Binding Interaction Mechanism Research Articles

Investigation of synthesis, spectroscopic characterization, crystal structure, and computational studies of 3-(4-(dimethylamino)phenyl)-1,5-di(thiophen-2- yl)pentane-1,5-dione as potent against Cathepsin S

The chief purpose of this work was to synthesize and characterize 3-(4-(dimethylamino)phenyl)-1,5-di(thiophen-2-yl)pentane-1,5-dione (4) whose structure was subsequently confirmed by single-crystal X-ray analysis. This molecule adopts a conformation approximating a three-bladed fan. In the crystal, C–H···O and C–H···S hydrogen bonds, together with C–H···π(ring) interactions form corrugated layers parallel to the bc plane. Electronic structure calculations were performed at the ωB97xd/def2tzvp level to explore the reactivity and topology of the molecule. Quantum theory of atoms in molecule (QTAIM) and NBO studies provide bonding characteristics and the extent of charge transfer with orbital energies computed from FMO theory together with optical and nonlinear optical (NLO) properties. A Hirschfeld surface analysis was performed to explore the nature of interactions in the crystal packing and the dispersion interactions were found to have a significant role in stabilizing the crystal structure. The H···H interactions are the most significant among the intermolecular interactions. Compound 4 was subjected to structural activity relationship analysis and exhibited potency against Cathepsin S. Molecular docking and molecular dynamics analysis were carried out to understand the binding interaction mechanism and stability of 4 in its complex with Cathepsin S.

Insight into the Binding Interaction Mechanism of the Ligand M1069 with Human Serum Albumin and A2A Adenosine Receptor—A Biophysical Approach

The study focuses on M1069, a promising drug for solid tumors functioning as an A2A adenosine receptor antagonist. Herein, we investigate the binding mechanism of the drug molecule M1069 by employing computational techniques to draw comparisons with Human serum albumin (HSA), shedding light on the intricate interactions between M1069 and its target as well. The molecular docking results suggest that the drug molecule binds very well with the HSA protein when compared to A2AAR with the docking score of −7.02 kcal/mol. To substantiate the molecular interactions between the drug and the protein structure, comprehensive molecular dynamic simulations were performed for a period of 100 ns. This approach facilitated an in-depth analysis of the dynamic relationships and behaviors between the drug and the protein, offering valuable insights into their intermolecular dynamics and stability. Subsequently, DFT analysis is conducted to assess the inhibitory efficacy of the drug, employing the B3LYP technique. Additionally, an investigation into the pharmacological ADMET parameters of the drug molecule resulted in gastrointestinal absorption. These outcomes contribute to a better understanding of the interaction dynamics between the drug and the proteins, providing valuable insights that can enhance the drug discovery process.

Chemical, antimicrobial, antioxidant, and molecular dynamic studies of spiro[chromane-3',2''-thiopyran]-4'-one 1''-oxide and spiro[chromane-3',2''-thiopyran]-4'-one 1'',1''-dioxide

Some of spiro[chromane-3',2''-thiopyran]-4'-ones were oxidized via m-chloroperbenzoic acid and/or hydrogen peroxide to afford the corresponding nine spiro[chromane-3',2''-thiopyran]-4'-one 1''-oxides and three spiro[chromane-3',2''-thiopyran]-4'-one 1'',1''-dioxides, which were confirmed by spectral data (IR, 1H NMR, 13C NMR, MS-ESI, and MS-EI). Whereas, the yield of oxidation using hydrogen peroxide is higher than that of oxidation using m-chloroperbenzoic acid. Moreover, Gram-negative bacteria (Escherichia coli ATCC 25922), and Gram-positive bacteria (Staphylococcus aureus ATCC 6538) were adopted to test the antimicrobial activity of 12 newly synthesized compounds (7a, 8a-c, 9a, 10a-c, 11a, 12a-c). The three sulfoxide derivatives 8b, 10b, and 10c showed antimicrobial activity. Also, antioxidant activity was evaluated for the newly synthesized compounds and shows that, all newly synthesized compounds (7a, 8a-c, 9a, 10a-c, 11a, 12a-c) have antioxidant activity. Molecular dynamic and system stability, Binding interaction mechanism based on binding free energy calculation, Identification of the critical residues responsible for ligands binding, Ligand–residue interaction network profiles, and In silico ADMET properties prediction were studied for the new compounds. The results of molecular dynamic studies were consistent with the in vitro antibacterial and antioxidant activity.

