Distal mutation v486m disrupts the catalytic activity of dpp4 by affecting the flap of the propeller domain

ABSTRACT Dipeptidyl peptidase-4 (DPP4) plays a crucial role in regulating the bioactivity of glucagon-like peptide-1 (GLP-1) that enhances insulin secretion and pancreatic β-cell

proliferation, making it a therapeutic target for type 2 diabetes. Although the crystal structure of DPP4 has been determined, its structure-function mechanism is largely unknown. Here, we

examined the biochemical properties of sporadic human DPP4 mutations distal from its catalytic site, among which V486M ablates DPP4 dimerization and causes loss of enzymatic activity.

Unbiased molecular dynamics simulations revealed that the distal V486M mutation induces a local conformational collapse in a β-propeller loop (residues 234–260, defined as the flap) and

disrupts the dimerization of DPP4. The “open/closed” conformational transitions of the flap whereby capping the active site, are involved in the enzymatic activity of DPP4. Further

site-directed mutagenesis guided by theoretical predictions verified the importance of the conformational dynamics of the flap for the enzymatic activity of DPP4. Therefore, the current

studies that combined theoretical modeling and experimental identification, provide important insights into the biological function of DPP4 and allow for the evaluation of directed DPP4

genetic mutations before initiating clinical applications and drug development. You have full access to this article via your institution. Download PDF SIMILAR CONTENT BEING VIEWED BY OTHERS

UNRAVELING THE FUNCTION AND STRUCTURE IMPACT OF DELETERIOUS MISSENSE SNPS IN THE HUMAN OX1R RECEPTOR BY COMPUTATIONAL ANALYSIS Article Open access 08 January 2024 A COMBINATION OF VIRTUAL

SCREENING, MOLECULAR DYNAMICS SIMULATION, MM/PBSA, ADMET, AND DFT CALCULATIONS TO IDENTIFY A POTENTIAL DPP4 INHIBITOR Article Open access 02 April 2024 COMBINED EFFECTS OF DOUBLE MUTATIONS

ON CATALYTIC ACTIVITY AND STRUCTURAL STABILITY CONTRIBUTE TO CLINICAL MANIFESTATIONS OF GLUCOSE-6-PHOSPHATE DEHYDROGENASE DEFICIENCY Article Open access 21 December 2021 INTRODUCTION

Dipeptidyl-peptidase 4 (DPP4) is a multifunctional type II cell surface glycoprotein that is widely expressed on epithelial cells, fibroblasts, and leukocyte subsets [1]. The appearance of

DPP4 in circulation reveals its dual existence as both membrane-bound and soluble isoforms, both of which have enzymatic activity [1, 2]. The cleavage of membrane-bound DPP4 could produce a

soluble form (amino acids 39–766). As a member of the serine peptidase subfamily S9B, which includes fibroblast-activation protein α (FAP), resident cytoplasmic proteins (DPP8 and DPP9), and

nonenzymatic members (DPP6 and DPP10) [1, 3, 4], DPP4 cleaves and inactivates several incretin hormones, chemokines, and cytokines. Therefore, it is involved in various physiological

processes, including endocrine systems, cancer, inflammation, and immune function [1, 5]. The functional cleavage of dipeptides by DPP4 occurs at the N-terminus of substrates by specifically

cleaving off the X-proline and X-alanine dipeptides from the substrates [6]. To date, the best-characterized substrates of DPP4 are glucagon-like peptide-1 (GLP-1) and gastric inhibitory

polypeptide (GIP), which are responsible for the incretin effect or 60% of insulin secreted in response to nutrients. Li et al. showed that DPP4 could rapidly inactive GLP-1 (half-life of 2 

min) and GIP (half-life of 2–3 min) [7]. Therefore, inhibiting the enzymatic activity of DPP4 will prolong the half-life of GLP-1, which provides a strategy to treat type 2 diabetes mellitus

(T2DM) [8]. The crystal structure of human DPP4 has revealed that DPP4 adopts a homodimeric architecture, of which each monomeric subunit is comprised of an α/β hydrolysis domain and a

β-propeller domain [9]. The α/β hydrolysis domain consists of residues 39–51 and 506–766, including the catalytic triad (S630, D708 and H740). The β-propeller domain (residues 55–497)

consists of eight blades, and each blade is made up of four antiparallel β-strands [10]. A propeller loop (residues 234–260) from propeller blade 4 is involved in both dimerization and

tetramerization interactions [11]. Three residues (Y238, Y248, and Y256) in the propeller loop that locate the interface of dimer have been identified their importance in the dimerization of

DPP4 [12]. However, the mechanism of action of the propeller loop in the dimerization and enzymatic activity of DPP4 remains largely unclear. Considering the complicated function of DPP4,

it is imperative to delineate the manner in which its enzymatic activity could be regulated. However, using experimental methods, such as X-ray crystallography, to observe the structural

dynamics of DPP4 is technically challenging and expensive. Recent studies [13,14,15,16,17,18] have revealed a growing interest in the theoretical prediction of protein structure-function

relationships by using molecular dynamics (MD) simulations together with experimental validation. In theory, MD simulations can investigate protein dynamics at the atomic level and achieve

very fine temporal resolution. Importantly, such simulations can capture how proteins respond to perturbations such as ligand binding/unbinding, protonation, or mutations. For example,

accumulating evidence indicates that MD simulations can identify key protein ligands [19,20,21], which is valuable in lead optimization. Many studies have also successfully determined the

impact of mutations on protein mechanical properties by using MD simulations [17, 18]. Recently, Maxwell et al. revealed over 50 cryptic epitopes by 0.1 s simulations of the SARS-CoV-2

proteome [22]. To date, MD simulations of DPP4 have been used for virtual screening and exploring the binding mechanism of inhibitors [23, 24]. As summarized in several reviews

