3.1.0]hexanes, and bicyclo[4.2.0]heptanes). The scope and limitations of the method were established, and applicability to the multigram synthesis of target bicyclic compounds was illustrated. Using the developed protocols, over 50 mono- and bifunctional building blocks relevant to medicinal chemistry were prepared. The synthesized compounds are promising isosteres of benzene and cycloalkane rings, which is confirmed by their physicochemical and structural characterization (pKa , LogP, and exit vector parameters (EVP)). "Rules of thumb" for the upcoming isosteric replacement studies were proposed.

Collective Synthesis of Sarpagine and Macroline Alkaloid-Inspired Compounds

Design strategies that can access natural-product-like chemical space in an efficient manner may facilitate the discovery of biologically relevant compounds. We have employed a divergent intermediate strategy to construct an indole alkaloid-inspired compound collection derived from two different molecular design principles, i.e. biology-oriented synthesis and pseudo-natural products. The divergent intermediate was subjected to acid-catalyzed or newly discovered Sn-mediated conditions to selectively promote intramolecular C- or N-acylation, respectively. After further derivatization, a collection totalling 84 compounds representing four classes was obtained. Morphological profiling via the cell painting assay coupled with a subprofile analysis showed that compounds derived from different design principles have different bioactivity profiles. The subprofile analysis suggested that a pseudo-natural product class is enriched in modulators of tubulin, and subsequent assays led to the identification of compounds that suppress in vitro tubulin polymerization and mitotic progression.

Recent advances in anti-inflammatory active components and action mechanisms of natural medicines

Inflammation is a series of reactions caused by the body's resistance to external biological stimuli. Inflammation affects the occurrence and development of many diseases. Anti-inflammatory drugs have been used widely to treat inflammatory diseases, but long-term use can cause toxic side-effects and affect human functions. As immunomodulators with long-term conditioning effects and no drug residues, natural products are being investigated increasingly for the treatment of inflammatory diseases. In this review, we focus on the inflammatory process and cellular mechanisms in the development of diseases such as inflammatory bowel disease, atherosclerosis, and coronavirus disease-2019. Also, we focus on three signaling pathways (Nuclear factor-kappa B, p38 mitogen-activated protein kinase, Janus kinase/signal transducer and activator of transcription-3) to explain the anti-inflammatory effect of natural products. In addition, we also classified common natural products based on secondary metabolites and explained the association between current bidirectional prediction progress of natural product targets and inflammatory diseases.

Scaling the Andean Shilajit: A Novel Neuroprotective Agent for Alzheimer's Disease

Alzheimer's disease (AD) is a multifactorial neurodegenerative disorder without a cure, despite the enormous number of investigations and therapeutic approaches. AD is a consequence of microglial responses to "damage signals", such as aggregated tau oligomers, which trigger a neuro-inflammatory reaction, promoting the misfolding of cytoskeleton structure. Since AD is the most prevalent cause of dementia in the elderly (>60 years old), new treatments are essential to improve the well-being of affected subjects. The pharmaceutical industry has not developed new drugs with efficacy for controlling AD. In this context, major attention has been given to nutraceuticals and novel bioactive compounds, such as molecules from the Andean Shilajit (AnSh), obtained from the Andes of Chile. Primary cultures of rat hippocampal neurons and mouse neuroblastoma cells were evaluated to examine the functional and neuroprotective role of different AnSh fractions. Our findings show that AnSh fractions increase the number and length of neuronal processes at a differential dose. All fractions were viable in neurons. The AnSh fractions inhibit tau self-aggregation after 10 days of treatment. Finally, we identified two candidate molecules in M3 fractions assayed by UPLC/MS. Our research points to a novel AnSh-derived fraction that is helpful in AD. Intensive work toward elucidation of the molecular mechanisms is being carried out. AnSh is an alternative for AD treatment or as a coadjuvant for an effective treatment.

Bioactive Natural Product Discovery via Deuterium Adduct Bioactivity Screening

The discovery of bioactive natural products lies at the forefront of human medicine. The continued discovery of these molecules is imperative in the fight against infection and disease. While natural products have historically dominated the drug market, discovery in recent years has slowed significantly, partly due to limitations in current discovery methodologies. This work demonstrates a new workflow, deuterium adduct bioactivity screening (DABS), which pairs untargeted isotope labeling with whole cell binding assays for bioactive natural product discovery. DABS was validated and led to the discovery of a new isoprenyl guanidine alkaloid, zillamycin, which showed anti-cancer and anti-microbial activities. DABS thus represents a new workflow to accelerate discovery of natural products with a wide range of bioactive potentials.