Novel composite structures based on cobalt phthalocyanine/graphene oxide: Identification of potential drug candidates to treat Alzheimer’s disease and diabetes

This study produced novel cobalt phthalocyanine (CoPc) (2) and its graphene oxide (GO) composites (2a-2f) and examined their impact on several metabolic enzymes, including α-glycosidase (α-Gly), achetylcholinesterase (AChE) and butyrylcholinesterase (BChE). IC50 values showed that when compared to conventional inhibitors, all the compounds demonstrated strong inhibitory effects against all targets. The ranges for the Ki values of the compounds containing the AChE, BChE, and α-glycosidase enzymes were 26.15 ± 3.85–48.26 ± 7.43, 5.46 ± 0.57–10.68 ± 0.78, and 2.20 ± 0.11–22.41 ± 2.60 nM, in that order. In addition, pharmacodynamic studies, the model form of new CoPc/GO composites, their structural orientations in the active sites of AChE, BChE and α-Gly enzymes, respectively, their binding interaction mechanism, and even their drug potential were investigated. The relevant compound (CoPc/GO) shows a binding energy trend of −12.40, −12.30 and −12.10 kcal/mol to α-Gly, AChE and BChE enzymes, respectively. In addition, it was determined that the compounds exhibited cytotoxic effects against human breast cancer cells. After more than 20 years of usage, cholinesterase inhibitors (ChEIs) are still a crucial component of the therapy of Alzheimer’s disease (AD). In multiple multicenter, well-controlled trials, only ChEIs have consistently demonstrated efficacy against AD; as a result, they have been widely approved by national regulatory authorities. Even if there have been a lot of ChEI discoveries recently, drug discovery is a continuous process that involves looking for novel strategies and chemotypes.

DFT Exploration of Metal Ion-Ligand Binding: Toward Rational Design of Chelating Agent in Semiconductor Manufacturing.

Chelating agents are commonly employed in microelectronic processes to prevent metal ion contamination. The ligand fragments of a chelating agent largely determine its binding strength to metal ions. Identification of ligands with suitable characteristics will facilitate the design of chelating agents to enhance the capture and removal of metal ions from the substrate in microelectronic processes. This study employed quantum chemical calculations to simulate the binding process between eleven ligands and the hydrated forms of Ni2+, Cu2+, Al3+, and Fe3+ ions. The binding strength between the metal ions and ligands was quantified using binding energy and binding enthalpy. Additionally, we explored the binding interaction mechanisms and explained the differences in binding abilities of the eleven ligands using frontier molecular orbitals, nucleophilic indexes, electrostatic potentials, and energy decomposition calculations based on molecular force fields. Based on our computational results, promising chelating agent structures are proposed, aiming to guide the design of new chelating agents to address metal ion contamination issues in integrated circuit processes.

Computer-aided approach for the identification of lead molecules as the inhibitors of cholinesterase’s and monoamine oxidases: Novel target for the treatment of Alzheimer disease

Molecular docking is a promising and reliable technology for the purpose of discovering lead compounds via virtual screening. In addition to allowing for the testing of a large number of compounds, it also allows for the determination of how the selected compounds inhibit the targeted protein/receptor based on the scoring function and ranking. Because selective cholinesterase and monoamine oxidase inhibitors play a critical role in the treatment of Alzheimer disease, this research focuses on elucidating the mechanism of binding interactions of a few quinolone derivatives within the active sites of cholinesterase (acetyl-cholinesterase (AChE) and butyrylcholinesterase (BChE) and monoamine oxidase (MAO, monoamine oxidase A & B). As a result of these discoveries, it is possible that the newly identified inhibitors will be used as lead compounds in the development of novel enzyme inhibitors for the treatment of specific diseases, hence enabling the development of novel therapeutic approaches.

