Protein Interaction Inhibitors Research Articles

Towards optimizing peptide-based inhibitors of protein-protein interactions: predictive saturation variation scanning (PreSaVS).

A simple-to-implement and experimentally validated computational workflow for sequence modification of peptide inhibitors of protein–protein interactions (PPIs) is described.

Query-guided protein-protein interaction inhibitor discovery.

Protein–protein interactions (PPIs) are central to biological mechanisms, and can serve as compelling targets for drug discovery. Yet, the discovery of small molecule inhibitors of PPIs remains challenging given the large and typically shallow topography of the interacting protein surfaces. Here, we describe a general approach to the discovery of orthosteric PPI inhibitors that mimic specific secondary protein structures. Initially, hot residues at protein–protein interfaces are identified in silico or from experimental data, and incorporated into secondary structure-based queries. Virtual libraries of small molecules are then shape-matched against the queries, and promising ligands docked to target proteins. The approach is exemplified experimentally using two unrelated PPIs that are mediated by an α-helix (p53/hDM2) and a β-strand (GKAP/SHANK1-PDZ). In each case, selective PPI inhibitors are discovered with low μM activity as determined by a combination of fluorescence anisotropy and 1H–15N HSQC experiments. In addition, hit expansion yields a series of PPI inhibitors with defined structure–activity relationships. It is envisaged that the generality of the approach will enable discovery of inhibitors of a wide range of unrelated secondary structure-mediated PPIs.

Identification of β-strand mediated protein-protein interaction inhibitors using ligand-directed fragment ligation.

β-Strand mediated protein–protein interactions (PPIs) represent underexploited targets for chemical probe development despite representing a significant proportion of known and therapeutically relevant PPI targets. β-Strand mimicry is challenging given that both amino acid side-chains and backbone hydrogen-bonds are typically required for molecular recognition, yet these are oriented along perpendicular vectors. This paper describes an alternative approach, using GKAP/SHANK1 PDZ as a model and dynamic ligation screening to identify small-molecule replacements for tranches of peptide sequence. A peptide truncation of GKAP functionalized at the N- and C-termini with acylhydrazone groups was used as an anchor. Reversible acylhydrazone bond exchange with a library of aldehyde fragments in the presence of the protein as template and in situ screening using a fluorescence anisotropy (FA) assay identified peptide hybrid hits with comparable affinity to the GKAP peptide binding sequence. Identified hits were validated using FA, ITC, NMR and X-ray crystallography to confirm selective inhibition of the target PDZ-mediated PPI and mode of binding. These analyses together with molecular dynamics simulations demonstrated the ligands make transient interactions with an unoccupied basic patch through electrostatic interactions, establishing proof-of-concept that this unbiased approach to ligand discovery represents a powerful addition to the armory of tools that can be used to identify PPI modulators.

Mapping Synthetic Dosage Lethal Genetic Interactions in Saccharomyces cerevisiae.

Synthetic dosage lethality (SDL) is a type of genetic interaction that occurs when increasing the expression of a gene causes a fitness defect, such as lethality, in a specific mutant background but has little effect on fitness in a wild-type background. SDL genetic interactions discovered in model organisms such as the budding yeast, Saccharomyces cerevisiae , represent candidate genetic interactions that may be conserved in human cells. In some cases, SDL genetic interactions can be applied to study the biological implications of genes overexpressed in cancer and to discover potential anticancer therapeutic drug targets. Here, we provide a protocol for screening a query overexpression gene against ordered arrays of yeast mutant strains to identify mutations that sensitize yeast to increased dosage of a specific gene product. We outline applications and procedures for screening with an inducibly overexpressed wild-type gene, a common feature of cancer cells, or with an inducibly overexpressed gene carrying a dominant-negative missense mutation as a model of protein-inhibitor interactions. This high-throughput screening platform is adapted from synthetic genetic array (SGA) technology and enables the generation of large-scale SDL genetic interaction networks that can be applied to study gene/pathway function and to identify cross-species cancer-relevant processes.

Scanning Protein Surfaces with DNA-Encoded Libraries.