[13,14,15,16], major improvements in MD sampling efficiency have expanded the impact of biomolecular simulations in drug discovery and design, which has increased the appeal of theoretical

simulations for researches. Previously, a novel DPP4 mutation, p.V486M (c.1456G>A) and other seven sporadic DPP4 variants (D65E, P290L, A291P, S323L, T351A, R492K, and K554Q) were

identified in our in-home database [25]. All eight mutations are far from the catalytic site, but even so, the V486M proband showed an extremely high GLP-1 level and reduced enzymatic

activity of DPP4 [25]. To determine the functional mechanisms of these distal mutations, in this study, biochemical characterization and MD simulations were combined and applied to the

wild-type and eight DPP4 variants. The results revealed that the “open/closed” transition of a flap in the β-propeller domain (residues 234–260) plays a crucial role in the enzymatic

activity of DPP4. The V486M mutant induces a local conformational collapse of the flap and disrupts the dimerization of DPP4. Furthermore, site-directed mutagenesis of the residues located

in the flap or interacting with the flap verified the importance of flap movement for the enzymatic activity of DPP4. Therefore, this study uncovered important aspects associated with DPP4

enzymatic activity and DPP4 gene variations in humans, which also offers a powerful combined approach of theoretical prediction and experimental validation for understanding the

structure-function mechanism of biomolecules. MATERIALS AND METHODS SINGLE-SITE-DIRECTED MUTAGENESIS The DNA encoding the DPP4 extracellular domain (residues 39–766) was amplified by PCR

from the full-length DPP4 gene and subsequently cloned into a modified vector pFastBac1 with six His residues at the C-terminus. Twelve DPP4 mutations, including eight mutations identified

from individuals (D65E, P290L, A291P, S323L, T351A, V486M, R492K, and K554Q) of which the detailed information refers to our previous study [25] and four mutations for confirmatory research

(K122D, D243A, P257A, and S664P) were introduced into DPP4 by using phanata master mix DNA polymerase (Vazyme Biotech, catalog number: P515, Nanjing, China), followed by digestion of the

template DNA with _Dpn_ I (Thermo Fisher Scientific, catalog number: ER1702, Waltham, MA, USA). PROTEIN EXPRESSION AND PURIFICATION The extracellular domain of human DPP4 (residues 39–766)

was expressed using a Bac-to-Bac baculovirus expression system. In brief, the DNA encoding hDPP4 was cloned into the _Eco_R I and _Hin_d III sites of pFastBac1. The final construct contains

the N-terminal melittin signal peptide to facilitate secretion and a C-terminal 6× histidine tag for purification. The constructed DNA was then transformed into bacterial DH10Bac competent

cells (Weidi Biotechnology, catalog number: DE1070, Shanghai, China), and the recombined bacmid DNA was extracted and transfected into Sf9 cells using Cellfectin II Reagent (Thermo Fisher

Scientific, catalog number: 10362100, Waltham, MA, USA). Recombinant baculovirus was generated by transposition using the Bac-to-Bac system. The virus was used to infect High Five cells. The

secreted glycosylated recombinant protein was isolated from the cell culture supernatant containing the target protein and harvested 72 h after infection. The target protein was loaded onto

nickel (Ni)-charged resin (GE Healthcare, catalog number: 17–5247, Little Chalfont, Bukinghamshire, UK) and eluted with 0.25 M imidazole. NONREDUCING AND REDUCING SDS-PAGE The recombinant

DPP4 was mixed with nonreducing SDS sample buffer (50 mM Tris-HCl, pH 6.8, 2% SDS, 10% glycerol, 0.1% bromophenol blue) or reducing SDS sample buffer (50 mM Tris-HCl, pH 6.8, 2% SDS, 10%

glycerol, 0.1% bromophenol blue, 1.5% dithiothreitol) and incubated at 100 °C for 10 min. The samples and protein marker were loaded onto the gels. Following electrophoresis, the gels were

stained overnight using Coomassie blue. Bands were quantitated using Image Lab 6.0. ENZYME ASSAYS DPP4 activity was assayed by a continuous fluorometric assay, which is cleaved by the enzyme

to release fluorescent aminomethylcoumarin (AMC). Liberation of AMC was monitored using an excitation wavelength of 355 nm and an emission wavelength of 460 nm using an Envision microplate

reader (PerkinElmer, Waltham, Massachusetts, USA). DPP4 activity was assayed in 100 mM HEPES buffer (pH 7.5) containing 0.1 mg/mL BSA (buffer A) in a total volume of 50 μL. All kinetic

constants were computed by direct fits of the data to the appropriate nonlinear equation using GraphPad Prism 8.0 software. Substrates, Gly-Pro-AMC, were obtained from GL Biochem (Shanghai,

China). Omarigliptin was obtained from Selleck Chemicals (Houston, Texas, USA). THERMAL SHIFT Purified DPP4, wild type (WT) or variants, was diluted to 0.25 mg/mL (0.7 μM) in buffer A

containing 5× SYPRO orange dye (Thermo Fisher Scientific, catalog number: S5692, Waltham, MA, USA) and 25 mM inhibitor (dissolved in DMSO). The samples were heated from 25 °C to 95 °C at a

rate of 1 °C/min, and the fluorescence signals were monitored by a real-time PCR system (Agilent Technologies, Santa Clara, CA, USA). MOLECULAR DYNAMIC SIMULATION Starting with the X-ray

structure (PDB ID: 2QT9) [26] by deleting its inhibitor, we evaluated and compared the conformational dynamics of the wild type and DPP4 mutants. The missing residues were built by