Spectroscopic and molecular docking investigation on the interaction of a water-soluble Cu(II) complex containing diethanolamine and dipicolinic acid ligands with human serum albumin

Under physiological conditions, spectroscopic techniques as well as molecular docking simulation have been used to investigate the binding interaction mechanism between Cu(II) complex containing Pyridine-2,6-dicarboxylic acid (PDCA) and Diethanolamine (DEA) ligands, [Cu(DEA)(PDCA)] and human serum albumin (HSA). UV spectral changes of protein in the presence of the Cu(II) complex suggested the formation of a Protein-Cu(II) complex conjugate with specific new structure. The Cu(II) complex quenches the intrinsic fluorescence of the HSA via a static mechanism in which van der Waals interactions along with hydrogen bonds are fundamental binding forces. Displacement experiments performed by warfarin and ibuprofen site probes predict that the Cu(II) complex is located in subdomain IIA, Sudlow site 1 of HSA. Molecular docking results showed close resemblance with experimental data. Communicated by Ramaswamy H. Sarma

Understanding the binding interaction mechanism of i-motif with fluorophores: A biophysical approach

DNA exists in many canonical and non-canonical forms. i-motif: a non-canonical, tetraplex, antiparallel strand rich in cytosine, formed by hemi protonated cytosine- cytosine+ base pairs under slightly acidic pH levels, i-motifs are utilised in the study of numerous fields of applications. These i-motif tend to exhibit the property of switching the fluorescent nature of ligands such as thiazole orange, crystal violet and berberine upon interaction. This work is focussed on a basic overview of i-motif and its interactions with ligands to form fluorescence probes which could be useful in bio imaging. Herein, we are trying to find the electronic properties of small molecules upon interacting with i-motif. In order to find the active binding site in i-motif, Molecular Docking simulation was performed. The best docked pose obtained from the docking studies were subjected to molecular dynamics simulations. Further, DFT studies, optimization and single point energy calculations were carried out for freeligands and those bounded with the secondary DNA structures to understand the intermolecular interaction and to study their electronic properties.

Rhamnetin, a nutraceutical flavonoid arrests cell cycle progression of human ovarian cancer (SKOV3) cells by inhibiting the histone deacetylase 2 protein

Overexpression of HDAC 2 promotes cell proliferation in ovarian cancer. HDAC 2 is involved in chromatin remodeling, transcriptional repression, and the formation of condensed chromatin structures. Targeting HDAC 2 presents a promising therapeutic approach for correcting cancer-associated epigenetic abnormalities. Consequently, HDAC 2 inhibitors have evolved as an attractive class of anti-cancer agents. This work intended to investigate the anti-cancer abilities and underlying molecular mechanisms of Rhamnetin in human epithelial ovarian carcinoma cells (SKOV3), which remain largely unexplored. We employed various in vitro methods, including MTT, apoptosis study, cell cycle analysis, fluorescence microscopy imaging, and in vitro enzymatic HDAC 2 protein inhibition, to examine the chemotherapeutic sensitivity of Rhamnetin in SKOV3 cells. Additionally, we conducted in silico studies using molecular docking, MD simulation, MM-GBSA, DFT, and pharmacokinetic analysis to investigate the binding interaction mechanism within Rhamnetin and HDAC 2, alongside the compound’s prospective as a lead candidate. The in vitro assay confirmed the cytotoxic effects of Rhamnetin on SKOV3 cells, through its inhibition of HDAC 2 activity. Rhamnetin, a nutraceutical flavonoid, halted at the G1 phase of the cell cycle and triggered apoptosis in SKOV3 cells. Furthermore, computational studies provided additional evidence of its stable binding to the HDAC 2 protein’s binding site cavity. Based on our findings, we conclude that Rhamnetin effectively promotes apoptosis and mitigates the proliferation of SKOV3 cells through HDAC 2 inhibition. These results highlight Rhamnetin as a potential lead compound, opening a new therapeutic strategy for human epithelial ovarian cancer. Communicated by Ramaswamy H. Sarma

