Recent developments in the medicinal chemistry of single boron atom-containing compounds

Novel pleuromutilin derivatives conjugated with phenyl-sulfide and boron-containing moieties as potent antibacterial agents against antibiotic-resistant bacteria

In response to the escalating threat of microbial resistance, a series of novel pleuromutilin derivatives, conjugated with phenyl-sulfide and boron-containing moieties, were designed and synthesized. Most derivatives, especially 14b and 16b, demonstrated significant efficacy against Gram-positive bacteria, including multidrug-resistant strains, as well as pleuromutilin-resistant strains. Compound 16b showed high stability in the liver microsomes of rats and humans, along with acceptable tolerance in vitro and in vivo. Additionally, compound 16b exhibited promising efficacy in MRSA-infected mouse models. Our data highlight the potential of conjugated pleuromutilin derivatives as valuable agents against drug-resistant bacteria.

Borolatonin limits cognitive deficit and neuron loss while increasing proBDNF in ovariectomised rats

BACKGROUND

Borolatonin is a potential therapeutic agent for some neuronal diseases such as Alzheimer's disease (AD). Its administration exerts ameliorative effects such as those induced by the equimolar administration of melatonin in behavioral tests on male rats and in neuronal immunohistochemistry assays.

OBJECTIVE

In this study, motivated by sex differences in neurobiology and the incidence of AD, the ability of borolatonin to induce changes in female rats was assessed.

METHODS

Effects of borolatonin were measured by the evaluation of both behavioral and immunohistopathologic approaches; additionally, its ability to limit amyloid toxicity was determined in vitro.

RESULTS

Surprisingly, behavioral changes were similar to those reported in male rats, but not those evaluated by immunoassays regarding neuronal survival; while pro-brain-derived neurotrophic factor (BDNF) immunoreactivity and the limitation of toxicity by amyloid in vitro were observed for the first time.

CONCLUSION

Borolatonin administration induced changes in female rats. Differences induced by the administration of borolatonin or melatonin could be related to the differences in the production of steroid hormones in sex dependence. Further studies are required to clarify the possible mechanism and origin of differences in disturbed memory caused by the gonadectomy procedure between male and female rats.

Discovery of α-Amidobenzylboronates as Highly Potent Covalent Inhibitors of Plasma Kallikrein

Hereditary angioedema (HAE), a rare genetic disorder, is associated with uncontrolled plasma kallikrein (PKa) enzyme activity leading to the generation of bradykinin swelling in subcutaneous and submucosal membranes in various locations of the body. Herein, we describe a series of potent α-amidobenzylboronates as potential covalent inhibitors of PKa. These compounds exhibited time-dependent inhibition of PKa (compound 20 IC50 66 nM at 1 min, 70 pM at 24 h). Further compound dissociation studies demonstrated that 20 showed no apparent reversibility comparable to d-Phe-Pro-Arg-chloromethylketone (PPACK) (23), a known nonselective covalent PKa inhibitor.

2-Phenylcyclopropylmethylamine (PCPMA) as a privileged scaffold for central nervous system drug design

The use of privileged scaffolds in medicinal chemistry is an effective way to accelerate the drug discovery process, especially at the hit/lead optimization stage. 2-Phenylcyclopropylmethylamine (PCPMA) is a less commonly used chemical scaffold in medicinal chemistry, but many PCPMA-containing compounds exert therapeutic effects for various diseases, in particular central nervous system (CNS) diseases such as depression, schizophrenia, sleep disorder, and Parkinson's disease. The backbone of the PCPMA scaffold enables a unique structure of an amino group linked to a benzene ring through an alkyl linker, making it a useful template for the design of bioactive compounds especially for CNS drug targets including aminergic GPCRs and transporters. This review summarizes the medicinal chemistry studies of PCPMA-containing drugs and drug-like molecules, their mechanisms of action, and biological activities. We conclude that PCPMA is a unique and useful privileged scaffold for CNS drug design.

The Rise of Boron-Containing Compounds: Advancements in Synthesis, Medicinal Chemistry, and Emerging Pharmacology

Boron-containing compounds (BCC) have emerged as important pharmacophores. To date, five BCC drugs (including boronic acids and boroles) have been approved by the FDA for the treatment of cancer, infections, and atopic dermatitis, while some natural BCC are included in dietary supplements. Boron's Lewis acidity facilitates a mechanism of action via formation of reversible covalent bonds within the active site of target proteins. Boron has also been employed in the development of fluorophores, such as BODIPY for imaging, and in carboranes that are potential neutron capture therapy agents as well as novel agents in diagnostics and therapy. The utility of natural and synthetic BCC has become multifaceted, and the breadth of their applications continues to expand. This review covers the many uses and targets of boron in medicinal chemistry.

Boron-containing carbonic anhydrases inhibitors

Over the last decades, the medicinal chemistry of boron-based compounds has been extensively explored, designing valuable small molecule drugs to tackle diseases and conditions, such as cancer, infections, inflammatory and neurological disorders. Notably, boron has proven to also be a valuable element for the development of inhibitors of the metalloenzymes carbonic anhydrases (CAs), a class of drug targets with significant potential in medicinal chemistry. Incorporating boron into carbonic anhydrase inhibitors (CAIs) can modulate the ligand ability to recognize the target and/or influence selectivity towards different CA isoforms, using the tail approach and boron-based tails. The electron-deficient nature of boron and its associated properties have also led to the discovery of novel zinc-binding CAIs, such as boronic acids and the benzoxaboroles, capable of inhibiting the CAs upon a Lewis acid-base mechanism of action. The present manuscript reviews the state-of-the-art of boron-based CAIs. As research in the applications of boron compounds in medicinal chemistry continues, it is anticipated that new boron-based CAIs will soon expand the current array of such compounds. However, further research is imperative to fully unlock the potential of boron-based CAIs and to advance them towards clinical applications.

A Metal-Free and Operationally Simple Radical Trifluoromethylative Borylation of Unactivated Alkenes

We herein describe a protocol to synthesize trifluoromethylated alkyl boronates from alkenes by the mutual activation of the Togni II and the bis(catecholato)diboron reagents in the absence of any catalyst and additives. This reaction enables synthesizing a series of trifluoromethylated alkyl boronates using unactivated alkenes, including natural products and drug derivatives, in a regioselective manner. Moreover, the synthetic utility of the boronic ester present in the product allows access to a range of trifluoromethyl containing compounds. The radical trapping and gas detection experiments reveal that the more Lewis acidic diboron reagent determines the rapid formation of trifluoromethyl and boron centered radicals.