Heck Macrocyclization in Forging Non-Natural Large Rings including Macrocyclic Drugs

The intramolecular Heck reaction is a well-established strategy for natural product total synthesis. When constructing large rings, this reaction is also referred to as Heck macrocyclization, which has proved a viable avenue to access diverse naturally occurring macrocycles. Less noticed but likewise valuable, it has created novel macrocycles of non-natural origin that neither serve as nor derive from natural products. This review presents a systematic account of the title reaction in forging this non-natural subset of large rings, thereby addressing a topic rarely covered in the literature. Walking through two complementary sections, namely (1) drug discovery research and (2) synthetic methodology development, it demonstrates that beyond the well-known domain of natural product synthesis, Heck macrocyclization also plays a remarkable role in forming synthetic macrocycles, in particular macrocyclic drugs.

"Magic Chloro": Profound Effects of the Chlorine Atom in Drug Discovery

Chlorine is one of the most common atoms present in small-molecule drugs beyond carbon, hydrogen, nitrogen, and oxygen. There are currently more than 250 FDA-approved chlorine-containing drugs, yet the beneficial effect of the chloro substituent has not yet been reviewed. The seemingly simple substitution of a hydrogen atom (R = H) with a chlorine atom (R = Cl) can result in remarkable improvements in potency of up to 100,000-fold and can lead to profound effects on pharmacokinetic parameters including clearance, half-life, and drug exposure in vivo. Following the literature terminology of the "magic methyl effect" in drugs, the term "magic chloro effect" has been coined herein. Although reports of 500-fold or 1000-fold potency improvements are often serendipitous discoveries that can be considered "magical" rather than planned, hypotheses made to explain the magic chloro effect can lead to lessons that accelerate the cycle of drug discovery.

Role of Stereochemistry on the Biological Activity of Nature-Inspired 3-Br-Acivicin Isomers and Derivatives

Chiral natural compounds are often biosynthesized in an enantiomerically pure fashion, and stereochemistry plays a pivotal role in biological activity. Herein, we investigated the significance of chirality for nature-inspired 3-Br-acivicin (3-BA) and its derivatives. The three unnatural isomers of 3-BA and its ester and amide derivatives were prepared and characterized for their antimalarial activity. Only the (5S, αS) isomers displayed significant antiplasmodial activity, revealing that their uptake might be mediated by the L-amino acid transport system, which is known to mediate the acivicin membrane's permeability. In addition, we investigated the inhibitory activity towards Plasmodium falciparum glyceraldehyde 3-phosphate dehydrogenase (PfGAPDH) since it is involved in the multitarget mechanism of action of 3-BA. Molecular modeling has shed light on the structural and stereochemical requirements for an efficient interaction with PfGAPDH, leading to covalent irreversible binding and enzyme inactivation. While stereochemistry affects the target binding only for two subclasses (1a-d and 4a-d), it leads to significant differences in the antimalarial activity for all subclasses, suggesting that a stereoselective uptake might be responsible for the enhanced biological activity of the (5S, αS) isomers.

Green Drug Discovery: Novel Fragment Space from the Biomass-Derived Molecule Dihydrolevoglucosenone (CyreneTM)

Biomass-derived molecules can provide a basis for sustainable drug discovery. However, their full exploration is hampered by the dominance of millions of old-fashioned screening compounds in classical high-throughput screening (HTS) libraries frequently utilized. We propose a fragment-based drug discovery (FBDD) approach as an efficient method to navigate biomass-derived drug space. Here, we perform a proof-of-concept study with dihydrolevoglucosenone (Cyrene^TM), a pyrolysis product of cellulose. Diverse synthetic routes afforded a 100-membered fragment library with a diversity in functional groups appended. The library overall performs well in terms of novelty, physicochemical properties, aqueous solubility, stability, and three-dimensionality. Our study suggests that Cyrene-based fragments are a valuable green addition to the drug discovery toolbox. Our findings can help in paving the way for new hit drug candidates that are based on renewable resources.

Benzoquinoline Chemical Space: A Helpful Approach in Antibacterial and Anticancer Drug Design

Benzoquinolines are used in many drug design projects as starting molecules subject to derivatization. This computational study aims to characterize e benzoquinone drug space to ease future drug design processes based on these molecules. The drug space is composed of all benzoquinones, which are active on topoisomerase II and ATP synthase. Topological, chemical, and bioactivity spaces are explored using computational methodologies based on virtual screening and scaffold hopping and molecular docking, respectively. Topological space is a geometrical space in which the elements composing it can be defined as a set of neighbors (which satisfy a particular axiom). In such space, a chemical space can be defined as the property space spanned by all possible molecules and chemical compounds adhering to a given set of construction principles and boundary conditions. In this chemical space, the potentially pharmacologically active molecules form the bioactivity space. Results show a poly-morphological chemical space that suggests distinct characteristics. The chemical space is correlated with properties such as steric energy, the number of hydrogen bonds, the presence of halogen atoms, and membrane permeability-related properties. Lastly, novel chemical compounds (such as oxadiazole methybenzamide and floro methylcyclohexane diene) with drug-like potential, active on TOPO II and ATP synthase have been identified.