Understanding the ligandability of a target protein, defined as the capability of a protein to bind drug‐like compounds on any site, can give important stimuli to drug‐development projects. For instance, inhibition of protein–protein interactions usually depends on the identification of protein surface binders. DNA‐encoded chemical libraries (DELs) allow scanning of protein surfaces with large chemical space. Encoded library selection screens uncovered several protein–protein interaction inhibitors and compounds binding to the surface of G protein‐coupled receptors (GPCRs) and kinases. The protein surface‐binding chemotypes from DELs are predominantly chemically modified and cyclized peptides, and functional small‐molecule peptidomimetics. Peptoid libraries and structural peptidomimetics have been less studied in the DEL field, hinting at hitherto less populated chemical space and suggesting alternative library designs. Roughly a third of bioactive molecules evolved from smaller, target‐focused libraries. They showcase the potential of encoded libraries to identify more potent molecules from weak, for example, fragment‐like, starting points.

Configuration Flipping in Distal Pocket of Multidrug Transporter MexB Impacts the Efflux Inhibitory Mechanism.

MexAB-OprM efflux pumps, found in Pseudomonas aeruginosa, play a major role in drug resistance by extruding out drugs and antibiotic molecules from cells. Inhibitors are used to cease the potency of the efflux pumps. In this study, in-silico models are used to investigate the nature of the binding pocket of the MexAB-OprM efflux pump. First, we have performed classical molecular dynamics (MD) simulations to shed light on different aspects of protein-inhibitor interaction in the binding pocket of the pump. Using classical MD simulations, quantum mechanics/molecular mechanics (QM/MM), and various types of analyses, it is found that D13-9001 has a higher binding affinity towards the binding pocket compared to D1 and D2; the results are in sync with the experimental dat. Two stable configurations of D13-9001 are discovered inside the distal pocket which could be one of the primary reasons for the greater efficacy of D13-9001. The free energy barrier upon changing one state to another is calculated by employing umbrella sampling method. Finally, F178 is mutated to have the complete picture as it contributes significantly to the binding energy irrespective of the three inhibitors. Our results may help to design a new generation of inhibitors for such an efflux pump.

Investigation of C-glycosylated apigenin and luteolin derivatives’ effects on protein tyrosine phosphatase 1B inhibition with molecular and cellular approaches

In our previous study, we investigated C-glycosylated apigenin and luteolin derivatives’ antidiabetic potential via protein tyrosine phosphatase 1B (PTP1B) inhibition in vitro, and found that they exhibited varying degrees of effect on PTP1B (IC50 = 17.76, 24.76, 7.62, 24.54, 6.70, and 57.11 µM for isovitexin, apigenin, vitexin, isoorientin, luteolin, and orientin, respectively). However, the precise molecular mechanisms in apigenin and luteolin derivatives’ PTP1B inhibition remain unclear. Therefore, in this study, we examined C-glycosylated apigenin and luteolin derivatives’ PTP1B inhibition via molecular docking simulation and PTP1B expression at the cellular level in insulin-resistant C2C12 cells. Kinetic studies revealed that apigenin, luteolin, and isoorientin were competitive, vitexin and isovitexin mixed-type, and orientin noncompetitive inhibitors of PTP1B. Docking simulations of these flavonoids demonstrated different negative binding energies and close proximity to residues in PTP1B’s binding pocket. The number of hydrogen bonds and other interactions determined the strength of the protein-inhibitor interaction. Further, we also found that apigenin and luteolin derivatives stimulate glucose uptake in insulin-resistant C2C12 cells. Therefore, we speculate that the C-glycosylation apigenin and luteolin derivatives at the C-6 and C-8 positions affect PTP1B inhibition greatly depending upon the type of mode of inhibition and binding affinity with the PTP1B expression level. Thus, the study contributes to our knowledge of the mechanisms by which C-glycosylated flavonoids exert varying degrees of PTP1B inhibition activity.

HDM2 protein-binding peptides screened from stapled α-helical peptide phage display libraries with different types of staple linkers

Chemically modified peptide ligands were identified from α-helix peptide phage libraries with different types of staple linkers. The hDM2-protein was used as a representative target of protein–protein interactions to screen ligands for p53 binding sites in hDM2. Two types of staple linkers were used for the chemical modification of the peptide phage display libraries before affinity selection. The identified stapled peptides could bind to hDM2 competitively with the p53 peptide. The stapled peptide phage libraries developed in this study will improve the discovery of protein–protein interaction inhibitors through the synergistic effect of peptide units and staple linkers.

Cyclic Peptide Inhibitors of the Tsg101 UEV Protein Interactions Refined through Global Docking and Gaussian Accelerated Molecular Dynamics Simulations.