On the origins of SARS-CoV-2 main protease inhibitors

In order to address the world-wide health challenge caused by the COVID-19 pandemic, the 3CL protease/SARS-CoV-2 main protease (SARS-CoV-2-Mpro) coded by its nsp5 gene became one of the biochemical targets for the design of antiviral drugs. In less than 3 years of research, 4 inhibitors of SARS-CoV-2-Mpro have actually been authorized for COVID-19 treatment (nirmatrelvir, ensitrelvir, leritrelvir and simnotrelvir) and more such as EDP-235, FB-2001 and STI-1558/Olgotrelvir or five undisclosed compounds (CDI-988, ASC11, ALG-097558, QLS1128 and H-10517) are undergoing clinical trials. This review is an attempt to picture this quite unprecedented medicinal chemistry feat and provide insights on how these cysteine protease inhibitors were discovered. Since many series of covalent SARS-CoV-2-Mpro inhibitors owe some of their origins to previous work on other proteases, we first provided a description of various inhibitors of cysteine-bearing human caspase-1 or cathepsin K, as well as inhibitors of serine proteases such as human dipeptidyl peptidase-4 or the hepatitis C protein complex NS3/4A. This is then followed by a description of the results of the approaches adopted (repurposing, structure-based and high throughput screening) to discover coronavirus main protease inhibitors.

Chitosan nanomedicine containing RGD peptide and PAD4 inhibitor based on phenyl boronate coupling inhibition of primary tumor growth and lung metastasis

Stimulus-responsive nanodrugs have been extensively studied and their structural changes in the cells are important for controlled intracellular drug release. Histone citrullination of peptidylarginine deiminase 4 (PAD4) regulates the expression of tumor suppressor genes. In our previous study, compounds such as YW3-56 (356) were developed as potent PAD4 inhibitors with excellent anti-tumor activity in vitro and in vivo. To enhance the antitumor activity and improve the bioavailability, we further optimized the structure by modifying the phenylboronic acid moiety to the PAD4 inhibitor (4B). Taking advantage of the oxidative stress responsiveness of the phenylboronic acid moiety, in this study, we covalently attached 4B to RGD sequence peptide modified chitosan (K-CRGDV) to construct this new oxidative stress responsive nanodrug (K-CRGDV-4B). The modification of RGD sequence peptide conferred the nanodrug the ability to actively target tumors. The release mechanism was verified by UV-Vis spectroscopy, NMR. The anti-tumor and anti-metastatic properties of K-CRGDV-4B were demonstrated by in vitro cytotoxicity assay and in vivo mouse Lewis lung cancer metastasis model. In addition, K-CRGDV-4B modulates the ratio of immune cells in LLC tumor-bearing mice. Immunosuppressive proteins such as PD1 were inhibited, while IFN-γ and IFN-β, which are stimulators of tumor immune responses, were upregulated. Overall, K-CRGDV-4B is a stimulus-responsive nanodrug that responds to the tumor microenvironment by inhibiting PAD4 activity, blocking the formation of neutrophil extracellular traps (NETs), and improving the tumor immune microenvironment.

Palladium-Catalyzed ipso-Borylation of Aryl Halides Promoted by Lewis Acid-Mediated Electrophilic Activation of Aryl(halo)palladium(II) Complex

Palladium-catalyzed ipso-borylation of aryl halides, well-known as Miyaura borylation, is one of the reliable synthetic methods for organoborons. This reaction involves base-mediated nucleophilic activation of diboron that enables transmetalation of an aryl(halo)palladium(II) intermediate with a diboron. As an alternative, herein, we have established Lewis acid-mediated conditions for borylating (pseudo)haloarenes that require no external base. The electrophilic activation of the aryl(halo)palladium(II) intermediate via dehalogenation with Lewis acidic zinc complexes promotes the borylation.

Elemental exchange: Bioisosteric replacement of phosphorus by boron in drug design

Continuous efforts are being directed toward the employment of boron in drug design due to its advantages and unique characteristics including a plethora of target engagement modes, lower metabolism, and synthetic accessibility, among others. Phosphates are components of multiple drug molecules as well as clinical candidates, since they play a vital role in various biochemical functions, being components of nucleotides, energy currency- ATP as well as several enzyme cofactors. This review discusses the unique chemistry of boron functionalities as phosphate bioisosteres - "the boron-phosphorus elemental exchange strategy" as well as the superiority of boron groups over other commonly employed phosphate bioisosteres. Boron phosphate-mimetics have been utilized for the development of enzyme inhibitors as well as novel borononucleotides. Both the boron functionalities described in this review-boronic acids and benzoxaboroles-contain a boron connected to two oxygens and one carbon atom. The boron atom of these functional groups coordinates with a water molecule in the enzyme site forming a tetrahedral molecule which mimics the phosphate structure. Although boron phosphate-mimetic molecules - FDA-approved Crisaborole and phase II/III clinical candidate Acoziborole are products of the boron-phosphorus bioisosteric elemental exchange strategy, this technique is still in its infancy. The review aims to promote the use of this strategy in future medicinal chemistry projects.

EasyDock: customizable and scalable docking tool

Docking of large compound collections becomes an important procedure to discover new chemical entities. Screening of large sets of compounds may also occur in de novo design projects guided by molecular docking. To facilitate these processes, there is a need for automated tools capable of efficiently docking a large number of molecules using multiple computational nodes within a reasonable timeframe. These tools should also allow for easy integration of new docking programs and provide a user-friendly program interface to support the development of further approaches utilizing docking as a foundation. Currently available tools have certain limitations, such as lacking a convenient program interface or lacking support for distributed computations. In response to these limitations, we have developed a module called EasyDock. It can be deployed over a network of computational nodes using the Dask library, without requiring a specific cluster scheduler. Furthermore, we have proposed and implemented a simple model that predicts the runtime of docking experiments and applied it to minimize overall docking time. The current version of EasyDock supports popular docking programs, namely Autodock Vina, gnina, and smina. Additionally, we implemented a supplementary feature to enable docking of boron-containing compounds, which are not inherently supported by Vina and smina, and demonstrated its applicability on a set of 55 PDB protein-ligand complexes.