Synthesis, crystal structure investigation, Hirshfeld and DFT studies of newly synthesized dihydroisoquinoline derivatives

Isoquinoline and its derivatives, which constitute an important category of heterocyclic compounds and are found in a variety of naturally occurring alkaloids, serve a variety of biological purposes such as a potent agonist for human melatonin receptors 1. This research was conducted in an attempt to develop new dihydroisoquinoline molecules (III and IV). Single-crystal X-ray crystallography study validated their structures. The Hirshfeld surface analysis identifies intermolecular interactions by using a 2-D fingerprint map to recognize each type's relative contribution H⋅⋅⋅Hconnections are discovered to be dominating. The interaction energies between chemical pairs in crystal structures were found using an energy framework analysis. The DFT investigation demonstrates the electronic stability and reactivity of the compounds using the HOMO-LUMO and global reactivity descriptors, indicating that IV has higher chemical reactivity than III. The derived polarizability (αo) and hyperpolarizability (βo) values were used to calculate the optical and nonlinear optical characteristics of III and IV. The IV's significant βo value (488.94 au) indicates that it has good optical and NLO qualities. Molecular docking simulation using human melatonin receptors 1 was used to better understand the binding interaction mechanism of the title compounds. In addition, ADMET evaluations were performed to establish the therapeutic potential of III and IV.

Unraveling the mechanisms of Cefoxitin resistance in methicillin-resistant Staphylococcus aureus (MRSA): structural and molecular simulation-based insights

Methicillin-resistant Staphylococcus aureus (MRSA) severely affects human health, including the skin glands, nasal cavity, wound infections, bone infections, and pneumonia. Among the most effective MRSA drugs, Cefoxitin also develops resistance due to mutations in the mecA gene. Four mutations at positions E229K, E239R, G246K, and E447K are classified as high-level resistance mutations. However, the resistance mechanism of MRSA towards Cefoxitin caused by these mutations is still unclear, as there is less information available regarding the structural and functional effects of the mutations against Cefoxitin. Therefore, our present study was designed to explore the mechanisms of binding interactions between wild-type and mutated PBP2a against Cefoxitin using molecular docking and MD simulations. Subsequently, we identified that the mutant form of PBP2a affects the activity of Cefoxitin. Interestingly, the binding of Cefoxitin with G246K and E239R mutants demonstrates unstable behavior compared to E447K-Cefoxitin and E229K-Cefoxitin. In this study, we propose the resistance mechanism of Cefoxitin at the atomic level. The proposed drug-resistance mechanism will provide valuable guidance for the design of MRSA drugs. This research might provide a new framework for designing new agents against the mutated form of PBP2a. Communicated by Ramaswamy H. Sarma

Exploring the binding mechanism and adverse toxic effects of degradation metabolites of pyrethroid insecticides to human serum albumin: Multi-spectroscopy, calorimetric and molecular docking approaches.

