Fluoroolefins as amide bond mimics in dipeptidyl peptidase IV inhibitors

Multireceptor Analysis for Evaluating the Antidiabetic Efficacy of Karanjin: A Computational Approach

BACKGROUND

Diabetes mellitus, notably type 2, is a rising global health challenge, prompting the need for effective management strategies. Common medications such as metformin, insulin, repaglinide and sitagliptin can induce side effects like gastrointestinal disturbances, hypoglycemia, weight gain and specific organ risks. Plant-derived therapies like Karanjin from Pongamia pinnata present promising alternatives due to their historical use, holistic health benefits and potentially fewer adverse effects. This study employs in silico analysis to explore Karanjin's interactions with diabetes-associated receptors, aiming to unveil its therapeutic potential while addressing the limitations and side effects associated with conventional medications.

METHODOLOGY

The research encompassed the selection of proteins from the Protein Data Bank (PDB), followed by structural refinement processes and optimization. Ligands such as Karanjin and standard drugs were retrieved from PubChem, followed by a comprehensive analysis of their ADMET profiling and pharmacokinetic properties. Protein-ligand interactions were evaluated through molecular docking using AutoDockTools 1.5.7, followed by the analysis of structural stability using coarse-grained simulations with CABS Flex 2.0. Molecular dynamics simulations were performed using Desmond 7.2 and the OPLS4 force field to explore how Karanjin interacts with proteins over 100 nanoseconds, focusing on the dynamics and structural stability.

RESULTS

Karanjin, a phytochemical from Pongamia pinnata, shows superior drug candidate potential compared to common medications, offering advantages in efficacy and reduced side effects. It adheres to drug-likeness criteria and exhibits optimal ADMET properties, including moderate solubility, high gastrointestinal absorption and blood-brain barrier penetration. Molecular docking revealed Karanjin's highest binding energy against receptor 3L2M (Pig pancreatic alpha-amylase) at -9.1 kcal/mol, indicating strong efficacy potential. Molecular dynamics simulations confirmed stable ligand-protein complexes with minor fluctuations in RMSD and RMSF, suggesting robust interactions with receptors 3L2M.

CONCLUSION

Karanjin demonstrates potential in pharmaceutical expansion for treating metabolic disorders such as diabetes, as supported by computational analysis. Prospects for Karanjin in pharmaceutical development include structural modifications for enhanced efficacy and safety. Nanoencapsulation may improve bioavailability and targeted delivery to pancreatic cells, while combination therapies could optimize treatment outcomes in diabetes management. Clinical trials and experimental studies are crucial to validate its potential as a novel therapeutic agent.

Silver-Catalyzed (Z)-β-Fluoro-vinyl Iodonium Salts from Alkynes: Efficient and Selective Syntheses of Z-Monofluoroalkenes

Monofluoroalkenes are stable and lipophilic amide bioisosteres used in medicinal chemistry. However, efficient and stereoselective methods for synthesizing Z-monofluoroalkenes are underdeveloped. We envisage (Z)-β-fluoro-vinyl iodonium salts (Z-FVIs) as coupling partners for the diverse and stereoselective synthesis of Z-monofluoroalkenes. Disclosed herein is the development and application of a silver(I)-catalyzed process for accessing a broad scope of (Z)-FVIs with exclusive Z-stereoselectivity and regioselectivity from alkynes in a single step. Experimental and computational studies provide insight into the mechanism of the catalytic cycle and the role of the silver(I) catalyst, and the reactivity of (Z)-FVIs is explored through several stereospecific derivatizations.

Defluoroalkylation of gem-Difluoroalkenes with Alcohols via C-F/C-H Coupling

A feasible and effective method to synthesize α-fluoroalkenyl alcohols was reported. With the cooperation of photoredox and hydrogen atom transfer (HAT) processes, defluoroalkylations of gem-difluoroalkenes occurred smoothly with alcohols under visible-light irradiation. Notably, the protocols feature broad scopes, mild conditions, and validity for the late-stage functionalization of bioactive molecule derivatives. Mechanistic studies suggested that the reaction occurred through the radical coupling of the alkyl radical and the fluoroalkenyl radical.

Visible-Light-Induced Monofluoroalkenylation and gem-Difluoroallylation of Inactivated C(sp3)-H Bonds via 1,5-Hydrogen Atom Transfer (HAT)

The direct monofluoroalkenylation of C(sp³)-H bonds is of great importance and quite challenging. Current methods have been restricted to the monofluoroalkenylation of activated C(sp³)-H bonds. Here, we reported the photocatalyzed C(sp³)-H monofluoroalkenylation of inactivated C(sp³)-H bonds with gem-difluoroalkenes via 1,5-hydrogen atom transfer. This process shows good functional group tolerance, such as halides (F, Cl), nitrile, sulfone, ester, and pyridine, and good γ-selectivity. Moreover, this method succeeds in the photocatalyzed gem-difluoroallylation of inactivated C(sp³)-H with α-trifluoromethyl alkenes.