Bioactive compound, polyphenol content, and antioxidant activity of Asparagus racemosus Linn. root extract

Asparagus racemosus Linn. is an ethnopharmacologically important plant having extensive uses in Ayurveda, Unani, and Siddha. This study was carried out to evaluate the chemical profile of A. racemosus Linn. using GC-MS and FT-IR analysis, and its polyphenol content and antioxidant effects. Plants were collected from Bhujiyaghat, Nainital (29.3159° N, 79.5245° E) in Kumaun Himalayas. GC-MS with FT-IR analysis identified multiple functional groups, including carboxylic acid derivatives. Methyl 11, 12-octadecadienoate, was screened as the major compounds by GC-MS. A. racemosus contains a high concentration of phenols (80.92 ± 0.57 mg of GAE/g of DW), flavonoids (58.22 ± 1.62 mg of QE/g of DW), and tannins (86.77 ± 0.81 mg of TAE/g of DW). DPPH (24.63 ± 0.21 g/ml) and FRAP (72.49483 ± 0.130549 mg of AAE/g of DW) assays revealed the presence of significant antioxidant activity in A. racemosus.

Anti-inflammatory Action of BT75, a Novel RARα Agonist, in Cultured Microglia and in an Experimental Mouse Model of Alzheimer's Disease

BT75, a boron-containing retinoid, is a novel retinoic acid receptor (RAR)α agonist synthesized by our group. Previous studies indicated that activation of retinoic acid (RA) signaling may attenuate progression of Alzheimer's disease (AD). Presently, we aimed to examine the anti-inflammatory effect of BT75 and explore the possible mechanism using cultured cells and an AD mouse model. Pretreatment with BT75 (1-25 µM) suppressed the release of nitric oxide (NO) and IL-1β in the culture medium of mouse microglial SIM-A9 cells activated by LPS. BMS195614, an RARα antagonist, partially blocked the inhibition of NO production by BT75. Moreover, BT75 attenuated phospho-Akt and phospho-NF-κB p65 expression augmented by LPS. In addition, BT75 elevated arginase 1, IL-10, and CD206, and inhibited inducible nitric oxide synthase (iNOS) and IL-6 formation in LPS-treated SIM-A9 cells, suggesting the promotion of M1-M2 microglial phenotypic polarization. C57BL/6 mice were injected intracerebroventricularly (icv) with streptozotocin (STZ) (3 mg/kg) to provide an AD-like mouse model. BT75 (5 mg/kg) or the vehicle was intraperitoneally (ip) injected to icv-STZ mice once a day for 3 weeks. Immunohistochemical analyses indicated that GFAP-positive cells and rod or amoeboid-like Iba1-positive cells, which increased in the hippocampal fimbria of icv-STZ mice, were reduced by BT75 treatment. Western blot results showed that BT75 decreased levels of neuronal nitric oxide synthase (nNOS), GFAP, and phosphorylated Tau, and increased levels of synaptophysin in the hippocampus of icv-STZ mice. BT75 may attenuate neuroinflammation by affecting the Akt/NF-κB pathway and microglial M1-M2 polarization in LPS-stimulated SIM-A9 cells. BT75 also reduced AD-like pathology including glial activation in the icv-STZ mice. Thus, BT75 may be a promising anti-inflammatory and neuroprotective agent worthy of further AD studies.

Boron-Containing Compounds for Prevention, Diagnosis, and Treatment of Human Metabolic Disorders

The application of natural and synthetic boron-containing compounds (BCC) in biomedical field is expanding. BCC have effects in the metabolism of living organisms. Some boron-enriched supplements are marketed as they exert effects in the bone and skeletal muscle; but also, BCC are being reported as acting on the enzymes and transporters of membrane suggesting they could modify the carbohydrate metabolism linked to some pathologies of high global burden, as an example is diabetes mellitus. Also, some recent findings are showing effects of BCC on lipid metabolism. In this review, information regarding the effects and interaction of these compounds was compiled, as well as the potential application for treating human metabolic disorders is suggested.

An update on the discovery and development of reversible covalent inhibitors

Small molecule drugs that covalently bind irreversibly to their target proteins have several advantages over conventional reversible inhibitors. They include increased duration of action, less-frequent drug dosing, reduced pharmacokinetic sensitivity, and the potential to target intractable shallow binding sites. Despite these advantages, the key challenges of irreversible covalent drugs are their potential for off-target toxicities and immunogenicity risks. Incorporating reversibility into covalent drugs would lead to less off-target toxicity by forming reversible adducts with off-target proteins and thus reducing the risk of idiosyncratic toxicities caused by the permanent modification of proteins, which leads to higher levels of potential haptens. Herein, we systematically review electrophilic warheads employed during the development of reversible covalent drugs. We hope the structural insights of electrophilic warheads would provide helpful information to medicinal chemists and aid in designing covalent drugs with better on-target selectivity and improved safety.

Graphical Abstract

Computational Design, Synthesis, and Biophysical Evaluation of β-Amido Boronic Acids as SARS-CoV-2 Mpro Inhibitors

The COVID-19 pandemic has given a strong impetus to the search for antivirals active on SARS-associated coronaviruses. Over these years, numerous vaccines have been developed and many of these are effective and clinically available. Similarly, small molecules and monoclonal antibodies have also been approved by the FDA and EMA for the treatment of SARS-CoV-2 infection in patients who could develop the severe form of COVID-19. Among the available therapeutic tools, the small molecule nirmatrelvir was approved in 2021. It is a drug capable of binding to the M^pro protease, an enzyme encoded by the viral genome and essential for viral intracellular replication. In this work, by virtual screening of a focused library of β-amido boronic acids, we have designed and synthesized a focused library of compounds. All of them were biophysically tested by microscale thermophoresis, attaining encouraging results. Moreover, they also displayed M^pro protease inhibitory activity, as demonstrated by performing enzymatic assays. We are confident that this study will pave the way for the design of new drugs potentially useful for the treatment of SARS-CoV-2 viral infection.

Inhibition of HIV-1 Protease by a Boronic Acid with High Oxidative Stability

HIV-1 protease is an important target for pharmaceutical intervention in HIV infection. Extensive structure-based drug design led to darunavir becoming a key chemotherapeutic agent. We replaced the aniline group of darunavir with a benzoxaborolone to form BOL-darunavir. This analogue has the same potency as darunavir as an inhibitor of catalysis by wild-type HIV-1 protease and, unlike darunavir, does not lose potency as an inhibitor of the common D30N variant. Moreover, BOL-darunavir is much more stable to oxidation than is a simple phenylboronic acid analogue of darunavir. X-ray crystallography revealed an extensive network of hydrogen bonds between the enzyme and benzoxaborolone moiety, including a novel direct hydrogen bond from a main-chain nitrogen to the carbonyl oxygen of the benzoxaborolone moiety that displaces a water molecule. These data highlight the utility of benzoxaborolone as a pharmacophore.