SWISS-MODEL [27], and the protein was mutated by PyMOL software [28]. The protonation states were predicted by the _H_++ web server using pH 7.5 [29]. The Amber 99SB*-ILDNP [30] force field

was used to parameterize the protein. Each system was solvated into a cubic box of TIP3P water extended by 10 Å. A rational number of counter ions of Na+ or Cl− were added to neutralize the

system. Finally, the total number of atoms in each system was ~80,000. All bonds involving hydrogen atoms were constrained with the LINCS algorithm [31]. All long-range electrostatic

interactions were calculated with the particle mesh Ewald [32] method with a 12 Å cut-off. Each system was first minimized using the steepest descent algorithm to remove bad contacts,

followed by 0.5 ns heating from 0 K to 300 K and 2 ns equilibrium simulations with constraints (10 kcal·mol−1·Å−2) on heavy atoms. Finally, a 1 μs production simulation on each system at 300

 K was performed with GROMACS5.1.4 software. To identify the conformational change of the flap, distance analysis was carried out by the _g_distance_ routine (GROMACS). The hydrogen bond

interactions of each system were analyzed along the 1 μs MD simulations. RESULTS A GENETICALLY DISTAL MUTATION, V486M, ABLATES THE CATALYTIC ACTIVITY OF THE DPP4 ENZYME In our previous

study, a novel DPP4 mutation (p.V486M) was identified in a proband who had low DPP4 enzymatic activity and high GLP-1 levels, together with two other family members who were carriers [25].

Meanwhile, additional seven sporadic DPP4 mutations, _viz_., D65E, P290L, A291P, S323L, T351A, R492K, and K554Q, were further verified from our in-home population database [25]. All eight

sporadic DPP4 mutations were far from the catalytic pocket, with the shortest distance of 23.7 Å for K554 (Fig. 1a). To comprehensively evaluate the effects of the genetic DPP4 distal

mutations on its enzymatic activities, we expressed all eight His-tagged DPP4 distal mutants in High Five cells, and they were subjected to biochemical assays after expression and

purification. By determining the enzyme kinetic constants (_K_m, _K_cat and _K_cat/_K_m) of the DPP4 mutants, we found that the V486M mutant showed complete loss of catalytic activity (Table

 1). In addition, P290L and S323L also exhibited blunted activity. A significant drop by approximately 10-fold in the second-order rate constant _K_cat/_K_m was observed in the T351A mutant,

whereas a small increase (~1.7-fold) in _K_cat was observed in the K554Q mutant (Fig. 1b and Table 1). V486M RETAINS THERMAL STABILITY AND SUBSTRATE BINDING ABILITY BUT DISRUPTS DPP4

DIMERIZATION To determine whether the distal mutation introduced in this study affects the overall conformational stability, we measured the thermal stability of the DPP4 mutants by

monitoring their melting temperature (_T_m). Surprisingly, the V486M mutant showed _T_m values equivalent to those of wild-type DPP4 (Fig. 2a), indicating that the protein backbone of the

V486M mutant was not disturbed. Moreover, the N-terminus of the substrates is essential since they have to be recognized and bonded. The DPP4 crystal structure has revealed how substrate

specificity is achieved, after which it preferentially cleaves after Xaa-Pro or Xaa-Ala (Xaa being any amino acid) [10]. To confirm the substrate binding of the V486M mutant, we applied a

thermal shift assay by using omarigliptin to mimic the substrate binding mode. The DPP4 inhibitor omagliptin binds rapidly and competitively to the active site of DPP4, which is a reversible

and highly selective process [33]. In wild-type DPP4, the _T_m values increased by 12.41 degrees compared to the DMSO control. Similarly, the _T_m values increased by 13.79 degrees in the

V486M mutant. In addition, we found that there was no significant change in substrate binding of the V486M mutant and wild-type DPP4 (Fig. 2b, c). Taken together, the ablated enzymatic

activity of the V486M mutant was clearly not a result of active site collapse or the entire protein. DPP4 has a monomeric glycoprotein subunit that homodimerizes to acquire enzymatic

activity. The formation of dimers is the prerequisite for DPP4 to exert enzymatic activity [9]. Measured by nonreduced SDS-PAGE, we explored the possibility that loss of activity of the

V486M mutant was associated with dimer formation. Interestingly, the V486M mutant resulted in an ~18.1% reduction in the dimer relative to the wild type (Fig. 2d, e). However, which factor

contributes to the dimer formulation of V486M is unknown. MOLECULAR DYNAMICS SIMULATION REVEALS THAT THE PROPELLER LOOP, NAMELY, THE FLAP, MEDIATES DPP4 ENZYMATIC ACTIVITY V486 lies in

strand 3 blade 8 (β8/3) of the β-propeller domain of DPP4, which is distant from the dimerization interface and catalytic triad (45.2 Å). Therefore, it is unlikely that V486 directly impacts

the dimerization or enzymatic activity of DPP4. However, the detailed mechanism by which V486M remotely regulates enzymatic activity is unclear. To understand this mechanism, we performed

long-time unbiased MD simulations to study the conformational dynamics of V486M at the atomic level compared with wild-type DPP4. As shown in Fig. 3, we found that the propeller loop

(residues 234–260) is flexible in wild-type DPP4, switching between two distinct conformations controlled by the propeller loop, “closed” and “open”; therefore, we defined it as a flap.