Development of potent cholinesterase inhibitors based on a marine pharmacophore

The management of neurological disorders such as dementia associated with Alzheimer's or Parkinson's disease includes the use of cholinesterase inhibitors. These compounds can slow down the progression of these diseases and can also be used in the treatment of glaucoma and myasthenia gravis. The majority of the cholinesterase inhibitors used in the clinic are derived from natural products and our current paper describes the use of a small marine pharmacophore to develop potent and selective cholinesterase inhibitors. Fourteen small inhibitors were designed based on recent discoveries about the inhibitory potential of a range of related marine secondary metabolites. The compounds were evaluated, in kinetic enzymatic assays, for their ability to inhibit three different cholinesterase enzymes and it was shown that compounds with a high inhibitory activity towards electric eel and human recombinant acetylcholinesterase (IC₅₀ between 20-70 μM) could be prepared. It was also shown that this compound class was particularly active against horse serum butyrylcholinesterase, with IC₅₀ values between 0.8-16 μM, which is an order of magnitude more potent than the clinically used positive control neostigmine. The compounds were further tested for off-target toxicity against both human umbilical vein endothelial cells and bovine and human erythrocytes and were shown to display a low mammalian cellular toxicity. Overall, the study illustrates how the brominated dipeptide marine pharmacophore can be used as a versatile natural scaffold for the design of potent, and selective cholinesterase inhibitors.

Synthesis and cytotoxicity of betulin and betulinic acid derived 30-oxo-amides

Betulin and betulinic acid derived 30-oxo-amides were prepared by hydroboration, subsequent oxidation and amidation; these novel compounds were screened for their cytotoxic activity by SRB assays. All of the compounds showed significant cytotoxic activity for different human tumor cell lines. Small changes in the structure, however, resulted in significant changes in the cytotoxicity of the compounds. Of special interest were compounds 11 and 12, each holding an extra ethylenediamine moiety. These C-30 amides which showed low EC₅₀ values, and both of them acted mainly by apoptosis.

A Brief Review of Machine Learning-Based Bioactive Compound Research

Bioactive compounds are often used as initial substances for many therapeutic agents. In recent years, both theoretical and practical innovations in hardware-assisted and fast-evolving machine learning (ML) have made it possible to identify desired bioactive compounds in chemical spaces, such as those in natural products (NPs). This review introduces how machine learning approaches can be used for the identification and evaluation of bioactive compounds. It also provides an overview of recent research trends in machine learning-based prediction and the evaluation of bioactive compounds by listing real-world examples along with various input data. In addition, several ML-based approaches to identify specific bioactive compounds for cardiovascular and metabolic diseases are described. Overall, these approaches are important for the discovery of novel bioactive compounds and provide new insights into the machine learning basis for various traditional applications of bioactive compound-related research.

Chemical Evolution of Natural Product Structure

Natural products are the result of Nature’s exploration of biologically relevant chemical space through evolution and an invaluable source of bioactive small molecules for chemical biology and medicinal chemistry. Novel concepts for the discovery of new bioactive compound classes based on natural product structure may enable exploration of wider biologically relevant chemical space. The pseudo-natural product concept merges the relevance of natural product structure with efficient exploration of chemical space by means of fragment-based compound development to inspire the discovery of new bioactive chemical matter through de novo combination of natural product fragments in unprecedented arrangements. The novel scaffolds retain the biological relevance of natural products but are not obtainable through known biosynthetic pathways which can lead to new chemotypes that may have unexpected or unprecedented bioactivities. Herein, we cover the workflow of pseudo-natural product design and development, highlight recent examples, and discuss a cheminformatic analysis in which a significant portion of biologically active synthetic compounds were found to be pseudo-natural products. We compare the concept to natural evolution and discuss pseudo-natural products as the human-made equivalent, i.e. the chemical evolution of natural product structure.

A brief overview of classical natural product drug synthesis and bioactivity

This manuscript briefly overviewed the total synthesis and structure–activity relationship studies of eight classical natural products, which emphasizes the important role of total synthesis in natural product-based drug development.