Pyrethroid insecticides (PIs), a class of structurally similar non-persistent organic pollutants, can be degraded and metabolized to more toxic, and longer half-life products. In this study, the binding interaction mechanisms between human serum albumin (HSA) and the main degradation metabolites of PIs, 3-phenoxybenzoic acid (3-PBA) and 4-fluoro-3-phenoxybenzoic acid (4-F-3-PBA), were studied by theoretical simulation and experimental verification. Steady state fluorescence spectra showed that the fluorescence quenching mechanism was static. According to the binding constant, 4-F-3-PBA (1.53×105Lmol-1) was bound more strongly to HSA than 3-PBA (1.42×105Lmol-1) in subdomain ⅡA (site I). It was found by isothermal titration calorimetry that the metabolites and HSA spontaneously combined mainly through hydrogen bond and van der Waals interaction. Ultraviolet absorption spectra and circular dichroism spectra showed that the metabolites caused slight changes in the microenvironment and conformation of HSA. The above results were proved by molecular docking. The toxicity properties of the metabolites were further analyzed by software, and 4-F-3-PBA was found to be more toxic than 3-PBA. Considering the high exposure level of these metabolites in food, the environment and human body, it is necessary to further explore the toxicity of PIs metabolites.

Synthesis, crystal structure characterization and computational investigation of new thieno[2,3-b]pyridine derivatives as potent against molecule p38 alpha MAP kinase

In this study, two new thieno[2,3-b]pyridine derivatives (2 and 3) have been synthesized and characterized by single X-ray diffraction. While compound 2 crystallizes in monoclinic space group P21/c, compound 3 crystallizes in triclinic space group P. These compounds were further subjected to molecular docking simulation with p38 alpha MAP kinase to understand the binding interaction mechanism, in addition to that ADMET analysis was also performed to explore the title compounds to characterize the future drug candidate. To rationalize their structure-activity relationship, a DFT study based on the B3LYP/6-311++G** theoretical level was also done in this study.

Analysis of the Binding Mechanism of Bioactive Coumarins with Ovalbumin: Further Investigation into the Inhibitory Effects toward Protein Fibrillation

Two bioactive coumarin derivatives, 7-hydroxycoumarin (7-HC) and 4-methyl-7-hydroxycoumarin (4-Me-7-HC), were used to investigate the molecular interactions with the main food allergen from egg white, ovalbumin (OVA), along with their inhibitory effects on OVA aggregation. The mechanism of binding interaction was elucidated by multispectroscopic and computational methods. Circular dichroism (CD) and Fourier transform infrared (FT-IR) experiments confirmed the ligand-induced conformational changes of OVA. The fluorescence spectroscopic experiments demonstrated that the quenching mechanism was an unusual static quenching method with binding constants (Kb) in the range of 104 M–1, indicating a moderate nature of binding between OVA and coumarins. Thioflavin T (ThT) and Congo red (CR) binding assays confirmed the production of OVA fibrils, and the aggregation was shown to be inhibited by the coumarin derivatives in vitro. Thermodynamic parameters for OVA-7-HC/4-Me-7-HC interactions showed positive ΔH and ΔS values, indicating hydrophobic forces predominated in the binding processes and a negative ΔG value, implying the spontaneity of the complex formation, which was then further confirmed by computational studies.

Biochemical interaction of human hemoglobin with ionic liquids of noscapinoids: Spectroscopic and computational approach

In this work, we have developed noscapine based ionic liquids i.e., Noscapine (MeNOS) and 9-Bromonoscapine (MeBrNOS) as cation supported with bis(trifluoromethylsulfonyl)amide (NTf2−) as anion. We have reported the mechanism of binding interaction between noscapine based ILs and human hemoglobin (Hb) using various spectroscopic and computational techniques. The corresponding thermodynamics studies showed that the binding is exothermic in nature and major forces responsible for binding are Van der waals and hydrogen bonding interaction. The fluorescence spectra showed that the intensity of Hb decreases in the presence of [MeNOS]NTf2 and [MeBrNOS]NTf2 both shows static quenching. The secondary structural changes in Hb were observed and calculated by using CD spectroscopy. Molecular docking studies revealed that both the ILs show strong binding in β1 fragment of the tetrameric structure of Hb, but the binding of [MeNOS]NTf2 is relatively stronger than [MeBrNOS]NTf2 and the results are supported by MD simulations.