During 1 μs MD simulations, the wild-type DPP4 underwent two-time transitions between “closed” and “open”, at approximately 540 ns and 900 ns, respectively. However, in the V486M mutant, the

flap was relatively rigid and remained “open” during the MD simulations, indicating that the conformational transition of the flap is important for the enzymatic activity of DPP4. To

further evaluate the relationship between this conformational transition and enzymatic activity, we analyzed the conformational transition of the flap in other seven DPP4 mutants. As shown

in Fig. 4, for the two mutants that lost enzymatic activity (P290L and S323L), their flaps also remained in an “open” state. For the other mutants that maintain DPP4 enzymatic activity,

their flaps are flexible between “closed” and “open”; for example, R492K underwent three transitions between “closed” and “open”, at approximately 20 ns, 400 ns and 450 ns, respectively.

Therefore, the results showed that the conformational switch between the “closed” and “open” states of the flap is necessary for the enzymatic activity of DPP4. MUTAGENESIS OF S664P RESULTS

IN MONOMERIC DPP4 WITHOUT CATALYTIC ACTIVITY To validate the importance of the flap’s conformational transition on enzymatic activity, we analyzed and compared the hydrogen bond interactions

formed by the flap in its “closed” and “open” structures. As shown in Fig. 5a, the hydrogen bond formed by K122 and D243 could stabilize the “closed” conformations, whereas the hydrogen

bond formed by P257 and S664, which lies in the root of the flap, could be found in both the “closed” and “open” conformations. In particular, the hydrogen bond between P257 and S664 was

formed by their main chain atoms. Therefore, we designed a mutagenesis study of these two hydrogen bonds. For D243-K122 interactions, the D243A mutant destabilizes the “closed”

conformations, thus maintaining enzymatic activity as a control, whereas the K122D mutant prevents DPP4 from shifting from “open” to “closed”, thus decreasing enzymatic activity. For the

P257-S664P interactions, the P257A mutant retains the interactions to maintain enzymatic activity as a control, whereas the S664P mutant disturbs the interactions to decrease enzymatic

activity. Therefore, we designed four mutants (K122D, D243A, P257A, and S664P) that are in the flap or interact with this region. We next performed enzyme kinetics studies to validate the

efficacy of the four mutants. The results showed that among the four mutations, the S664P single-site mutation abolished the enzymatic activity of DPP4, and K122D significantly decreased

_K_cat/_K_m by approximately 50%, indicating that conformational transitions of the flaps were indeed critical for the enzymatic activity of DPP4. In addition, D243A and P257A retained some

of the enzymatic activity of DPP4 (Fig. 5b, c and Table 2). The flap lies in the dimer interface, and disrupting the “open/closed” conformational transitions may affect the dimer formation

of DPP4. To confirm whether such transitions affect the dimer formation, we employed a nonreduced SDS-PAGE assay. The single mutation, S664P, disrupted DPP4 dimerization with a concomitant

loss of enzymatic activity, while other three mutations had no change compared with the wild type (Fig. 5d). These results indicated that the “open/closed” conformational transitions of the

flap, to some extent, were associated with dimer formation. During 1 μs MD simulations, we found that the flap of S664P is kept in the “open” conformation and we also sampled many unstable

conformations resulting from the disturbance of the interactions between S664P and V665/N263 (Fig. 6a, b). Therefore, these results indicated that S664 possibly supports the overall protein

backbone and that the S664P mutation may disturb the overall protein structure and stability. To confirm this hypothesis, the structural stability of the S664P mutant was further assayed by

thermal shift. Consistent with the prediction of the MD simulation, the _T_m values of the S664P mutant dramatically dropped by 25 degrees (Fig. 6c). In summary, we found that the movement

is critical for the dimerization and consequently the enzymatic activity of DPP4, as illustrated by mutagenesis tests of S664P and K122D. Furthermore, the collapse of the conformational

transition of the flap in the human DPP4 mutation V486M, together with P290L and S323L, led to a loss of enzyme activity. DISCUSSION DPP4 is recognized as an important T2DM therapeutic

target [34]. It is a protease with a ubiquitous expression profile and it is involved in many physiological processes, including glucose homeostasis [35], inflammation [36,37,38], and tumor

growth [39, 40]. Circulating levels of DPP4 activity and sDPP4 are increased in humans with T2DM [41], suggesting that inhibiting the activity of DPP4 could be used as a treatment for T2DM.