Polyphenolic Boronates Inhibit Tumor Cell Proliferation: Potential Mitigators of Oxidants in the Tumor Microenvironment

Boronate-based compounds have been used in brain cancer therapy, either as prodrugs or in combination with other modalities. Boronates containing pro-luminescent and fluorescent probes have been used in mouse models of cancer. In this study, we synthesized and developed polyphenolic boronates and mitochondria-targeted polyphenolic phytochemicals (e.g., magnolol [MGN] and honokiol [HNK]) and tested their antiproliferative effects in brain cancer cells. Results show that mitochondria-targeted (Mito) polyphenolic boronates (Mito-MGN-B and Mito-HNK-B) were slightly more potent than Mito-MGN and Mito-HNK in inhibiting proliferation of the U87MG cell line. Similar proliferation results also were observed in other cancer cell lines, such as MiaPaCa-2, A549 and UACC-62. Independent in vitro experiments indicated that reactive nitrogen species (e.g., peroxynitrite) and reactive oxygen species (e.g., hydrogen peroxide) stoichiometrically react with polyphenolic boronates and Mito-polphenolic boronates, forming polyphenols and Mito-polyphenols as major products. Previous reports suggest that both Mito-MGN and Mito-HNK activate cytotoxic T cells and inhibit immunosuppressive immune cells. We propose that Mito-polyphenolic boronate-based prodrugs may be used to inhibit tumor proliferation and mitigate oxidant formation in the tumor microenvironment, thereby generating Mito-polyphenols in situ, as well as showing activity in the tumor microenvironment.

Synthesis of Novel Multifunctional bora-Ibuprofen Derivatives

A unique class of β-boron-functionalized non-steroidal anti-inflammatory compound (pinB-NSAID) was previously synthesized via copper-catalyzed 1,2-difunctionalization of the respective vinyl arene with CO2 and B2pin2 reagents. Here, pinacolylboron-functionalized ibuprofen (pinB-ibuprofen) was used as a model substrate to develop the conditions for pinacol deprotection and subsequent boron functionalization. Initial pinacol-boronic ester deprotection was achieved by transesterification with diethanolamine (DEA) from the boralactonate organic salt. The resulting DEA boronate adopts a spirocyclic boralactonate structure rather than a diazaborocane–DABO boronate structure. The subsequent acid-mediated hydrolysis of DEA and transesterification/transamination provided a diverse scope of new boron-containing ibuprofen derivatives.

Role of Nanomedicine-Based Therapeutics in the Treatment of CNS Disorders

Central nervous system disorders, especially neurodegenerative diseases, are a public health priority and demand a strong scientific response. Various therapy procedures have been used in the past, but their therapeutic value has been insufficient. The blood-brain barrier (BBB) and the blood-cerebrospinal fluid barrier is two of the barriers that protect the central nervous system (CNS), but are the main barriers to medicine delivery into the CNS for treating CNS disorders, such as brain tumors, Parkinson's disease, Alzheimer's disease, and Huntington's disease. Nanotechnology-based medicinal approaches deliver valuable cargos targeting molecular and cellular processes with greater safety, efficacy, and specificity than traditional approaches. CNS diseases include a wide range of brain ailments connected to short- and long-term disability. They affect millions of people worldwide and are anticipated to become more common in the coming years. Nanotechnology-based brain therapy could solve the BBB problem. This review analyzes nanomedicine's role in medication delivery; immunotherapy, chemotherapy, and gene therapy are combined with nanomedicines to treat CNS disorders. We also evaluated nanotechnology-based approaches for CNS disease amelioration, with the intention of stimulating the immune system by delivering medications across the BBB.

Development of a New Methodology for Dearomative Borylation of Coumarins and Chromenes and Its Applications to Synthesize Boron-Containing Retinoids

Dearomative borylation of coumarins and chromenes via conjugate addition represents a relatively unexplored and challenging task. To address this issue, herein, we report a new and general copper (I) catalyzed dearomative borylation process to synthesize boron-containing oxacycles. In this report, the borylation of coumarins, chromones, and chromenes comprising functional groups, such as esters, nitriles, carbonyls, and amides, has been achieved. In addition, the method generates different classes of potential boron-based retinoids, including the ones with oxadiazole and anthocyanin motifs. The borylated oxacycles can serve as suitable intermediates to generate a library of compounds.

Design and Synthesis of New Boron-Based Benzo[c][1,2,5]oxadiazoles and Benzo[c][1,2,5]thiadiazoles as Potential Hypoxia Inhibitors

Benzo[c][1,2,5]oxadiazoles and benzo[c][1,2,5]thiadiazoles are recognized to possess potent pharmacological activities including anticancer potential. In continuation of our research endeavors in the development of boron-based heterocycles as potential therapeutic agents, herein we report the design and synthesis of new series of boron-based benzo[c][1,2,5]oxadiazoles and benzo[c][1,2,5]thiadiazoles as anticancer agents targeting tumor hypoxia. A series of seventeen compounds were synthesized in two steps in an efficient manner via substitution reactions followed by subsequent hydrolysis of aryltrifluoroboronate salts into corresponding boronic acid derivatives in the presence of silica. This is the first example to develop boron-based hypoxia agents. The synthesized hybrids were characterized by suitable spectroscopic techniques. The biological studies are currently underway.

Boron- and phosphorus-containing molecular/nano platforms: exploiting pathological redox imbalance to fight cancer

Cancer is currently the second leading cause of death globally. Despite multidisciplinary efforts, therapies to fight various types of cancer still remain inefficient. Reducing high recurrence rates and mortality is thus a major challenge to tackle. In this context, redox imbalance is an undervalued characteristic of cancer. However, it may be targeted by boron- and phosphorus-containing materials to selectively or systemically fight cancer. In particular, boron and phosphorus derivatives are attractive building blocks for rational drug discovery due to their unique and wide regioselective chemistry, high degree of tuneability and chemical stability. Thus, they can be meticulously employed to access tunable molecular platforms to selectively exploit the redox imbalance of cancer cells towards necrosis/apoptosis. This field of research holds a remarkable potential; nevertheless, it is still in its infancy. In this mini-review, we underline recent advances in the development of boron- or phosphorus-derivatives as molecular/nano platforms for rational anticancer drug design. Our goal is to provide comprehensive information on different methodologies that bear an outstanding potential to further develop this very promising field of research.