Tsg101 UEV domain proteins are potential targets for virus infection therapy, especially for HIV and Ebola viruses. Peptides are key in curbing virus transmission, and cyclic peptides have a greater survival time than their linear peptides. To date, the accurate prediction of cyclic peptide-protein receptors binding conformations still is challenging because of high peptide flexibility. Here, a useful approach combined the global peptide docking, Gaussian accelerated molecular dynamics (GaMD), two-dimensional (2D) potential of mean force (PMF), normal molecular dynamics (cMD), and solvated interaction energy (SIE) techniques. Then we used this approach to investigate the binding conformations of UEV domain proteins with three cyclic peptides inhibitors. We reported the possible cyclic peptide-UEV domain protein binding conformations via 2D PMF free energy profiles and SIE free energy calculations. The residues Trp145, Tyr147, and Trp148 of the native cyclic peptide (CP1) indeed play essential roles in the cyclic peptides-UEV domain proteins interactions. Our findings might increase the accuracy of cyclic peptide-protein conformational prediction, which may facilitate cyclic peptide inhibitor design. Our approach is expected to further aid in addressing the challenges in cyclic peptide inhibitor design.

Design, Synthesis, and Structure-Activity Relationships of Indoline-Based Kelch-like ECH-Associated Protein 1-Nuclear Factor (Erythroid-Derived 2)-Like 2 (Keap1-Nrf2) Protein-Protein Interaction Inhibitors.

The Keap1 (Kelch-like ECH-associated protein 1)-Nrf2 (nuclear factor erythroid 2-related factor 2)-ARE (antioxidant response element) pathway is the major defending mechanism against oxidative stresses, and directly disrupting the Keap1-Nrf2 protein-protein interaction (PPI) has been an attractive strategy to target oxidative stress-related diseases, including cardiovascular diseases. Here, we describe the design, synthesis, and structure-activity relationships (SARs) of indoline-based compounds as potent Keap1-Nrf2 PPI inhibitors. Comprehensive SAR analysis and thermodynamics-guided optimization identified 19a as the most potent inhibitor in this series, with an IC50 of 22 nM in a competitive fluorescence polarization assay. Further evaluation indicated the proper drug-like properties of 19a. Compound 19a dose-dependently upregulated genes and protein level of Nrf2 as well as its downstream markers and showed protective effects against lipopolysaccharide-induced injury in both H9c2 cardiac cells and mouse models. Collectively, we reported here a novel indoline-based Keap1-Nrf2 PPI inhibitor as a potential cardioprotective agent.

NO is involved in H2-induced adventitious rooting in cucumber by regulating the expression and interaction of plasma membrane H+-ATPase and 14-3-3.

NO was involved in H2-induced adventitious rooting by regulating the protein and gene expressions of PM H+-ATPase and 14-3-3. Simultaneously, the interaction of PM H+-ATPase and 14-3-3 protein was also involved in this process. Hydrogen gas (H2) and nitric oxide (NO) have been shown to be involved in plant growth and development. The results in this study revealed that NO was involved in H2-induced adventitious root formation. Western blot (WB) analysis showed that the protein abundances of plasma membrane H+-ATPase (PM H+-ATPase) and 14-3-3 protein were increased after H2, NO, H2 plus NO treatments, whereas their protein abundances were down regulated when NO scavenger carboxy-2-(4-carboxyphenyl)-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide (cPTI O) was added. Moreover, the mRNA abundances of the HA3 and 14-3-3(7) gene as well as the activities of PM H+-ATPase (EC 3.6.1.35) and H+ pump were in full agreement with the changes of protein abundance. Phosphorylation of PM H+-ATPase and the interaction of PM H+-ATPase and 14-3-3 protein were detected by co-immunoprecipitation analysis. H2 and NO significantly up regulated the phosphorylation of PM H+-ATPase and the interaction of PM H+-ATPase and 14-3-3 protein. Conversely, the stimulation of PM H+-ATPase phosphorylation and protein interaction were significantly diminished by cPTIO. Protein interaction activator fusicoccin (FC) and inhibitor adenosine monophosphate (AMP) of PM H+-ATPase and 14-3-3 were used in this study, and the results showed that FC significantly increased the abundances of PM H+-ATPase and 14-3-3, while AMP showed opposite trends. We further proved the critical roles of PM H+-ATPase and 14-3-3 protein interaction in NO-H2-induced adventitious root formation. Taken together, our results suggested that NO might be involved in H2-induced adventitious rooting by regulating the expression and the interaction of PM H+-ATPase and 14-3-3 protein.