There are a few studies about DPP4 genetic alterations and their association with T2DM and other diseases. Bouchard et al. reported DPP4 polymorphisms associated with blood pressure, lipids,

and diabetes-related phenotypes in obese patients [42]. In addition, single nucleotide polymorphisms rs6741949 in the DPP4 gene interacts with body adiposity and negatively affects GLP-1

levels, insulin secretion, and glucose tolerance [43]. It is unclear that biofunction of the entire lost activity of DPP4 in humans, although ablation of DPP4 activity has been studied in

both rat and mouse models. C57BL/6 DPP4-KO mice exhibited enhanced glucose tolerance, lower plasma glucose, and higher plasma insulin [44]. The long-term physiological effects of loss of

function of DPP4 have not yet been reported. In our work, we followed up on the continuous changes in plasma glucose, lipid metabolism and tumor markers in the proband who carried the V486M

mutation. Surprisingly, the proband did not report any hypoglycemic events despite high GLP-1 levels over the past 6 years (data not shown). This discrepancy might be due to certain

physiological compensations to maintain glucose homeostasis at the whole organism level. For the V486M carrier proband, a half dosage reduction of DPP4 activity seems to be relatively

benign, at least through 46 years old. This result suggests that long-term inhibition of DPP4 activity may have no serious adverse effects. Thus, the functional variations in DPP4 may have

important clinical significance. In addition, this study can help an understanding of the biochemical properties of D65E, P290L, A291P, S323L, T351A, V486M, R492K, and K554Q mutations in

Chinese individuals. The enzymatic activity of DPP4 was found to be influenced by mutations that lie far from the active site. The finding of the “open/closed” conformational transitions of

the flap domain neighboring the active site explained the functional mechanism of the distal mutations in our MD simulations. The flap domain is highly conserved among the S9B subfamily.

Previously, Rasmussen et al. crystallized the DPP4 structure and revealed that this domain stabilizes the dimeric structure and may act as a lid on the side entrance to the catalytic pocket

[10]. In particular, residues Y238, Y248, and Y256 in the flap domain are essential to DPP4 dimerization [12]. Similar to DPP4, its close gene family member Prolyl oligopeptidase (POP), has

loop A (residues 189–209) and loop B (residues 577–608) at the domain interface implicated in substrate entry to the active site [45]. However, exactly how this domain impacts DPP4

dimerization and enzymatic activity remains unknown. To understand the structure-function mechanism at the atomic level, we applied MD simulations together with experimental validation.

Observation of the conformational dynamics of DPP4 mutants in MD simulations revealed that the flap (residues 234–260) regulates enzymatic activity. We showed that the “open/closed”

conformational transitions of the flap are of significance for the enzymatic activity of DPP4. Furthermore, according to our hydrogen bond analyses, four DPP4 mutants were designed to

validate the necessity of the flap conformational transitions for enzymatic activity, _viz_. K122D, D243A, P257A, and S664P. The K122D and S664P mutants were designed to decrease DPP4

enzymatic activity, while the D243A and P257A mutants were designed as controls that retained enzymatic activity. Enzyme kinetics experiments validated the predictions of the four mutants,

especially the S664P mutant, which abolished the enzymatic activity of DPP4, revealing the reliability of our MD simulations. Further simulations of S664P revealed that the flap remained in

the “open” state, again suggesting the necessity of the conformational transition of the flap. In summary, molecules that reduce or even disrupt the conformational transition have the

potential to be developed for the treatment of T2DM. Subsequently, residue S664 was found to be essential for the enzymatic activity and dimerization of DPP4. The nonreduced SDS-PAGE assay

revealed a disrupted dimerization of S664P, and the thermal shift assay showed decreased _T_m values, indicating that S664 might play a crucial role in DPP4 protein stability. During the MD

simulations, S664P maintains a stable conformation except for the flap region. As a result, conformational changes in the flap distort the substrate binding pocket, which then leads to

significantly reduced enzymatic activity directly or indirectly. Indeed, kinetic assays suggested that S664P has undetectable enzymatic activity. Additionally, the V486M mutant also had an

“open” flap during the MD simulations, which may be further explained by the findings in the flap crystal structure of the V486M protein. According to Fig. 4, the conformational transition

frequency of the flap might be associated with the enzymatic activity of DPP4. For example, in the wild type and R492K mutant, the flap underwent two and three transitions between “closed”

and “open” states, respectively. Enzyme kinetics experiments revealed that R492K has similar catalytic activity to the wild type. However, in the K554Q mutant, the flap underwent over ten

conformational transitions. Correspondingly, the catalytic activity of the K554Q mutant was higher than that of the wild type. These results suggest that there might be a positive

correlation between conformational transition frequency and catalytic activity. Therefore, our current findings provide new insights into developing novel inhibitors that block dimerization

and activators that either open or remove this flap. Our method of a combination of MD simulation and experimental validation for describing the structure-function mechanism of DPP4 may be

helpful for studying other key enzymes. CONCLUSION DPP4 is recognized as a crucial therapeutic target for T2DM and more than twenty inhibitors were already approved for type 2 diabetes

therapy. With the Human Genome Project progresses to the whole genome sequence of the population, varieties of single nucleotide polymorphism were identified. Eight sporadic DPP4 variants

(D65E, P290L, A291P, S323L, T351A, V486M, R492K, and K554Q) that are distant from both the catalytic pocket and the dimerization interface, were identified in Chinese population. In

addition, the V486M mutant showed a reduced enzymatic activity. To determine the functional mechanisms of these distal mutations, in this study, biochemical characterization and MD

simulations were combined and applied to the wild-type and eight DPP4 variants. The results showed that the single point mutations that damage activity of DPP4 could cause conformational

transition failure of the propeller flap and disrupts the dimerization of DPP4. Further site-directed mutagenesis of K122D, D243A, P257A, and S664P predicted by MD simulations verified the

importance of the flap’s conformational dynamics for DPP4 enzymatic activity. In addition, the conformational transition frequency of the flap might be associated with the enzymatic activity

of DPP4. Therefore, this finding may have implications for understanding the structure-function mechanism of DPP4 and open an avenue for the development of specific DPP4 inhibitors that may

have diagnostic and therapeutic applications in humans. REFERENCES * Rohrborn D, Wronkowitz N, Eckel J. DPP4 in diabetes. Front Immunol. 2015;6:386. Article  PubMed  PubMed Central  CAS 

Google Scholar  * Zhong J, Maiseyeu A, Davis SN, Rajagopalan S. DPP4 in cardiometabolic disease: recent insights from the laboratory and clinical trials of DPP4 inhibition. Circ Res.