The current progress in the use of boron as a platform for novel antiviral drug design

INTRODUCTION

Boron has attracted extensive interest due to several FDA-approved boron-containing drugs and other pharmacological agents in clinical trials. As a semimetal, it has peculiar biochemical characteristics which could be utilized in designing novel drugs against drug-resistant viruses. Emerging and reemerging viral pandemics are major threats to human health. Accordingly, we aim to comprehensively review the current status of antiviral boron-containing compounds.

AREAS COVERED

This review focuses on the utilization of boron to design molecules against viruses from two perspectives: (i) single boron atom-containing compounds acting on miscellaneous viral targets and (ii) boron clusters. The peculiar properties of antiviral boron-containing compounds and their diverse binding modes with viral targets are described in detail in this review.

EXPERT OPINION

Compounds bearing boronic acid can interact with viral targets by forming covalent or robust hydrogen bonds. This feature is valuable for combating resistant viruses. Furthermore, boron clusters can form dihydrogen bonds and bear features such as three-dimensional aromaticity, hydrophobicity, and biological stability. All these features demonstrated boron as a probable essential element with immense potential for drug design.

Design, synthesis, and biological evaluation of novel sulfamoylbenzamide derivatives as HBV capsid assembly modulators

Capsid assembly modulators (CAMs) represent a novel class of antiviral agents targeting hepatitis B virus (HBV) capsid to disrupt the assembly process. NVR 3-778 is the first CAM to demonstrate antiviral activity in patients infected with HBV. However, the relatively low aqueous solubility and moderate activity in the human body halted further development of NVR 3-778. To improve the anti-HBV activity and the drug-like properties of NVR 3-778, we designed and synthesized a series of NVR 3-778 derivatives. Notably, phenylboronic acid-bearing compound 7b (EC50 = 0.83 ± 0.33 µM, CC50 = 19.4 ± 5.0 µM) displayed comparable anti-HBV activity to NVR 3-778 (EC50 = 0.73 ± 0.20 µM, CC50 = 23.4 ± 7.0 µM). Besides, 7b showed improved water solubility (328.8 µg/mL, pH 7) compared to NVR 3-778 (35.8 µg/mL, pH 7). Size exclusion chromatography (SEC) and quantification of encapsidated viral RNA were used to demonstrate that 7b behaves as a class II CAM similar to NVR 3-778. Moreover, molecular dynamics (MD) simulations were conducted to rationalize the structure-activity relationships (SARs) of these novel derivatives and to understand their key interactions with the binding pocket, which provide useful indications for guiding the further rational design of more effective anti-HBV drugs.

Inorganic nanomaterials for intelligent photothermal antibacterial applications

Antibiotics are currently the main therapeutic agent for bacterial infections, but they have led to bacterial resistance, which has become a worldwide problem that needs to be addressed. The emergence of inorganic nanomaterials provides a new opportunity for the prevention and treatment of bacterial infection. With the continuous development of nanoscience, more and more inorganic nanomaterials have been used to treat bacterial infections. However, single inorganic nanoparticles (NPs) are often faced with problems such as large dosage, strong toxic and side effects, poor therapeutic effect and so on, so the combination of inorganic nano-materials and photothermal therapy (PTT) has become a promising treatment. PTT effectively avoids the problem of bacterial drug resistance, and can also reduce the dosage of inorganic nanomaterials to a certain extent, greatly improving the antibacterial effect. In this paper, we summarize several common synthesis methods of inorganic nanomaterials, and discuss the advantages and disadvantages of several typical inorganic nanomaterials which can be used in photothermal treatment of bacterial infection, such as precious metal-based nanomaterials, metal-based nanomaterials and carbon-based nanomaterials. In addition, we also analyze the future development trend of the remaining problems. We hope that these discussions will be helpful to the future research of near-infrared (NIR) photothermal conversion inorganic nanomaterials.

Palladium-Catalyzed Borylative Cyclizations of α-(2-Bromoaryl) Ketones to Form 1,2-Benzoxaborinines

Herein, we report that palladium catalyzes the borylative cyclization of α-(2-bromoaryl) ketones to afford 1,2-benzoxaborinines. The developed system is compatible with a variety of functionalities (Me, t-Bu, OMe, NMe₂, F, Cl, CN, CF₃, CO₂Me, and heteroaryl groups) and is applicable to the synthesis of B-O-containing tri- and tetracyclic fused-ring compounds.

Activity Screening of Fatty Acid Mimetic Drugs Identified Nuclear Receptor Agonists

Fatty acid mimetics (FAM) are bioactive molecules acting through the binding sites of endogenous fatty acid metabolites on enzymes, transporters, and receptors. Due to the special characteristics of these binding sites, FAMs share common chemical features. Pharmacological modulation of fatty acid signaling has therapeutic potential in multiple pathologies, and several FAMs have been developed as drugs. We aimed to elucidate the promiscuity of FAM drugs on lipid-activated transcription factors and tested 64 approved compounds for activation of RAR, PPARs, VDR, LXR, FXR, and RXR. The activity screening revealed nuclear receptor agonism of several FAM drugs and considerable promiscuity of NSAIDs, while other compound classes evolved as selective. These screening results were not anticipated by three well-established target prediction tools, suggesting that FAMs are underrepresented in bioactivity data for model development. The screening dataset may therefore valuably contribute to such tools. Oxaprozin (RXR), tianeptine (PPARδ), mycophenolic acid (RAR), and bortezomib (RAR) exhibited selective agonism on one nuclear receptor and emerged as attractive leads for the selective optimization of side activities. Additionally, their nuclear receptor agonism may contribute relevant and valuable polypharmacology.

ROS-removing nano-medicine for navigating inflammatory microenvironment to enhance anti-epileptic therapy

As a neurological disorder in the brain, epilepsy is not only associated with abnormal synchronized discharging of neurons, but also inseparable from non-neuronal elements in the altered microenvironment. Anti-epileptic drugs (AEDs) merely focusing on neuronal circuits frequently turn out deficient, which is necessitating comprehensive strategies of medications to cover over-exciting neurons, activated glial cells, oxidative stress and chronic inflammation synchronously. Therefore, we would report the design of a polymeric micelle drug delivery system that was functioned with brain targeting and cerebral microenvironment modulation. In brief, reactive oxygen species (ROS)-sensitive phenylboronic ester was conjugated with poly-ethylene glycol (PEG) to form amphiphilic copolymers. Additionally, dehydroascorbic acid (DHAA), an analogue of glucose, was applied to target glucose transporter 1 (GLUT1) and facilitate micelle penetration across the blood‒brain barrier (BBB). A classic hydrophobic AED, lamotrigine (LTG), was encapsulated in the micelles via self-assembly. When administrated and transferred across the BBB, ROS-scavenging polymers were expected to integrate anti-oxidation, anti-inflammation and neuro-electric modulation into one strategy. Moreover, micelles would alter LTG distribution in vivo with improved efficacy. Overall, the combined anti-epileptic therapy might provide effective opinions on how to maximize neuroprotection during early epileptogenesis.