Druggable binding sites in the multicomponent assemblies that characterise DNA double-strand-break repair through non-homologous end joining.

Non-homologous end joining (NHEJ) is one of the two principal damage repair pathways for DNA double-strand breaks in cells. In this review, we give a brief overview of the system including a discussion of the effects of deregulation of NHEJ components in carcinogenesis and resistance to cancer therapy. We then discuss the relevance of targeting NHEJ components pharmacologically as a potential cancer therapy and review previous approaches to orthosteric regulation of NHEJ factors. Given the limited success of previous investigations to develop inhibitors against individual components, we give a brief discussion of the recent advances in computational and structural biology that allow us to explore different targets, with a particular focus on modulating protein–protein interaction interfaces. We illustrate this discussion with three examples showcasing some current approaches to developing protein–protein interaction inhibitors to modulate the assembly of NHEJ multiprotein complexes in space and time.

Predicting 19F NMR Chemical Shifts: A Combined Computational and Experimental Study of a Trypanosomal Oxidoreductase–Inhibitor Complex

AbstractThe absence of fluorine from most biomolecules renders it an excellent probe for NMR spectroscopy to monitor inhibitor–protein interactions. However, predicting the binding mode of a fluorinated ligand from a chemical shift (or vice versa) has been challenging due to the high electron density of the fluorine atom. Nonetheless, reliable 19F chemical‐shift predictions to deduce ligand‐binding modes hold great potential for in silico drug design. Herein, we present a systematic QM/MM study to predict the 19F NMR chemical shifts of a covalently bound fluorinated inhibitor to the essential oxidoreductase tryparedoxin (Tpx) from African trypanosomes, the causative agent of African sleeping sickness. We include many protein–inhibitor conformations as well as monomeric and dimeric inhibitor–protein complexes, thus rendering it the largest computational study on chemical shifts of 19F nuclei in a biological context to date. Our predicted shifts agree well with those obtained experimentally and pave the way for future work in this area.

Predicting 19 F NMR Chemical Shifts: A Combined Computational and Experimental Study of a Trypanosomal Oxidoreductase-Inhibitor Complex.

The absence of fluorine from most biomolecules renders it an excellent probe for NMR spectroscopy to monitor inhibitor–protein interactions. However, predicting the binding mode of a fluorinated ligand from a chemical shift (or vice versa) has been challenging due to the high electron density of the fluorine atom. Nonetheless, reliable 19F chemical‐shift predictions to deduce ligand‐binding modes hold great potential for in silico drug design. Herein, we present a systematic QM/MM study to predict the 19F NMR chemical shifts of a covalently bound fluorinated inhibitor to the essential oxidoreductase tryparedoxin (Tpx) from African trypanosomes, the causative agent of African sleeping sickness. We include many protein–inhibitor conformations as well as monomeric and dimeric inhibitor–protein complexes, thus rendering it the largest computational study on chemical shifts of 19F nuclei in a biological context to date. Our predicted shifts agree well with those obtained experimentally and pave the way for future work in this area.

Biochemical characterization and inhibition of the alternative oxidase enzyme from the fungal phytopathogen Moniliophthora perniciosa

Moniliophthora perniciosa is a fungal pathogen and causal agent of the witches’ broom disease of cocoa, a threat to the chocolate industry and to the economic and social security in cocoa-planting countries. The membrane-bound enzyme alternative oxidase (MpAOX) is crucial for pathogen survival; however a lack of information on the biochemical properties of MpAOX hinders the development of novel fungicides. In this study, we purified and characterised recombinant MpAOX in dose-response assays with activators and inhibitors, followed by a kinetic characterization both in an aqueous environment and in physiologically-relevant proteoliposomes. We present structure-activity relationships of AOX inhibitors such as colletochlorin B and analogues which, aided by an MpAOX structural model, indicates key residues for protein-inhibitor interaction. We also discuss the importance of the correct hydrophobic environment for MpAOX enzymatic activity. We envisage that such results will guide the future development of AOX-targeting antifungal agents against M. perniciosa, an important outcome for the chocolate industry.