Cu-catalyzed cascade difluoroalkylation/5-endo cyclization/β-fluorine cleavage of ynones

A copper-catalyzed, redox-neutral cascade difluoroalkylation/5-endo annulation/β-fluorine cleavage of ynones is developed, providing a direct and stereoselective method to access synthetically important α-monofluoroalkenyl cyclopentanones. Mechanistic studies suggest an unprecedented Cu^II-assisted β-fluorine fragmentation, which may be valuable for the challenging but important C-F bond activation. Moreover, the in situ generated difluorocarbene was found to serve as an effective reductant for the regeneration of copper(I) catalyst, thus avoiding the addition of external reductants.

Formation of Fluorovinyl Spiro-[imidazole-indene] and α-Amino-β-naphthalenones via Rh(III)-Catalyzed Cascade C-H Functionalization

An efficacious method for building fluorovinyl spiro-[imidazole-indene] and α-amino-β-naphthalenone skeletons synchronously has been shown to consist of Rh(III)-catalyzed C-H functionalization between 2H-imidazoles and difluoromethylene alkynes. This protocol demonstrates a practical and straightforward route for installing fluorine elements in the envisioned position of heterocyclic compounds.

Design and Synthesis of New α-hydroxy β-fluoro/β-trifluoromethyl and Unsaturated Phosphonates from Carbohydrate-Derived Building Blocks via Pudovik and Horner–Wadsworth–Emmons Reactions

Herein, we present the application of fluorinated carbohydrate-derived building blocks for α-hydroxy β-fluoro/β-trifluoromethyl and unsaturated phosphonates synthesis. Pudovik and Horner–Wadsworth–Emmons reactions were applied to achieve this goal. The proposed pathway of the key reactions is supported by the experimental results, as well as quantum chemical calculations. The structure of the products was established by spectroscopic (1D, 2D NMR) and spectrometric (MS) techniques. Based on our data received, we claim that the progress of the Pudovik and HWE reactions is significantly influenced by the acidic protons present in the molecules as assessed by pKa values of the reagent.

Design and synthesis of efficient fluororethylene-peptidomimetic inhibitors of dipeptidyl peptidase III (DPP3)

Dipeptidyl peptidase III (DPP3) is a ubiquitously expressed zinc-dependent peptide cutting enzyme and selectively hydrolyses amide bonds to cleave N-terminal dipeptide fragments off of physiologically important oligopeptides. DPP3 has been found in a multitude of different types of cells and appears to be involved in various physiological processes (e.g. nociception, blood pressure control, protein turnover). Using the slowly converted peptide substrate tynorphin (VVYPW) as starting point, we have replaced the scissile bond with a fluoroethylene bioisostere to design ground state inhibitors, which led to the so far most effective peptide-based inhibitor of DPP3.

Iron-catalyzed decarboxylative and oxidative decarbonylative cross-coupling: a new strategy for the synthesis of monofluoroalkenes

Herein, an iron(ii)-catalyzed decarboxylative and oxidative decarbonylative cross-coupling of α-fluoro cinnamic acids with aliphatic aldehydes is presented.

Csp3‒H Monofluoroalkenylation via Stereoselective C‒F Bond Cleavage

A practical nickel- and photoredox-catalyzed Csp3‒H monofluoroalkenylation through chelation-assisted Csp2‒F bond cleavage of gem-difluoroalkenes has been developed, which provides an expedient access to the synthesis of tetrasubstituted fluoroalkenes with complete...

Copper-catalyzed direct monofluoroalkenylation of C(sp3)–H bonds via decarboxylation of α-fluoroacrylic acids

Herein, a protocol for the copper-catalyzed direct monofluoroalkenylation of C(sp3)–H bonds is reported.

gem-Heteroatom-Substituted Fluoroalkenes as Mimics of Amide Derivatives or Phosphates: A Comprehensive Review

gem-Heteroatom-substituted fluoroalkenes have received little attention despite their great potential in medicinal chemistry or in fine chemistry. Indeed, due to the electronic and steric similarity between the fluoroalkene moiety and the amide bond as well as the high strength of the carbon-fluorine bond, these gem-heteroatom-substituted fluoroalkenes could be envisioned as stable mimics of various important organic functions, such as phosphates, carbamates, S-thiocarbamates and ureas. We present herein an overview describing the syntheses over the last decade of heteroatom-substituted fluoroalkenes in geminal position. This review will be divided into several sections covering each the common following heteroatom: oxygen-, nitrogen-, sulfur-, phosphorus-, boron- and silicon-substituted fluoroalkenes.

