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Homology modeling and molecular docking study of corticotrophin-releasing hormone: An approach to treat stress-related diseases

  • Nasir Ahmad , Khalid Khan , Sher Wali Khan , Haroon Ur Rashid EMAIL logo , Irum , Muhammad Zahoor EMAIL logo , Muhammad Naveed Umar , Riaz Ullah and Essam A. Ali
Published/Copyright: July 25, 2024
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Open Chemistry
From the journal Open Chemistry Volume 22 Issue 1

Abstract

Corticotropin-releasing hormone receptors (CRHRs), also termed corticotropin-releasing factor receptors, are linked to G-protein-coupled receptor class. Corticotropin-releasing hormone (CRH) is medically significant in stress, immune response, gastrointestinal motility, and eating patterns. It serves as a releasing hormone and is encoded by the CRH gene. It has been established that there are two subtypes of CRHRs: CRH1-R and CRH2-R. These receptors, representing types 1 and 2, respectively, play a crucial role in regulating biological functions triggered by CRH. To treat stress-related gut abnormalities and stress-related disorders, regulation and optimization of CRH1-R and CRH2-R have turned into a novel idea. The three-dimensional (3D) structure of CRH is not completely recognized, and it is believed that the peptide key unit is helical and both the ultimate edges are relatively unsaturated. We can envisage its 3D structure from the amino acid order of a model protein by homology modeling procedures using Molecular Operating Environment and the Iterative Threading Assembly Refinement program. The assessment and authentication of the 3D structure were performed with RAMPAGE and ERRATE online servers. Utilizing the 3D structure of the target protein and predictions of its active site assists us in the development of new drug candidates aimed at treating disorders associated with stress. CRHR was docked with 19 CP376395 analogs acting as antagonists.

Graphical abstract

Keywords: homology modeling; molecular docking; corticotrophin; adenylate cyclase; nucleotides

1 Introduction

G-protein-coupled receptors (GPCRs) facilitate most of our biological feedback to neurotransmitters, hormones, and environmental stimulants, and so they possess a significant potential to act as therapeutic targets for a variety of diseases. [1]. The structure of GPCRs is usually comprised of seven α-helical transmembrane (TM) domains, an intracellular C-terminus, and an extracellular N-terminus [2,3]. Hydrophobic seven TM helical central core domain is linked by three intracellular and three extracellular loops. In extracellular loops 1 and 2, two cysteine residues are conserved to form a disulfide bridge, which is important for the stabilization and packing of a restricted number of conformations of seven TMs [4,5]. They are included in the cell membranes of a wide range of organisms including invertebrates, microorganisms, plants, and mammals [6,7]. All types of GPCRs share a common membrane topology, the N-terminus is outside, and the C-terminus is inside with seven alpha-helical TM segments (Figure 1) [8,9].

Figure 1 GPCR in the plasma membrane with seven α-helical TM sections. Heterotrimeric G-protein is characterized diagrammatically by the letters α, β, and γ in the cytoplasm. Diagram showing label A, an agonist in its binding pocket; C, receptor C-terminus in the cytoplasm; and N, receptor extracellular N-terminus. [Ref. 6] The figure is recorded under the Creative Commons Attribution 4.0 International Agreement, which approves unconditional practice, distribution, amendment, and replication in any means, http://creativecommons.org/licenses/by/4.0/.
Figure 1

GPCR in the plasma membrane with seven α-helical TM sections. Heterotrimeric G-protein is characterized diagrammatically by the letters α, β, and γ in the cytoplasm. Diagram showing label A, an agonist in its binding pocket; C, receptor C-terminus in the cytoplasm; and N, receptor extracellular N-terminus. [Ref. 6] The figure is recorded under the Creative Commons Attribution 4.0 International Agreement, which approves unconditional practice, distribution, amendment, and replication in any means, http://creativecommons.org/licenses/by/4.0/.

GPCRs represent the largest group of plasma membrane receptors. Rhodopsin and adrenergic receptors are the most common types of GPCRs.