A phase I, open-label, dose-escalation trial of BI 1701963 as monotherapy and in combination with trametinib in patients with KRAS mutated advanced or metastatic solid tumors.

TPS3651 Background: Activating mutations of KRAS drive many types of cancer. Activation of KRAS relies on guanine nucleotide exchange factors, such as SOS1, to mediate exchange of GDP for GTP. BI 1701963 is a small-molecule protein–protein interaction inhibitor that prevents the interaction between KRAS and SOS. Binding of BI 1701963 to the catalytic site of SOS1 inhibits binding of SOS1 to RAS–GDP, thereby hindering the exchange from RAS–GDP (inactive form) to RAS–GTP (active form). In preclinical studies this has been shown to lead to cytostasis in cancer cells addicted to KRAS signaling. Methods: NCT04111458 is a first-in-human trial of BI 1701963 in patients aged ≥18 years with tumors harboring KRAS mutations. Primary objectives are to determine the maximum tolerated dose (MTD) and recommended Phase II dose of BI 1701963 as monotherapy and in combination with trametinib, based on dose-limiting toxicities (DLTs). Secondary objectives are to evaluate safety, tolerability, pharmacokinetics/-dynamics and preliminary efficacy. The study will have two arms (mono- and combination therapy), and be divided into dose escalation (Part A), confirmation (Part B) and expansion (Part C, combination only) phases. Inclusion criteria include activating KRAS mutation, ≥1 evaluable lesion (RECIST 1.1), ECOG PS ≤1 and adequate organ function. Exclusion criteria include history of: RAS, MAPK or SOS1 targeting therapies; retinal vein occlusion; retinal pigment epithelial detachment; and decreased cardiac function. Parts B and C will be conducted in patients with advanced NSCLC. Treatment will continue until confirmed clinical benefit, defined toxicities, or withdrawal of consent. The primary endpoints are: Part A, the MTD, and the number of patients with DLTs during Cycle 1; Part B (monotherapy), the number of patients with DLTs; Part C, objective response (OR, RECIST 1.1). Starting doses of BI 1701963 in Part A will be 50 mg once daily (QD) orally (monotherapy) and 100 mg QD (combination, once proved safe as monotherapy) and will be escalated until the MTD is reached. The starting dose of trametinib will be 1 mg QD, escalated to the MTD or a max. of 2 mg QD. Dose cohorts will include ≥3 patients, with two therapeutic relevant doses (TRDs) established in each arm. In Part B, patients will be randomized to groups receiving one of the TRDs. If an OR is observed at a TRD in the combination arm, additional patients will be recruited into expansion cohorts receiving the relevant dose. As of Feb 11, 2020 three patients have been treated. Clinical trial information: NCT04111458 .

Validating Signal Transducer and Activator of Transcription (STAT) Protein-Inhibitor Interactions Using Biochemical and Cellular Thermal Shift Assays.

Signal transducer and activator of transcription (STAT) proteins have important biological functions; however, deregulation of STAT signaling is a driving force behind the onset and progression of inflammatory diseases and cancer. While their biological roles suggest that STAT proteins would be valuable targets for developing therapeutic agents, STAT proteins are notoriously difficult to inhibit using small drug-like molecules, as they do not have a distinct inhibitor binding site. Despite this, a multitude of small-molecule STAT inhibitors have been proposed, primarily focusing on inhibiting STAT3 protein to generate novel cancer therapies. Demonstrating that inhibitors bind to their targets in cells has historically been a very challenging task. With the advent of modern target engagement techniques, such as the cellular thermal shift assay (CETSA), interactions between experimental compounds and their biological targets can be detected with relative ease. To investigate interactions between STAT proteins and inhibitors, we herein developed STAT CETSAs and evaluated known STAT3 inhibitors for their ability to engage STAT proteins in biological settings. While potent binding was detected between STAT proteins and peptidic STAT inhibitors, small-molecule inhibitors elicited variable responses, most of which failed to stabilize STAT3 proteins in cells and cell lysates. The described STAT thermal stability assays represent valuable tools for evaluating proposed STAT inhibitors.

Beclin 1-ATG14L Protein-Protein Interaction Inhibitor Selectively Inhibits Autophagy through Disruption of VPS34 Complex I.