A biophysical approach of cytarabine anticancer drug insights into human serum albumin and checkpoint kinase 1

The present studies used biophysical techniques to examine the binding interaction mechanism of cytarabine anticancer drugs with human serum albumin (HSA) and checkpoint kinase 1. The UV–vis absorption spectrum of the cytarabine-HSA complex reveals a blue shift due to the presence of the cytarabine drug. The results of the fluorescence spectroscopy indicate that static quenching happened as the cytarabine drug concentration in HSA was increased and thermodynamical parameters, binding constant (K) were calculated at different temperatures (293 K, 298 K, 303 K) results have good agreement with molecular docking studies. Molecular docking and molecular dynamics studies were carried out for both HSA and Chk1 protein complexes. In continuing with docking, we have also carried out DFT analysis at the cytarabine drug binding active site of HSA and Chk1 molecule to understand the internal stability at the atomic level.

Interaction thermodynamics investigation of bovine serum albumin with black phosphorus quantum dots via spectroscopic and molecular simulation techniques

In this paper, the binding interaction thermodynamics of black phosphorus quantum dots (BPQDs) with bovine serum albumin (BSA) was explored systematically and comprehensively to interpret the influence of BPQDs on both the conformational structure and the biological function of BSA. The results of a variety of spectroscopic strategies and molecular simulation technique revealed that the endogenous fluorescence of BSA was quenched by BPQDs spontaneously via the static quenching mechanism based on the main binding forces of van der Waals interaction and hydrogen bonds formation. BPQDs interacted strongly with the Sudlow's site I of BSA via stoichiometric ratio of 1:1 to construct the novel stable ground-state complex. The results of three-dimensional fluorescence spectrometry and circular dichroism spectroscopy showed that BPQDs reduced the prominent α-helix structure content and the thermal stability of BSA through concentration-dependent manner. These results not only disclose the binding interaction mechanism of BPQDs with BSA comprehensively but also illustrate the variation of the secondary structure of BSA after its association with BPQDs carefully. Such research paves the way for the targeted design of black phosphorus derivatives with excellent biocompatibility and the safety application of such nanoparticles in the clinic diagnosis and the effective therapy of serious diseases in human beings.

Functional Characterization of the Venus Flytrap Domain of the Human TAS1R2 Sweet Taste Receptor.

The human sweet taste receptor is a heterodimeric receptor composed of two distinct G-protein-coupled receptors (GPCRs), TAS1R2 and TAS1R3. The TAS1R2 and TAS1R3 subunits are members of a small family of class C GPCRs whose members share the same architecture, comprising a Venus Flytrap (VFT) module linked to the seven transmembrane domains (TMDs) by a short cysteine-rich region (CRR). The VFT module of TAS1R2 contains the primary binding site for most of the sweet-tasting compounds, including natural sugars and artificial and natural sweeteners. However, cellular assays, molecular docking and site-directed mutagenesis studies have revealed that the VFT, CRR and TMD of TAS1R3 interact with some sweeteners, including the sweet-tasting protein brazzein. The aim of this study was to better understand the contribution of TAS1R2-VFT in the binding of sweet stimuli. To achieve this, we heterologously expressed human TAS1R2-VFT (hTAS1R2-VFT) in Escherichia coli. Circular dichroism spectroscopic studies revealed that hTAS1R2-VFT was properly folded with evidence of secondary structures. Using size-exclusion chromatography coupled with light scattering, we found that hTAS1R2-VFT behaves as a monomer. Ligand binding quantified by intrinsic tryptophan fluorescence showed that hTAS1R2-VFT is capable of binding sweet stimuli with Kd values, in agreement with physiological detection. Furthermore, we investigated whether the impact of point mutations, already shown to have deleterious effects on cellular assays, could impact the ability of hTAS1R2-VFT to bind sweet ligands. As expected, the ligand affinities of hTAS1R2-VFT were drastically reduced through the introduction of single amino acid substitutions (D278A and E382A) known to abolish the response of the full-length TAS1R2/TAS1R3 receptor. This study demonstrates the feasibility of producing milligram quantities of hTAS1R2-VFT to further characterize the mechanism of binding interaction and perform structural studies.