2015;116:1491–504. Article  CAS  PubMed  PubMed Central  Google Scholar  * Gorrell MD. Dipeptidyl peptidase IV and related enzymes in cell biology and liver disorders. Clin Sci.

2005;108:277–92. Article  CAS  Google Scholar  * Deacon CF. Physiology and pharmacology of DPP-4 in glucose homeostasis and the treatment of type 2 diabetes. Front Endocrinol. 2019;10:80.

Article  Google Scholar  * Gorrell MD, Gysbers V, McCaughan GW. CD26: a multifunctional integral membrane and secreted protein of activated lymphocytes. Scand J Immunol. 2001;54:249-64. *

Elmansi AM, Awad ME, Eisa NH, Kondrikov D, Hussein KA, Aguilar-Perez A, et al. What doesn’t kill you makes you stranger: dipeptidyl peptidase-4 (CD26) proteolysis differentially modulates

the activity of many peptide hormones and cytokines generating novel cryptic bioactive ligands. Pharmacol Ther. 2019;198:90–108. Article  CAS  PubMed  PubMed Central  Google Scholar  * Li N,

Wang LJ, Jiang B, Li XQ, Guo CL, Guo SJ, et al. Recent progress of the development of dipeptidyl peptidase-4 inhibitors for the treatment of type 2 diabetes mellitus. Eur J Med Chem.

2018;151:145–57. Article  PubMed  CAS  Google Scholar  * Trzaskalski NA, Fadzeyeva E, Mulvihill EE. Dipeptidyl peptidase-4 at the interface between inflammation and metabolism. Clin Med

Insights Endocrinol Diabetes. 2020;13:1179551420912972. Article  PubMed  PubMed Central  Google Scholar  * Chien CH, Huang LH, Chou CY, Chen YS, Han YS, Chang GG, et al. One site mutation

disrupts dimer formation in human DPP-IV proteins. J Biol Chem. 2004;279:52338–45. Article  CAS  PubMed  Google Scholar  * Rasmussen HB, Branner S, Wiberg FC, Wagtmann N. Crystal structure

of human dipeptidyl peptidase IV/CD26 in complex with a substrate analog. Nat Struct Biol. 2003;10:19–25. Article  CAS  PubMed  Google Scholar  * Engel M, Hoffmann T, Wagner L, Wermann M,

Heiser U, Kiefersauer R, et al. The crystal structure of dipeptidyl peptidase IV (CD26) reveals its functional regulation and enzymatic mechanism. Proc Natl Acad Sci USA. 2003;100:5063–68.

Article  CAS  PubMed  PubMed Central  Google Scholar  * Tang HK, Chen KC, Liou GG, Cheng SC, Chien CH, Tang HY, et al. Role of a propeller loop in the quaternary structure and enzymatic

activity of prolyl dipeptidases DPP-IV and DPP9. FEBS Lett. 2011;585:3409–14. Article  CAS  PubMed  Google Scholar  * Do PC, Lee EH, Le L. Steered molecular dynamics simulation in rational

drug design. J Chem Inf Model. 2018;58:1473–82. Article  CAS  PubMed  Google Scholar  * Liu X, Shi D, Zhou S, Liu H, Liu H, Yao X. Molecular dynamics simulations and novel drug discovery.

Expert Opin Drug Discov. 2018;13:23–37. Article  CAS  PubMed  Google Scholar  * Wade RC, Salo-Ahen OMH. Molecular modeling in drug design. Molecules. 2019;24:321. Article  PubMed Central 

CAS  Google Scholar  * Hollingsworth SA, Dror RO. Molecular dynamics simulation for all. Neuron. 2018;99:1129–43. Article  CAS  PubMed  PubMed Central  Google Scholar  * McCoy MD, Shivakumar

V, Nimmagadda S, Jafri MS, Madhavan S. SNP2SIM: a modular workflow for standardizing molecular simulation and functional analysis of protein variants. BMC Bioinforma. 2019;20:171. Article 

Google Scholar  * Azadi S, Tafazzoli-Shadpour M, Omidvar R. Steered molecular dynamics simulation study of quantified effects of point mutation induced by breast cancer on mechanical

behavior of E-cadherin. Mol Biol. 2018;52:723–31. Article  CAS  Google Scholar  * Zhang C, Feng LJ, Huang Y, Wu D, Li Z, Zhou Q, et al. Discovery of novel phosphodiesterase-2A inhibitors by

structure-based virtual screening, structural optimization, and bioassay. J Chem Inf Model. 2017;57:355–64. Article  PubMed  CAS  Google Scholar  * Hucke O, Coulombe R, Bonneau P,

Bertrand-Laperle M, Brochu C, Gillard J, et al. Molecular dynamics simulations and structure-based rational design lead to allosteric HCV NS5B polymerase thumb pocket 2 inhibitor with

picomolar cellular replicon potency. J Med Chem. 2014;57:1932–43. Article  CAS  PubMed  Google Scholar  * Spahn V, Del Vecchio G, Labuz D, Rodriguez-Gaztelumendi A, Massaly N, Temp J, et al.