GPCRs are the receptors for a large amount of different signals. The most important among them are the chemosensory GPCRs, which act as receptors for the external origin that are odors, pheromones, or tastes. Mainly other GPCRs react to endogenous signals such as peptides, lipids, neurotransmitters, or nucleotides [4]. They represent essential plasma membrane proteins that transmit signals from extracellular ligands in intracellular relay proteins, the heterotrimeric GTP-binding proteins (G proteins). The G proteins initiate pleiotropic modifications in numerous targets by coupling to several downstream effectors. Thus, the extracellular signal is characteristically intensified to create vigorous, wide-ranging, and cell-specific responses [10]. GPCRs can be triggered by various exterior stimuli, including peptides, chemoattractants, hormones, neurotransmitters, phospholipids, odorants, photons, and taste ligands [11,12,13]. GPCRs are activated through ligands and are signaled through G proteins that are made of α, β, and γ subunits. The α- and β/γ-subunits disintegrate and discretely trigger several conventional effectors such as phospholipases and adenylyl cyclases. They also modulate the action of several kinases, ion transporters, and ion channels.

GPCRs are classified into five families. Its classification is based on the similarity of amino acid sequences within the seven TM helical segments.

Class A, the rhodopsin family, consists of 701 members.

Class B1, the secretin family, consists of 15 members.

Class B2, the adhesion family, consists of 24 members.

Class C, the glutamate family, consists of 15 members.

Class F, the frizzled/taste 2 family, consists of 24 members [14,15].

Corticotropin-releasing hormone (CRH) targets a membrane-bound GPCR and acts as a primary hormone in the flight or fight responses. It is a 41-amino acid polypeptide made from 196 amino acids, a precursor of CRH by C-terminal cleavage. The peptide of CRH can be segmented into three useful parts. The residues (1–16) are believed to be vital for receptor activation and agonist binding. The residues (17–31) containing the CRH-binding protein (CRHBP) control the structural conformation of the protein, while the residues (32–41) are essential for receptor binding [16,17]. CRH has been recognized and identified in mammals, amphibians, fishes, and birds [18].

CRH is made in smaller quantities by certain white blood cells, and it causes swelling particularly that of the gut. Moreover, it is also secreted by the paraventricular nucleus of the hypothalamus [19]. CRH is principally produced in the hypothalamus. Additionally, it is also discharged into the hypophyseal portal passage in response to stress [20].

CRH is accountable for autonomic, endocrine, behavioral, and immunological responses to stress in mammals [21]. The key central regulator of the hypothalamic–pituitary–adrenal (HPA) axis is CRH, which regulates the HPA through the initiation of the proopiomelanocortin gene and the discharge of corticotropin adrenocorticotropic hormone from the anterior pituitary [22,23]. Stress has a suppressive effect on the male and female reproductive systems; the stress system is triggered in a synchronized way, which influences the chief and peripheral roles that are vital for survival and adaptation during stress [24]. In humans and other mammals, two receptor genes have been identified to date. Both receptors of CRH consist of seven TM regions that are coupled to adenylate cyclase. CRH and its receptors are present in a variety of tissues including the immune system, blood–brain barrier, gastrointestinal tract, and parasympathetic ganglion [20]. The distribution of both receptors in various tissues is different. CRH-R1 is present all over the brain and is greatly expressed in the anterior pituitary [24]. Corticotropin-releasing hormone receptor 2 (CRHR2) is dispersed in the wider regions of the human brain. Its subtype CRH-R2a is exclusively present in the brain and has a wider distribution than the CRH-R1. CRH-R2b is highly expressed in skeletal muscles and the heart. The expression of CRH-R2a and CRH-R2b in different regions suggests their different functional roles [17,22,25]. CRH and its receptors are found in the male and female reproductive system in addition to their presence in the different extrahypothalamic sites of the central nervous system [24].

CRHBP is considered to act as a secreted protein that modulates the actions of CRH. The CRHBPs are synthesized in the liver in addition to their expression in the human brain. They have a significant impact on the availability of CRH. [22]. The CRH, its binding protein, and both receptors are crucial for regulating the HPA axis. Women have a higher level of plasma CRHBPs than men. CRHBP contains ten cysteine residues, and its secondary structure consists of five loops [26].