Recent Progress in Fabrication and Application of BN Nanostructures and BN-Based Nanohybrids

Due to its unique physical, chemical, and mechanical properties, such as a low specific density, large specific surface area, excellent thermal stability, oxidation resistance, low friction, good dispersion stability, enhanced adsorbing capacity, large interlayer shear force, and wide bandgap, hexagonal boron nitride (h-BN) nanostructures are of great interest in many fields. These include, but are not limited to, (i) heterogeneous catalysts, (ii) promising nanocarriers for targeted drug delivery to tumor cells and nanoparticles containing therapeutic agents to fight bacterial and fungal infections, (iii) reinforcing phases in metal, ceramics, and polymer matrix composites, (iv) additives to liquid lubricants, (v) substrates for surface enhanced Raman spectroscopy, (vi) agents for boron neutron capture therapy, (vii) water purifiers, (viii) gas and biological sensors, and (ix) quantum dots, single photon emitters, and heterostructures for electronic, plasmonic, optical, optoelectronic, semiconductor, and magnetic devices. All of these areas are developing rapidly. Thus, the goal of this review is to analyze the critical mass of knowledge and the current state-of-the-art in the field of BN-based nanomaterial fabrication and application based on their amazing properties.

Access to Unexplored 3D Chemical Space: cis ‐Selective Arene Hydrogenation for the Synthesis of Saturated Cyclic Boronic Acids

A new class of saturated boron‐incorporated cyclic molecules has been synthesized employing an arene‐hydrogenation methodology. cis‐Selective hydrogenation of easily accessible, and biologically important molecules comprising benzoxaborole, benzoxaborinin, and benzoxaboripin derivatives is reported. Among the various catalysts tested, rhodium cyclic(alkyl)(amino)carbene [Rh‐CAAC] (1) pre‐catalyst revealed the best hydrogenation activity confirming turnover number up to 1400 with good to high diastereoselectivity. A broad range of functional groups was tolerated including sensitive substituents such as −F, −CF₃, and −silyl groups. The utility of the synthesized products was demonstrated by the recognition of diols and sugars under physiological conditions. These motifs can have a substantial importance in medicinal chemistry as they possess a three‐dimensional structure, are highly stable, soluble in water, form hydrogen bonds, and interact with diols and sugars.

Osteogenesis Performance of Boronized Ti6Al4V/HA Composites Prepared by Microwave Sintering: In Vitro and In Vivo Studies

The boronized Ti6Al4V/HA composite is deemed to be an important biomaterial because of its potential remarkable mechanical and biological properties. This paper reports the osteogenesis performance of the boronized Ti6Al4V/HA composite, which was prepared by microwave sintering of powders of Ti6Al4V, hydroxyapatite (HA), and TiB₂ in high-purity Ar gas at 1050 °C for 30 min, as dental implant based on both cell experiments in vitro and animal experiments in vivo. The comparison between the boronized Ti6Al4V/HA composite and Ti, Ti6Al4V, and boronized Ti6Al4V in the terms of adhesion, proliferation, alkaline phosphate (ALP) activity, and mineralization of MG-63 cells on their surfaces confirmed that the composite exhibited the best inductive osteogenesis potential. It exerted a more significant effect on promoting the early osteogenic differentiation of osteoblasts and exhibited the maximum optical density (OD) value in the MTT assay and the highest levels of ALP activity and mineralization ability, primarily ascribed to its bioactive HA component, porous structure, and relatively rough micro-morphology. The in vivo study in rabbits based on the micro-computed tomography (micro-CT) analysis, histological and histomorphometric evaluation, and biomechanical testing further confirmed that the boronized Ti6Al4V/HA composite had the highest new bone formation potential and the best osseointegration property after implantation for up to 12 weeks, mainly revealed by the measured values of bone volume fraction, bone implant contact, and maximum push-out force which, for example, reached 48.64%, 61%, and 150.3 ± 6.07 N at the 12th week. Owing to these inspiring features, it can serve as a highly promising dental implant.

Carboranes in drug discovery, chemical biology and molecular imaging

There exists a paucity of structural innovation and limited molecular diversity associated with molecular frameworks in drug discovery and biomolecular imaging/chemical probe design. The discovery and exploitation of new molecular entities for medical and biological applications will necessarily involve voyaging into previously unexplored regions of chemical space. Boron clusters, notably the carboranes, offer an alternative to conventional (poly)cyclic organic frameworks that may address some of the limitations associated with the use of novel molecular frameworks in chemical biology or medicine. The high thermal stability, unique 3D structure and aromaticity, kinetic inertness to metabolism and ability to engage in unusual types of intermolecular interactions, such as dihydrogen bonds, with biological receptors make carboranes exquisite frameworks in the design of probes for chemical biology, novel drug candidates and biomolecular imaging agents. This Review highlights the key developments of carborane derivatives made over the last decade as new design tools in medicinal chemistry and chemical biology, showcasing the versatility of this unique family of boron compounds.

Substitution at boron in BODIPYs

Recent synthetic achievements have led to 4,4-disubstituted-4-bora-3a,4a-diaza-s-indacenes (BODIPYs) with varying substituents at the meso, pyrrolic and/or boron sites, with each influencing photophysical properties and utility. This Feature article gives an overview of chemistry at the boron atom in BODIPYs, highlighting our contributions that evolved from synthetic curiosities and now offer this dipyrrolic skeleton potential across a wider range of applications. We first summarise preparative routes to BODIPYs through complexation of boron with the dipyrrinato ligand. The role of boron in protecting dipyrrins is then discussed, followed by strategies by which to achieve facile substitution at the boron atom.