Autophagy, a catabolic recycling process, has been implicated as a critical pathway in cancer. Its role in maintaining cellular homeostasis helps to nourish hypoxic, nutrient-starved tumors and protects them from chemotherapy-induced death. Recent efforts to target autophagy in cancer have focused on kinase inhibition, which has led to molecules that lack specificity due to the multiple roles of key kinases in this pathway. For example, the lipid kinase VPS34 is present in two multiprotein complexes responsible for the generation of phosphatidylinositol-3-phosphate. Complex I generates the autophagosome, and Complex II is crucial for endosomal trafficking. Molecules targeting VPS34 inhibit both complexes, which inhibits autophagy but causes undesirable defects in vesicle trafficking. The lack of specific autophagy modulators has limited the utility of autophagy inhibition as a therapeutic strategy. We hypothesize that disruption of the Beclin 1-ATG14L protein-protein interaction, which is required for the formation, proper localization, and function of VPS34 Complex I but not Complex II, will disrupt Complex I formation and selectively inhibit autophagy. To this end, a high-throughput, cellular NanoBRET assay was developed targeting this interaction. An initial screen of 2560 molecules yielded 19 hits that effectively disrupted the interaction, and it was confirmed that one hit disrupted VPS34 Complex I formation and inhibited autophagy. In addition, the molecule did not disrupt the Beclin 1-UVRAG interaction, critical for VPS34 Complex II, and thus had little impact on vesicle trafficking. This molecule is a promising new tool that is critical for understanding how modulation of the Beclin 1-ATG14L interaction affects autophagy. More broadly, its discovery demonstrates that targeting protein-protein interactions found within the autophagy pathway is a viable strategy for the discovery of autophagy-specific probes and therapeutics.

Structure–Activity Relationship Study on Col-003, a Protein–Protein Interaction Inhibitor between Collagen and Hsp47

This study demonstrates the structure-activity relationship of Col-003, a potent collagen-heat-shock protein 47 (Hsp47) interaction inhibitor. Col-003 analogues were successfully synthesized by Pd(0)-catalyzed cross-coupling reactions of 5-bromosalicylaldehyde derivatives with alkyl-metal species, and the inhibitory activities of the synthetic analogues were evaluated using surface plasmon resonance analysis (BIAcore). We succeeded in discovering two potent inhibitors that showed 85 and 81% inhibition at a concentration of 1.9 µM against the collagen-Hsp47 interaction. This indicates that elongation of an alkyl linker between two aromatic rings could considerably improve inhibitory activity due to the adjustment of a pendant phenyl moiety to an appropriate position, in addition to the hydrophobic interaction with an alkyl linker moiety.

Proton Transport in Mitochondrial UCP2 is Regulated by a Matrix-Oriented Salt-Bridge Network

Uncoupling proteins (UCPs) are ion carrier proteins causing regulated proton leak across the mitochondrial inner membrane, thus reducing the rate of ATP synthesis. Despite this important impact, the mechanism of UCP-mediated proton transport has not been fully understood. It has been speculated that the mitochondrial carrier family members contain two interconnected salt-bridge networks facilitating the substrate transport. One of these networks is close to the matrix side (matrix network) and the other is close to the intermembrane space. This study focuses on the role of matrix network on the regulation of proton transport in UCP2. UCP2 and eleven mutants (in matrix network) are expressed recombinantly in the E. coli inner membrane. Six mutants disrupt a single salt-bridge link by maintaining either a single negative (K to Q mutation) or positive (D to N mutation) charge on one end of the salt-bridge (K38Q, K141Q, K239Q, D35N, D138N and D236N). Two mutants (K38Q/K239Q and D138N/D236N) disrupt two salt-bridges, while the other two, lacking three salt-bridges, disrupt the total matrix network (K38Q/K141Q/K239Q and D35N/D138N/D236N). In the last mutant, the matrix network is inversed by switching the salt-bridge forming couples (D35K/K38D/D236K/K239D/D138K/K141D). Results show that the matrix network has a regulatory role, and perturbation of the network increases the rate of proton transport. It seems that individual salt-bridges within the network are cooperatively and equally responsible for regulation of transport. Various alterations of the constituting elements of matrix salt-bridge network do not have a considerable effect on inhibitor-protein interactions. Conformational analysis of the protein (CD and fluorescence) and MD simulations provided molecular insights into the role of UCP2 in proton transport. This study characterizes the physicochemical role of the matrix-oriented salt-bridge network on proton transport in UCP2 and its inhibition by purine nucleotides.