The three-dimensional (3D) structure of CRH is not established. In an ideal situation, we can predict the protein structure accurately. With the help of computer software as experimental tools, we perform homology modeling. A 3D model of the protein is needed, which can be constructed using the homology modeling technique, as neither X-ray crystallography nor NMR spectroscopy is capable of determining such a model [10,27]. The models built through homology modeling provide a great deal of information about how the protein functions. A suitably designed model will closely resemble unknown proteins. The quality of the model is evaluated, and the best model is selected among the obtained models. The model quality is directly proportional to the similarity with the target and template protein. The quality of the model decreases with the decrease in the similarity of the target and model. Protein Data Bank (PDB) provides the foundation of homology modeling via known 3D structures (templates) available in it.

Our study aims to predict a potential 3D model of CRH via homology modeling and molecular docking techniques for the discovery of novel drug molecules to treat stress-related conditions. It is important to mention that the current study is theoretical and speculative. Consequently, experimental investigations would be necessary in the future to endorse the results obtained in this in silico work.

2 Methodology

2.1 Protein sequence retrieval

The primary sequences of CRH with accession no G3CIS4 were received from Universal Protein Resources (UniProt) [28] in FASTA format (Fast protein or nucleotide comparison). Its 3D structure was unavailable and was therefore designed via homology modeling employing Iterative Threading Assembly Refinement (I-TASSER) [29,30] and Molecular Operating Environment (MOE) [31].

2.2 Homology model prediction by GPCR I-TASSER server

GPCR I-TASSER method [29] is a hybrid method for the estimation of the 3D structure of GPCRs. The I-TASSER server includes the following major steps:

  1. The amino acid arrangement of a single protein is copied and pasted, an optional name is given to the protein, and the job is run.

  2. I-TASSER applies a Local Meta-Threading Server, version 3 (LOMETS) [32] with additional threading programs, i.e., FUGUE [33], HHSEARCH [34], MUSTER [35], PROSPECT [36], PPA [37], SP3 [38], and SPARKS [39]. Using the Z-score, the top template alignments were selected for further consideration. The standard of the template arrangement is determined through the Z-score.

  3. In template structures, fragments were excised from the threading alignments, and structure assembly was performed.

  4. Model selection and refinement occurred on the I-TASSER second run. Subsequently, structure-based functional annotation is performed.

When the job run was completed, the I-TASSER result page was available in the inbox (via email).

2.3 Homology model construction through MOE

A 3D model of CRH was made through MOE. To produce the precise 3D design of CRH, key steps, i.e., recovery of the pattern, sequence arrangement, generation of the design, justification, and refinement, were followed. Before the aforementioned steps for model generation, parameters such as the force field Amber 99 and model scoring to GB/VI (Generalized Born/Volume Integral) were adjusted. After the sequence alignment, root mean square deviation (RMSD) values for αC atoms, side row atoms, and backbone atoms, and each arrangement of all heavy atoms were calculated. The most stable structure was recognized after the method that was then recovered in PDB layout.

2.4 Molecular docking

Molecular docking is a computational technique through which the most appropriate orientation between two molecules is predicted. The technique is used to predict protein binding sites, pockets, and clefts of the ligands [40,41]. The 3D framework of CRHR was made by homology modeling for molecular docking. The 3D protonation and energy minimization of the receptor molecule was performed via force field Amber 99. For the molecular docking of CP376395 derivatives, the default domain of the MOE-dock database was used. At the end of docking, the binding interactions of all derivatives (Figure 2) with homology-modeled CRHR were predicted.

Figure 2 Chemical structures of CP376395 and its derivatives.
Figure 2 Chemical structures of CP376395 and its derivatives.
Figure 2

Chemical structures of CP376395 and its derivatives.

2.5 Primary sequence retrieval

The principal arrangement of CRH with accession no G3CIS4 in FASTA format was taken from UniProt containing 430 amino acid sequences (Figure 3).

Figure 3 Query sequence of G3CIS4 having 430 residues.
Figure 3

Query sequence of G3CIS4 having 430 residues.