In vitro antifungal activity of heterocyclic organoboron compounds against Trichophyton mentagrophytes and Microsporum canis obtained from clinical isolates

The aim of this study was to investigate the in vitro activity of thirty-eight heterocyclic organoboron compounds (1a-o, 2a-j, 3a-m) against clinically isolated dermatophytes Trichophyton mentagrophytes and Microsporum canis. Minimum inhibitory concentrations (MICs) of compounds (1a-o, 2a-j, 3a-m) were determined according to published protocol Clinical and Laboratory Standards Institute (CLSI) M38-A2 broth microdilution method. The minimum fungicidal concentrations (MFCs) for both T. mentagrophytes and M. canis were found by subculturing each fungal suspension on potato dextrose agar. According to the results, heterocyclic organoboron compounds (1a-o, 2a-j, 3a-m) were found to be more effective against dermatophyte M. canis (MIC = 3.12-25 µg/ml) than T. mentagrophytes (MIC = 12.5-100 µg/ml). Our findings showed that 7-membered heterocyclic organoboron compounds (3a-m) (MIC = 12.5-50 µg/ml) have stronger in vitro antifungal activity against T. mentagrophytes than 5-membered heterocyclic organoboron compounds (1a-o, 2a-j) (MIC = 25-100 µg/ml). The MFC values for all compounds ranged from 6.25 to 200 µg/ml. The limited number of systemic antifungal agents used in the treatment of dermatophyte infections and the presence of side effects have led to the search for new treatment resources in recent years. Therefore, investigation of the effect of heterocyclic organoboron compounds against dermatophytes will be promising for the discovery of new antifungal compounds that have gained great importance today.

Boron-Containing heterocycles as promising pharmacological agents

The incorporation of the "magic" boron atom has been established as an important new strategy in the field of medicinal chemistry as boron compounds have been shown to form various bonds with their biological targets. Currently, a number of boron-based drugs (e.g. bortezomib, crisaborole, and tavaborole) have been FDA approved and are in the clinic, and several other boron-containing compounds are in clinical trials. Boron-based heterocycles have an incredible potential in the ongoing quest for new therapeutic agents owing to their plethora of biological activities and useful pharmacokinetic profiles. The present perspective is intended to review the pharmacological applications of boron-based heterocycles that have been published. We have classified these compounds into groups exhibiting shared pharmacological activities and discussed their corresponding biological targets focusing mainly on the most potent therapeutic compounds.

Possible therapeutic effects of boron citrate and oleoylethanolamide supplementation in patients with COVID-19: A pilot randomized, double-blind, clinical trial

BACKGROUND

The present study aimed to assess the therapeutic effects of boron citrate and oleoylethanolamide supplementation in patients with COVID-19.

METHODS

Forty adult patients with a diagnosis of COVID-19 were recruited in the present study. Patients were randomized in a 1:1:1:1 allocation ratio to 1of 4 treatment groups: (A) 5 mg of boron citrate twice a day, (B) 200 mg of oleoylethanolamide twice a day, (C) both therapies, or (D) routine treatments without any study medications. At pre-and post-intervention phase, some clinical and biochemical parameters were assessed.

RESULTS

Supplementation with boron citrate alone or in combination with oleoylethanolamide significantly improved O2 saturation and respiratory rate (p < 0.01). At the end of the study, significant increases in white blood cell and lymphocyte count were observed in the boron citrate and combined groups (p < 0.001). Boron citrate supplementation led to a significant decrease in serum lactate dehydrogenase (p = 0.026) and erythrocyte sedimentation rate (p = 0.014), compared with other groups. Furthermore, boron citrate in combination with oleoylethanolamide resulted in a significant reduction in the high-sensitivity C-reactive protein and interleukin-1β concentrations (p = 0.031 and p = 0.027, respectively). No significant differences were found among four groups post-intervention, in terms of hemoglobin concentrations, platelet count, and serum interleukin-6 levels. At the end of the study, common symptoms of COVID-19 including cough, fatigue, shortness of breath, and myalgia significantly improved in the supplemented groups, compared to the placebo (p < 0.05).

CONCLUSION

Supplementation with boron citrate alone or in combination with oleoylethanolamide could improve some clinical and biochemical parameters in COVID-19 patients.

Boron Chemicals in Drug Discovery and Development: Synthesis and Medicinal Perspective

A standard goal of medicinal chemists has been to discover efficient and potent drug candidates with specific enzyme-inhibitor abilities. In this regard, boron-based bioactive compounds have provided amphiphilic properties to facilitate interaction with protein targets. Indeed, the spectrum of boron-based entities as drug candidates against many diseases has grown tremendously since the first clinically tested boron-based drug, Velcade. In this review, we collectively represent the current boron-containing drug candidates, boron-containing retinoids, benzoxaboroles, aminoboronic acid, carboranes, and BODIPY, for the treatment of different human diseases.In addition, we also describe the synthesis, key structure-activity relationship, and associated biological activities, such as antimicrobial, antituberculosis, antitumor, antiparasitic, antiprotozoal, anti-inflammatory, antifolate, antidepressant, antiallergic, anesthetic, and anti-Alzheimer's agents, as well as proteasome and lipogenic inhibitors. This compilation could be very useful in the exploration of novel boron-derived compounds against different diseases, with promising efficacy and lesser side effects.

Synthesis, In Silico, and Biological Evaluation of a Borinic Tryptophan-Derivative That Induces Melatonin-like Amelioration of Cognitive Deficit in Male Rat

Preclinical and clinical evidence supports melatonin and its analogues as potential treatment for diseases involving cognitive deficit such as Alzheimer's disease. In this work, we evaluated by in silico studies a set of boron-containing melatonin analogues on MT1 and MT2 receptors. Then, we synthesized a compound (borolatonin) identified as potent agonist. After chemical characterization, its evaluation in a rat model with cognitive deficit showed that it induced ameliorative effects such as those induced by equimolar administration of melatonin in behavioral tests and in neuronal immunohistochemistry assays. Our results suggest the observed effects are by means of action on the melatonin system. Further studies are required to clarify the mechanism(s) of action, as the beneficial effects on disturbed memory by gonadectomy in male rats are attractive.

The Boron Advantage: The Evolution and Diversification of Boron’s Applications in Medicinal Chemistry

In this review, the history of boron’s early use in drugs, and the history of the use of boron functional groups in medicinal chemistry applications are discussed. This includes diazaborines, boronic acids, benzoxaboroles, boron clusters, and carboranes. Furthermore, critical developments from these functional groups are highlighted along with recent developments, which exemplify potential prospects. Lastly, the application of boron in the form of a prodrug, softdrug, and as a nanocarrier are discussed to showcase boron’s emergence into new and exciting fields. Overall, we emphasize the evolution of organoboron therapeutic agents as privileged structures in medicinal chemistry and outline the impact that boron has had on drug discovery and development.