A nontoxic pain killer designed by modeling of pathological receptor conformations. Science. 2017;355:966–9. Article  CAS  PubMed  Google Scholar  * Zimmerman MI, Porter JR, Ward MD, Singh

S, Vithani N, Meller A, et al. SARS-CoV-2 simulations go exascale to predict dramatic spike opening and cryptic pockets across the proteome. Nat Chem. 2021;13:651–9. Article  CAS  PubMed 

PubMed Central  Google Scholar  * Meduru H, Wang YT, Tsai JJ, Chen YC. Finding a potential dipeptidyl peptidase-4 (DPP-4) inhibitor for type-2 diabetes treatment based on molecular docking,

pharmacophore generation, and molecular dynamics simulation. Int J Mol Sci. 2016;17:920. Article  PubMed Central  CAS  Google Scholar  * Hou H, Wang Y, Li C, Wang J, Cao Y. Dipeptidyl

peptidase-4 is a target protein of epigallocatechin-3-gallate. Biomed Res Int. 2020;2020:5370759. PubMed  PubMed Central  Google Scholar  * Zhao DD, Zhao SQ, Wang X, Su MB, Liu W, Ma QY, et

al. Clinical and physiological characterization of elevated plasma glucagon-like peptide-1 levels (hyperglipemia) in a dipeptidyl peptidase iv mutation carrier. Front Endocrinol. 2018;9:62.

Article  Google Scholar  * Kaelin DE, Smenton AL, Eiermann GJ, He H, Leiting B, Lyons KA, et al. 4-arylcyclohexylalanine analogs as potent, selective, and orally active inhibitors of

dipeptidyl peptidase IV. Bioorg Med Chem Lett. 2007;17:5806–11. Article  CAS  PubMed  Google Scholar  * Waterhouse A, Bertoni M, Bienert S, Studer G, Tauriello G, Gumienny R, et al.

SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Res. 2018;46:W296–W303. Article  CAS  PubMed  PubMed Central  Google Scholar  * DeLano WL. The PyMOL user’s

manual. San Carlos, CA: DeLano Scientific; 2002. p. 452. Google Scholar  * Anandakrishnan R, Aguilar B, Onufriev AV. H++ 3.0: automating pK prediction and the preparation of biomolecular

structures for atomistic molecular modeling and simulations. Nucleic Acids Res. 2012;40:W537–41. Article  CAS  PubMed  PubMed Central  Google Scholar  * Aliev AE, Kulke M, Khaneja HS,

Chudasama V, Sheppard TD, Lanigan RM. Motional timescale predictions by molecular dynamics simulations: case study using proline and hydroxyproline sidechain dynamics. Proteins.

2014;82:195–215. Article  CAS  PubMed  PubMed Central  Google Scholar  * Ryckaert JP, Ciccotti G, Berendsen HJ. Numerical integration of the cartesian equations of motion of a system with

constraints: molecular dynamics of n-alkanes. J Comput Phys. 1977;23:327–41. Article  CAS  Google Scholar  * Darden T, York D, Pedersen L. Particle mesh Ewald: An N⋅log (N) method for Ewald

sums in large systems. J Chem Phys. 1993;98:10089–92. Article  CAS  Google Scholar  * Burness CB. Omarigliptin: first global approval. Drugs. 2015;75:1947–52. Article  CAS  PubMed  Google

Scholar  * Holst JJ, Deacon CF. Inhibition of the activity of dipeptidyl-peptidase IV as a treatment for type 2 diabetes. Diabetes. 1998;47:1663–70. Article  CAS  PubMed  Google Scholar  *

Mulvihill EE, Varin EM, Gladanac B, Campbell JE, Ussher JR, Baggio LL, et al. Cellular sites and mechanisms linking reduction of dipeptidyl peptidase-4 activity to control of incretin

hormone action and glucose homeostasis. Cell Metab. 2017;25:152–65. Article  CAS  PubMed  Google Scholar  * Silva Junior WS, Souza M, Kraemer-Aguiar LG. Dipeptidyl peptidase 4 (DPP4),

adipose inflammation, and insulin resistance: is it time to look to the hepatocyte? Hepatobiliary Surg Nutr. 2018;7:499–500. Article  PubMed  PubMed Central  Google Scholar  * Baggio LL,

Varin EM, Koehler JA, Cao X, Lokhnygina Y, Stevens SR, et al. Plasma levels of DPP4 activity and sDPP4 are dissociated from inflammation in mice and humans. Nat Commun. 2020;11:3766. Article

  CAS  PubMed  PubMed Central  Google Scholar  * Fen Z, Ni Y, Nagashimada M, Nagata N, Xu L, Mukaida N, et al. DPP-4 inhibition by linagliptin attenuates obesity-related inflammation and

insulin resistance by regulating M1/M2 macrophage polarization. Diabetes. 2016;65:2966–79. Article  CAS  Google Scholar  * Barreira da Silva R, Laird ME, Yatim N, Fiette L, Ingersoll MA,

Albert ML. Dipeptidylpeptidase 4 inhibition enhances lymphocyte trafficking, improving both naturally occurring tumor immunity and immunotherapy. Nat Immunol. 2015;16:850–8. Article  CAS 

PubMed  Google Scholar  * Hollande C, Boussier J, Ziai J, Nozawa T, Bondet V, Phung W, et al. Inhibition of the dipeptidyl peptidase DPP4 (CD26) reveals IL-33-dependent eosinophil-mediated

control of tumor growth. Nat Immunol. 2019;20:257–64. Article  CAS  PubMed  Google Scholar  * Varin EM, Mulvihill EE, Beaudry JL, Pujadas G, Fuchs S, Tanti JF, et al. Circulating levels of

soluble dipeptidyl peptidase-4 are dissociated from inflammation and induced by enzymatic DPP4 inhibition. Cell Metab. 2019;29:320–34. e5 Article  CAS  PubMed  Google Scholar  * Bouchard L,

Faucher G, Tchernof A, Deshaies Y, Lebel S, Hould FS, et al. Comprehensive genetic analysis of the dipeptidyl peptidase-4 gene and cardiovascular disease risk factors in obese individuals.