2.6 Homology model prediction by GPCR I-TASSER server

The 3D framework of CRH was built with the online server GPCR I-TASSER. In total, five patterns were predicted, and the TM-score, C-score, and RMSD values for the first design are given. The C-score is an approximation of the grade of the projected model. The C-score value generally falls within the range of [−5, 2], where a higher score indicates a model of superior quality. In the top five patterns, the first one with a greater C-score of −0.45 was downloaded in PDB format. TM score shows the constitutional resemblance between the projected model and the original structure. TM score value typically ranges in [0, 1]. The predicted TM score and RMSD values for the initial design are 0.66 ± 0.13 and 8.0 ± 4.4 Å, respectively (Table 1). These values are acceptable for further studies. The 3D structure of CRH (first ranked model) contains seven TM helices (7TM), intracellular C-terminal G-protein-coupled site, CRH-binding site extracellular N-terminus, and extra and intracellular loops (Figure 4).

Table 1

Statistical analysis of a 3D model of CRH

C-score Predicted TM score Predicted RMSD score
−0.45 0.66 ± 0.13 8.0 ± 4.4 Å
Figure 4 3D structure of CRH via I-TASSER.
Figure 4

3D structure of CRH via I-TASSER.

2.7 Homology modeling construction through MOE

MOE 2011-12 package was employed for the generation of the design. At the end of the process, ten models were generated and the most stable ones were selected and recovered in the PDB form. The native model was overlaid on the template to generate a superimposed model. A close homology was confirmed by an RMSD value of 1.24 Å (Figure 5).

Figure 5 MOE generated 3D structure of CRHR.
Figure 5

MOE generated 3D structure of CRHR.

2.8 Justification and assessment of the final model

To justify the quality and accuracy of the final model, several steps were performed during the analysis of the final 3D model. For the stereochemical quality analysis, a Ramachandran plot was obtained. Ramachandran plot was obtained using the RAMPAGE server [42,43]. The results (Figure 6) were obtained to give the relation between the torsional angle with the Ramachandran plot and protein structure. Psi angle is between the carboxylic group and α-carbon. The results show that 91.1%, 6.8%, and 2.1% of the residues fell within the favored, allowed, and disallowed zones of the Ramachandran plot, respectively (Table 2). Almost 98% of the residues have fallen in the most favored and allowed regions. Through MOE2011-12 software, the Ramachandran plot analysis also showed that the residues PRO-6, ILE-300, TRP 55, ARG-66, SER-58, ALA-168, PHE-269, PRO-164, and GLN-62 were out of the dynamically favored zones. The residues remaining in the central zones of the Ramachandran plot indicate the high consistency of the last structure.

Figure 6 Ramachandran plot shows the results of CRH. Rampage results showed 91.1% favored, 6.8% allowed, and 2.1% disallowed. PRO-6, ILE-300, ALA-168, GLN-62, SER-58, PHE-269, TRP-59, ARG-66, and PRO-164 were out of the energetically favorable region.
Figure 6

Ramachandran plot shows the results of CRH. Rampage results showed 91.1% favored, 6.8% allowed, and 2.1% disallowed. PRO-6, ILE-300, ALA-168, GLN-62, SER-58, PHE-269, TRP-59, ARG-66, and PRO-164 were out of the energetically favorable region.

Table 2

Plot statistics of the modeled CRHRs

Plot investigation
Residues fell in the favored region (98.0%) projected (390) 91.1%
Residue fell in the allowed region (2%) projected (29) 0.68%
Residue fell in the disallowed region (9) 2.1%

The total caliber of the final design was predicted through the ERRATE server [44,45]. An ERRATE score of 82.816 was obtained. This value shows that it is a high-quality model as a 50 score is considered good. ERRATE is generally applied to explain the non-bonded interactions between various atoms. The gray bar indicates the zone of error, the black bar shows the misfolded zone, and the white bars reveal the zone for the folding of a protein possessing less error rate (Figure 7a and b).

Figure 7 (a) and (b) An overall quality factor of CRH predicted by ERRAT 2.
Figure 7

(a) and (b) An overall quality factor of CRH predicted by ERRAT 2.

2.9 Molecular docking of CRH with CP376395 derivatives

According to the molecular docking results, derivative A exhibited a maximum of two interactions with a docking score of −15.74 kcal/mol within the enzyme’s binding pocket. A total of seven amino acid fragments are situated in the binding pocket of the receptor, whereas the Lys 11 residue lies in TM domain 1 (TM1) and forms two interactions. Lys11 residue shows a hydrogen bonding interaction and an arene–cationic interaction with the electrophile NH2 of cyclobutane and the SH group of the benzene ring, respectively. The RMSD value was noted to be 3.734 Å.