Realization of a Model-Free Pathway for Quantum Dot-Protein Interaction Beyond Classical Protein Corona or Protein Complex.

Although in recent times nanoparticles (NPs) are being used in various biological applications, their mechanism of binding interactions still remains hazy. Usually, the binding mechanism is perceived to be mediated through either the protein corona (PC) or protein complex (PCx). Herein, we report that the nanoparticle (NP)-protein interaction can also proceed via a different pathway without forming the commonly observed PC or PCx. In the present study, the NP-protein interaction between less-toxic zinc-silver-indium-sulfide (ZAIS) quantum dots (QDs) and bovine serum albumin (BSA) was investigated by employing spectroscopic and microscopic techniques. Although the analyses of data obtained from fluorescence and thermodynamic studies do indicate the binding between QDs and BSA, they do not provide clear experimental evidence in favor of PC or PCx. Quite interestingly, high-resolution transmission electron microscopy (HRTEM) studies have shown the formation of a new type of species where BSA protein molecules are adsorbed onto some portion of a QD surface rather than the entire surface. To the best of our knowledge, we believe that this is the first direct experimental evidence in favor of a model-free pathway for NP-protein interaction events. Thus, the outcome of the present study, through experimental evidence, clearly suggests that NP-protein interaction can proceed by following a pathway that is different from classical PC and PCx.

α-Amylase inhibition, anti-glycation property and characterization of the binding interaction of citric acid with α-amylase using multiple spectroscopic, kinetics and molecular docking approaches

• Kinetics, fluorescence, UV–Vis, FT-IR, Mol. Docking affirmed α-amylase-CA interaction. • CA inhibited α-amylase activity by a mixed inhibition, K ic < K iu ; with moderate IC 50 . • AMY intrinsic fluorescence was quenched by CA via static mechanism. • CA binding altered AMY native conformation. • CA suppressed Advanced Glycation End-products (AGEs) formation. The quest to suppress complications associated with diabetes mellitus is ever increasing, while food additives and preservatives are currently being considered to play additional roles besides their uses in food enhancement and preservation. In the present study, the protective prowess of a common food preservative (citric acid, CA) against advanced glycation end-products (AGEs) formation and its binding interaction mechanism with α-amylase (AMY), an enzyme linked with hyperglycemia management, were examined. Enzyme inhibition kinetics, intrinsic fluorescence, synchronous and 3D fluorescence spectroscopies, ultraviolet–visible (UV–Vis) absorption spectroscopy, Fourier transform-infrared (FT-IR) spectroscopy, thermodynamics, and molecular docking analyses were employed. Results obtained showed that citric acid decreased α-amylase activity via mixed inhibition (IC 50 = 5.01 ± 0.87 mM, K ic = 2.42 mM, K iu = 160.34 mM) and suppressed AGEs formation (IC 50 = 0.795 ± 0.001 mM). The intrinsic fluorescence of free α-amylase was quenched via static mechanism with high bimolecular quenching constant (K q ) and binding constant (K a ) values. Analysis of thermodynamic properties revealed that AMY-CA complex was spontaneously formed (ΔG < 0), entropy driven (TΔS > ΔH), with involvement of electrostatic forces. UV–Vis, FT-IR and 3D fluorescence spectroscopies affirmed alterations in α-amylase native conformation due to CA binding interaction. CA interacted with His-101, Asp-197, His-299, and Glu-233 within AMY active site. Our findings indicated that CA could impair formation of AGEs and interact with α-amylase to slow down starch hydrolysis; vital properties in management of type 2 diabetes complications.