Recent Medicinal Chemistry Approach for the Development of Dipeptidyl Peptidase IV Inhibitors

BACKGROUND

Diabetes, a metabolic disease, occurs due to a decreased or no effect of insulin on the blood glucose level. The current oral medications stimulate insulin release, increase glucose absorption and its utilization, and decrease hepatic glucose output. Two major incretin hormones like Glucose-dependent insulinotropic polypeptide (GIP) and glucagonlike peptide - 1 (GLP-1) stimulate insulin release after a meal, but their action is inhibited by enzyme dipeptidyl peptidase- IV.

OBJECTIVE

The activity of endogenous GLP-1 and GIP prolongs and extends with DPP IV inhibitors, which are responsible for the stimulation of insulin secretion and regulation of blood glucose level. DPP IV inhibitors have shown effectiveness and endurability with a neutral effect on weight as well as less chances of hypoglycemia in the management of type 2 diabetes. These journeys started from Sitagliptin (marketed in 2006) to Evogliptin (marketed in 2015, Korea).

CONCLUSION

Treatment of type 2 diabetes includes lifestyle changes, oral medications, and insulin. Newer and superior therapies are needed more than currently prescribed drugs. Various heterocyclic derivatives have been tried, but due to masking of DASH proteins, CYP enzymes, and hERG channel, they showed side effects. Based on these, the study has been focused on the development of safe, influential, selective, and long-lasting inhibitors of DPP IV.

Highly Stereoselective Intramolecular Carbofluorination of Internal α,β-Ynones Promoted by Selectfluor

Herein, we report a metal-free intramolecular carbofluorination protocol for the synthesis of tetrasubstituted monofluoroalkenes from internal α,β-ynones and Selectfluor with both high stereoselectivity and broad functional group tolerance. The chelation between tetrafluoroborate anion and the oxygen present in the aldehyde group rendered the reaction highly stereoselective, with the tetrafluoroborate serving as the direct fluorine source. Therefore, with addition of sodium tetrafluoroborate, Selectfluor could be reused several times without sacrificing reactivity.

(2-Fluoroallyl)pyridinium tetrafluoroborates: novel fluorinated electrophiles for Pd-catalyzed allylic substitution

An efficient two-step approach to 2-fluoroallyl amines was developed that involves the synthesis of (2-fluoroallyl)pyridinium tetrafluoroborates from readily available gem-bromofluorocyclopropanes and the application of the former as novel and stable 2-fluoroallyl electrophiles for Pd-catalyzed allylic substitution.

A Difluoromethylene Linchpin/Synthon: Application in Conjunction with Anion Relay Chemistry (ARC) Permits Ready Access to Diverse Difluoromethylene Scaffolds

Organodifluorine synthons, in conjuction with three-component diastereoselective anion relay chemistry (ARC), permit ready access to diverse difluoromethylene scaffolds. Initiated via [1,2]-addition of an organolithium reagent to a β-difluoromethylene silyl aldehyde, an alkoxide intermediate is formed, which is capable of undergoing a [1,4]-Brook rearrangement to generate a stabilized α-difluoromethylene carbanion, which, upon electrophile capture, affords a three-component adduct. This three component synthetic tactic represents a novel one-pot divergent strategy for the construction of diverse organodifluorine containing compounds.

Stereodivergent Alkyne Hydrofluorination Using Protic Tetrafluoroborates as Tunable Reagents

The discovery of safe, general, and practical procedures to prepare vinyl fluorides from readily available precursors remains a synthetic challenge. The metal-free hydrofluorination of alkynes constitutes an attractive though elusive strategy for their preparation. Introduced here is an inexpensive and easily handled reagent that enables the development of simple and scalable protocols for the regioselective hydrofluorination of alkynes to access both the E and Z isomers of vinyl fluorides. These reaction conditions were suitable for a diverse collection of alkynes, including several highly functionalized pharmaceutical derivatives. Computational and experimental mechanistic studies support C-F bond formation through vinyl cation intermediates, with the E- and Z-hydrofluorination products forming under kinetic and thermodynamic control, respectively.