Indolylarylsulfones bearing phenylboronic acid and phenylboronate ester functionalities as potent HIV‑1 non-nucleoside reverse transcriptase inhibitors

To explore the chemical space around the entrance channel of the HIV-1 reverse transcriptase (RT) binding pocket, we innovatively designed and synthesized a series of novel indolylarylsulfones (IASs) bearing phenylboronic acid and phenylboronate ester functionalities at the indole-2-carboxamide as new HIV-1 non-nucleoside reverse transcriptase inhibitors (NNRTIs) through structure-based drug design. All the newly synthesized compounds exhibited excellent to moderate potency against wild-type (WT) HIV-1 with EC₅₀ values ranging from 6.7 to 42.6 nM. Among all, (3-ethylphenyl)boronic acid substituted indole-2-carboxamide and (4-ethylphenyl) boronate ester substituted indole-2-carboxamide were found to be the most potent inhibitors (EC₅₀ = 8.5 nM, SI = 3310; EC₅₀ = 6.7 nM, SI = 3549, respectively). Notably, (3-ethylphenyl)boronic acid substituted indole-2-carboxamide maintained excellent activities against the single HIV-1 mutants L100I (EC₅₀ = 7.3 nM), K103N (EC₅₀ = 9.2 nM), as well as the double mutant V106A/F227L (EC₅₀ = 21.1 nM). Preliminary SARs and molecular modelling studies are also discussed in detail.

Diversity of effects induced by boron-containing compounds on immune response cells and on antibodies in basal state

BACKGROUND

It has been reported that boron induces changes in the immune response, including in inflammatory processes. Recently, the effect of boric acid has been documented on the differentiation of lymphocyte clusters in mice and rats. However, the differences among boron-containing compounds (BCC) have been poorly explored.

METHODS

In this study, we analyzed the effects after oral administration of boric acid (BOR), methylboronic (MET), 3-thyenylboronic (3TB), 4-hydroxymethyl-phenylboronic (4MP) and 4-methanesulfonyl-phenylboronic (4SP) acids on the populations of lymphocytes from spleen and Peyer's patch (PP) as well as on antibodies. Groups of six male BALB/c were orally treated with 4.6 mg/kg of body weight with BOR, MET, 3TB, 4MP, and 4SP/daily for 10 days or vehicle (VEH) as a control group. After euthanasia, the spleen and small intestine were dissected. We conducted flow cytometry assays to assess B, CD3⁺ T, CD4⁺ T, and CD8⁺ T cells. Levels of IgG and IgM in serum, and IgA in intestinal fluid samples were analyzed by enzyme immunoassay.

RESULTS

In particular, we observed the effects of the administration of boronic acids on the number of lymphocytes; these changes were more notable in spleen than in PP. We found different profiles for each boron-containing compound, that is BOR induced an increase in the percentage of CD8⁺ T and CD19⁺/IgA⁺ cells in spleen, but a decrease in CD8⁺ T and B220⁺/CD19⁺ cells in PP. Meanwhile MET induced a decrease of CD4⁺ T in spleen, but induced an increase of CD4⁺ T cells and a decrease in the number of CD8⁺ T cells in PP. Boronic acids with an aromatic ring moiety induced changes in serum immunoglobulins levels, while 3TB acid induced a notable increase in S-IgA.

CONCLUSIONS

Effects in lymphocyte populations and antibodies are different for each tested compound. These results highlight the establishment of the necessary structure-activity relationship for BCC as immunomodulatory drugs. This is relevant in the biomedical field due to their attractiveness for selecting compounds to develop therapeutic tools.

Targeting Metalloenzymes by Boron-Containing Metal-Binding Pharmacophores

Metalloenzymes have critical roles in a wide range of biological processes and are directly involved in many human diseases; hence, they are considered as important targets for therapeutic intervention. The specific characteristics of metal ion(s)-containing active sites make exploitation of metal-binding pharmacophores (MBPs) critical to inhibitor development targeting metalloenzymes. This Perspective focuses on boron-containing MBPs, which display unique binding modes with metalloenzyme active sites, particularly via mimicking native substrates or tetrahedral transition states. The design concepts regarding boron-containing MBPs are highlighted through the case analyses on five distinct classes of clinically relevant nucleophilic metalloenzymes from medicinal chemistry perspectives. The challenges (e.g., selectivity) faced by some boron-containing MBPs and possible strategies (e.g., bioisosteres) for metalloenzyme inhibitor transformation are also discussed.

The modern role of boron as a 'magic element' in biomedical science: chemistry perspective

Boron was misconstrued as a toxic element for animals, which retarded the growth of boron-containing drug discovery in the last century. Nevertheless, modern applications of boronic acid derivatives are attractive in biomedical applications after the declaration that boron is a 'probable essential element' for humans by the WHO. Additionally, the approval of five boronic acid-containing drugs by the FDA has vastly impacted the use of boron in medicinal chemistry, chemical biology, drug delivery, biomaterial exploration, pharmacological improvements, and nutrition. This review article focuses on the chemistries attributed to boronic acids at physiological pH, enticing chemists to multidisciplinary applications. Prospective uses of boronic acid in pharma and chemical biology, along with prospects and challenges, are also part of the deliberation. Understanding these fundamental chemistries and interactions of boronic acid in biological systems will enable solving future challenges in drug discovery and executing space-age applications.

Exploring Covalent Docking Mechanisms of Boron-Based Inhibitors to Class A, C and D β-Lactamases Using Time-dependent Hybrid QM/MM Simulations

Recently, molecular covalent docking has been extensively developed to design new classes of inhibitors that form chemical bonds with their biological targets. This strategy for the design of such inhibitors, in particular boron-based inhibitors, holds great promise for the vast family of β-lactamases produced, inter alia, by Gram-negative antibiotic-resistant bacteria. However, the description of covalent docking processes requires a quantum-mechanical approach, and so far, only a few studies of this type have been presented. This study accurately describes the covalent docking process between two model inhibitors - representing two large families of inhibitors based on boronic-acid and bicyclic boronate scaffolds, and three β-lactamases which belong to the A, C, and D classes. Molecular fragments containing boron can be converted from a neutral, trigonal, planar state with sp2 hybridization to the anionic, tetrahedral sp3 state in a process sometimes referred to as morphing. This study applies multi-scale modeling methods, in particular, the hybrid QM/MM approach which has predictive power reaching well beyond conventional molecular modeling. Time-dependent QM/MM simulations indicated several structural changes and geometric preferences, ultimately leading to covalent docking processes. With current computing technologies, this approach is not computationally expensive, can be used in standard molecular modeling and molecular design works, and can effectively support experimental research which should allow for a detailed understanding of complex processes important to molecular medicine. In particular, it can support the rational design of covalent boron-based inhibitors for β-lactamases as well as for many other enzyme systems of clinical relevance, including SARS-CoV-2 proteins.