Acta Diabetol. 2009;46:13–21. Article  CAS  PubMed  Google Scholar  * Bohm A, Wagner R, Machicao F, Holst JJ, Gallwitz B, Stefan N, et al. DPP4 gene variation affects GLP-1 secretion,

insulin secretion, and glucose tolerance in humans with high body adiposity. PLoS One. 2017;12:e0181880. Article  PubMed  PubMed Central  CAS  Google Scholar  * Marguet D, Baggio L,

Kobayashi T, Bernard AM, Pierres M, Nielsen PF, et al. Enhanced insulin secretion and improved glucose tolerance in mice lacking CD26. Proc Natl Acad Sci USA. 2000;97:6874–9. Article  CAS 

PubMed  PubMed Central  Google Scholar  * Szeltner Z, Juhasz T, Szamosi I, Rea D, Fulop V, Modos K, et al. The loops facing the active site of prolyl oligopeptidase are crucial components in

substrate gating and specificity. Biochim Biophys Acta. 2013;1834:98–111. Article  CAS  PubMed  Google Scholar  Download references ACKNOWLEDGEMENTS This work was supported by the National

Natural Science Foundation of China (No. 92057116), the National Science and Technology Major Project (2018ZX09711002-018), the Strategic Priority Research Program of Chinese Academy of

Sciences grant (XDA12040204), the Shanghai Commission of Science and Technology (18431900900), and National Key R&D Program of China (2016YFA0502301 and 2017YFB0202601). The molecular

dynamics simulations were partially run at the TianHe 1 supercomputer in Tianjin and TianHe 2 supercomputer in Guangzhou. AUTHOR INFORMATION Author notes * These authors contributed equally:

Teng-teng Li, Cheng Peng AUTHORS AND AFFILIATIONS * State Key Laboratory of Drug Research, the National Drug Screening Center, Shanghai Institute of Materia Medica, Chinese Academy of

Sciences, Shanghai, 201203, China Teng-teng Li, Ming-bo Su, Jia Li & Jing-ya Li * School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China Teng-teng Li 

& Jia Li * CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China Cheng

Peng, Zhi-jian Xu & Wei-liang Zhu * School of Pharmacy, University of Chinese Academy of Sciences, Beijing, 100049, China Cheng Peng, Zhi-jian Xu & Wei-liang Zhu * Department of

Endocrinology and Metabolism, China National Research Center for Metabolic Diseases, National Key Laboratory for Medical Genomes, Ruijin Hospital, Shanghai Jiao Tong University School of

Medicine (SJTUSM), Shanghai, 200025, China Ji-qiu Wang Authors * Teng-teng Li View author publications You can also search for this author inPubMed Google Scholar * Cheng Peng View author

publications You can also search for this author inPubMed Google Scholar * Ji-qiu Wang View author publications You can also search for this author inPubMed Google Scholar * Zhi-jian Xu View

author publications You can also search for this author inPubMed Google Scholar * Ming-bo Su View author publications You can also search for this author inPubMed Google Scholar * Jia Li

View author publications You can also search for this author inPubMed Google Scholar * Wei-liang Zhu View author publications You can also search for this author inPubMed Google Scholar *

Jing-ya Li View author publications You can also search for this author inPubMed Google Scholar CONTRIBUTIONS JYL and WLZ put forward to conception and contributed to research design. TTL

planned and carried out the biochemistry experiments and analyzed the data. MBS participated in the enzymatic experiments. CP performed molecular dynamics simulations and analyzed the data.

ZJX participated in the molecular dynamics simulations experimental design. JQW contributed clinical flowing-up data of DPP4-V486M carrier and project discussion. JL contributed reagents and

analytic tools. TTL and CP contributed to writing the paper, and JYL and WLZ reviewed/edited the paper. CORRESPONDING AUTHORS Correspondence to Wei-liang Zhu or Jing-ya Li. ETHICS

DECLARATIONS COMPETING INTERESTS The authors declare no competing interests. RIGHTS AND PERMISSIONS Reprints and permissions ABOUT THIS ARTICLE CITE THIS ARTICLE Li, Tt., Peng, C., Wang, Jq.

_et al._ Distal mutation V486M disrupts the catalytic activity of DPP4 by affecting the flap of the propeller domain. _Acta Pharmacol Sin_ 43, 2147–2155 (2022).

https://doi.org/10.1038/s41401-021-00818-x Download citation * Received: 15 August 2021 * Accepted: 06 November 2021 * Published: 14 December 2021 * Issue Date: August 2022 * DOI:

https://doi.org/10.1038/s41401-021-00818-x SHARE THIS ARTICLE Anyone you share the following link with will be able to read this content: Get shareable link Sorry, a shareable link is not

currently available for this article. Copy to clipboard Provided by the Springer Nature SharedIt content-sharing initiative KEYWORDS * DPP4 * distal mutation * enzymatic activity * molecular

dynamics simulation * structure-function mechanism