Rhodium-Catalyzed Merging of 2-Arylquinazolinone and 2,2-Difluorovinyl Tosylate: Diverse Synthesis of Monofluoroolefin Quinazolinone Derivatives

An efficient method for the synthesis of 2-(o-monofluoroalkenylaryl)quinazolinone derivatives was developed. In this context, the quinazolinone ring served as the inherent directing group, 2,2-difluorovinyl tosylate was used as the monofluoroolefin synthon, and Rh(III)-catalyzed C-H bond difluorovinylation of 2-arylquinazolinons was performed to give the corresponding monofluoroalkene-containing quinazolinons in yields of 65-92%. The method is characterized by broad synthetic utility, mild conditions, and high efficiency.

Intermolecular fluoroamination of allenes towards substituted vinyl fluorides

Allene difunctionalization: Selectfluor mediated intermolecular aminofluorination of allenes with triazole and tetrazole nucleophiles towards vinyl fluorides.

Integrated Protocol to Design Potential Inhibitors of Dipeptidyl Peptidase- 4 (DPP-4)

BACKGROUND

A strategy for the treatment of type II diabetes mellitus is the inhibition of the enzyme known as dipeptidyl peptidase-4 (DPP-4).

AIMS

This study aims to investigate the main interactions between DPP-4 and a set of inhibitors, as well as proposing potential candidates to inhibit this enzyme.

METHODS

We performed molecular docking studies followed by the construction and validation of CoMFA and CoMSIA models. The information provided from these models was used to aid in the search for new candidates to inhibit DPP-4 and the design of new bioactive ligands from structural modifications in the most active molecule of the studied series.

RESULTS

We were able to propose a set of analogues with biological activity predicted by the CoMFA and CoMSIA models, suggesting that our protocol can be used to guide the design of new DPP-4 inhibitors as drug candidates to treat diabetes.

CONCLUSION

Once the integration of the techniques mentioned in this article was effective, our strategy can be applied to design possible new DPP-4 inhibitors as candidates to treat diabetes.

Applications of amide isosteres in medicinal chemistry

Isosteric replacement of amide groups is a classic practice in medicinal chemistry. This digest highlights the applications of most commonly employed amide isosteres in drug design aiming at improving potency and selectivity, optimizing physicochemical and pharmacokinetic properties, eliminating or modifying toxicophores, as well as providing novel intellectual property of lead compounds.

Stereoselective synthesis of α-fluoroacrylonitriles via organocatalytic cyanation of gem-difluoroalkenes and TMSCN

DBU-catalyzed cyanation of gem-difluoroalkenes with TMSCN, a highly stereoselective synthesis of α-fluoroacrylonitriles.

Activity and selectivity cliffs for DPP-IV inhibitors: Lessons we can learn from SAR studies and their application to virtual screening

The inhibition of dipeptidyl peptidase-IV (DPP-IV) has emerged over the last decade as one of the most effective treatments for type 2 diabetes mellitus, and consequently (a) 11 DPP-IV inhibitors have been on the market since 2006 (three in 2015), and (b) 74 noncovalent complexes involving human DPP-IV and drug-like inhibitors are available at the Protein Data Bank (PDB). The present review aims to (a) explain the most important activity cliffs for DPP-IV noncovalent inhibition according to the binding site structure of DPP-IV, (b) explain the most important selectivity cliffs for DPP-IV noncovalent inhibition in comparison with other related enzymes (i.e., DPP8 and DPP9), and (c) use the information deriving from this activity/selectivity cliff analysis to suggest how virtual screening protocols might be improved to favor the early identification of potent and selective DPP-IV inhibitors in molecular databases (because they have not succeeded in identifying selective DPP-IV inhibitors with IC₅₀ ≤ 100 nM). All these goals are achieved with the help of available homology models for DPP8 and DPP9 and an analysis of the structure-activity studies used to develop the noncovalent inhibitors that form part of some of the complexes with human DPP-IV available at the PDB.

Fluorine and Fluorinated Motifs in the Design and Application of Bioisosteres for Drug Design

The electronic properties and relatively small size of fluorine endow it with considerable versatility as a bioisostere and it has found application as a substitute for lone pairs of electrons, the hydrogen atom, and the methyl group while also acting as a functional mimetic of the carbonyl, carbinol, and nitrile moieties. In this context, fluorine substitution can influence the potency, conformation, metabolism, membrane permeability, and P-gp recognition of a molecule and temper inhibition of the hERG channel by basic amines. However, as a consequence of the unique properties of fluorine, it features prominently in the design of higher order structural metaphors that are more esoteric in their conception and which reflect a more sophisticated molecular construction that broadens biological mimesis. In this Perspective, applications of fluorine in the construction of bioisosteric elements designed to enhance the in vitro and in vivo properties of a molecule are summarized.

(2-Fluoroallyl)boronates: new reagents for diastereoselective 2-fluoroallylboration of aldehydes

New reagents for anti-selective 2-fluoroallylboration of aromatic and aliphatic aldehydes—(2-fluoroallyl)pinacolboranes, were prepared by Pd-catalyzed borylation of 2-fluoroallyl chlorides.

Recent advances in the synthesis of functionalised monofluorinated compounds

Over the past few years, we have tackled the synthesis of interesting monofluorinated organic molecules, such as: dihydronaphthalene derivatives, β-fluoro sulfones and related carbonyl compounds, fluorohydrins and allylic alcohols.

Rh(iii)-Catalyzed α-fluoroalkenylation of N-nitrosoanilines with 2,2-difluorovinyl tosylates via C–H bond activation

Rh(iii)-Catalyzed α-fluoroalkenylation of N-nitrosoanilines with 2,2-difluorovinyl tosylates has been realized, leading to the synthesis of monofluoroalkenes with high Z-selectivity with respect to the olefin.

Manganese-catalyzed synthesis of monofluoroalkenes via C–H activation and C–F cleavage

A redox-neutral manganese-catalyzed α-fluoroalkenylation of arenes via C–H activation and C–F cleavage has been described.

Palladium-Catalyzed Defluorinative Coupling of 1-Aryl-2,2-Difluoroalkenes and Boronic Acids: Stereoselective Synthesis of Monofluorostilbenes

The palladium-catalyzed defluorinative coupling of 1-aryl-2,2-difluoroalkenes with boronic acids is described. Broad functional-group tolerance arises from a redox-neutral process by a palladium(II) active species which is proposed to undergo a β-fluoride elimination to afford the products. The monofluorostilbene products were formed with excellent diastereoselectivity (≥50:1) in all cases, and it is critical, as traditional chromatographic techniques often fail to separate monofluoroalkene isomers. As a demonstration of this method's unique combination of reactivity and functional-group tolerance, a Gleevec® analogue, using a monofluorostilbene as an amide isostere, was synthesized.

Comprehensive analysis of the Co-structures of dipeptidyl peptidase IV and its inhibitor

Background

We comprehensively analyzed X-ray cocrystal structures of dipeptidyl peptidase IV (DPP-4) and its inhibitor to clarify whether DPP-4 alters its general or partial structure according to the inhibitor used and whether DPP-4 has a common rule for inhibitor binding.

Results

All the main and side chains in the inhibitor binding area were minimally altered, except for a few side chains, despite binding to inhibitors of various shapes. Some residues (Arg125, Glu205, Glu206, Tyr662 and Asn710) in the area had binding modes to fix a specific atom of inhibitor to a particular spatial position in DPP-4. We found two specific water molecules that were common to 92 DPP-4 structures. The two water molecules were close to many inhibitors, and seemed to play two roles: maintaining the orientation of the Glu205 and Glu206 side chains through a network via the water molecules, and arranging the inhibitor appropriately at the S2 subsite.

Conclusions

Our study based on high-quality resources may provide a necessary minimum consensus to help in the discovery of a novel DPP-4 inhibitor that is commercially useful.

Electronic supplementary material

The online version of this article (doi:10.1186/s12900-016-0062-8) contains supplementary material, which is available to authorized users.

Molecular docking studies and 2D analyses of DPP-4 inhibitors as candidates in the treatment of diabetes

Dipeptidyl peptidase-4 (DPP-4) is an important biological target related to the treatment of diabetes as DPP-4 inhibitors can lead to an increase in the insulin levels and a prolonged activity of glucagon-like peptide-1 (GLP-1) and gastric inhibitory polypeptide (GIP), being effective in glycemic control. Thus, this study analyses the main molecular interactions between DPP-4 and a series of bioactive ligands. The methodology used here employed molecular modeling methods, such as HQSAR (Hologram Quantitative Structure-Activity) analyses and molecular docking, with the aim of understanding the main structural features of the compound series that are essential for the biological activity. Analyses of the main interactions in the active site of DPP-4, in particular, the contribution of the hydroxyl coordination between Tyr547 and Ser630 by the water molecule, which is described in the literature as important for the coordinated interactions in the active site, were performed. Significant correlation coefficients of the best 2D model (r(2) = 0.942 and q(2) = 0.836) were obtained, indicating the predictive power of this model for untested compounds. Therefore, the final model constructed in this study, along with the information from the contribution maps, could be useful in the design of novel DPP-4 ligands with improved activity.