Only one interaction is shown by derivative B. A total of four amino acid fragments are located in the binding pocket of the receptor, and an arene–arene interaction is shown by Tyr 281 (lying in the TM5) with the benzene ring. The docking score and RMSD value were noted to be −11.57 Kcal/mol and 1.662 Å, respectively.

Two interactions are shown by the derivative C. A total of four amino acid fragments are situated in the binding pocket of the receptor. The residues Arg 403 and Arg 174 lie in the TM7 and TM4, respectively. Both the residues show arene–arene interactions with the benzene ring. The docking score and RMSD value were noted to be −14.88 Kcal/mol and 4.102 Å, respectively.

A maximum of two interactions are shown by derivative D. A total of four amino acids are situated in the binding pocket of the receptor. The residues Arg 392 and Arg 395 are located in TM6, and both establish arene–cationic bonds with the same benzene skeleton. The docking score and RMSD value were recorded to be −15.60 kcal/mol and 2.126 Å, respectively.

A maximum of three interactions are shown by derivative E. A total of four amino acids are situated in the binding pocket of the receptor. The residues Arg 403 and Arg 174 are located in TM7 and TM4, respectively. Two arene–cationic interactions are established by Arg 403 with a benzene ring. On the other hand, the residue Arg 174 forms an arene–cationic bonding with another benzene skeleton. The docking score and RMSD value were noted to be −14.25 kcal/mol and 3.624 Å, respectively.

A maximum of two interactions are formed by derivative F. A total of four amino acids are situated in the binding pocket of the receptor. The residues Arg 403 and Arg 174 are located in TM7 and TM4, respectively. Both the residues form arene–cationic bondings with the same benzene skeleton. The docking score and RMSD value were recorded to be 20.06 kcal/mol and 4.353 Å, respectively.

Only one interaction is shown by derivative G. A total of five amino acids are situated in the binding pocket of the receptor. The residue His 4 is located at the N-terminal and forms an arene–arene bonding with the benzene skeleton. The docking score and RMSD value were recorded to be −19.41 kcal/mol and 2.246 Å, respectively.

Only one interaction is shown by derivative H. A total of eight amino acids are situated in the binding pocket of the receptor. The residue Arg 145 is situated in TM3 and forms an arene–cationic bonding with the benzene skeleton. The docking score and RMSD value were verified to be −16.42 kcal/mol and 3.443 Å, respectively.

A maximum of three interactions are shown by derivative I. A total of nine amino acids are situated in the binding pocket of the receptor. The residue Trp 266 is located in TM5, and the two residues (Ala 190 and Asn 186) are situated in TM4. An arene–arene interaction is noted between the residue Trp 266 and the benzene moiety. The residues Ala 190 and Asn 186 form hydrogen bonding separately with the same oxygen. The docking score and RMSD value were confirmed to be −18.57 kcal/mol and 2.824 Å, respectively.

Two interactions are formed by derivative J. A total of eight amino acids are situated in the binding pocket of the receptor. The residue Arg 145 (located in TM3) forms an arene–cationic bonding with the benzene moiety, and the residue Ser 146 (located in TM3) establishes a hydrogen bonding with the hydroxyl moiety connected to a benzene ring. The docking score and RMSD value were noted to be −15.60 kcal/mol and 2.126 Å 2.824 Å, respectively.

The overall docking results of the CRH with CP376395 derivatives (A–J) are provided in Figure 8 and Table 3.

Figure 8 2D and 3D interaction images of CRH with CP376395 derivatives (A–J).
Figure 8 2D and 3D interaction images of CRH with CP376395 derivatives (A–J).
Figure 8 2D and 3D interaction images of CRH with CP376395 derivatives (A–J).
Figure 8 2D and 3D interaction images of CRH with CP376395 derivatives (A–J).
Figure 8

2D and 3D interaction images of CRH with CP376395 derivatives (A–J).

Table 3

Docking results of CP376395 derivatives (A–J)

CP376395 analogs Docking score (kcal/mol) RMSD (Å) Number of interactions
A −15.74 03.734 02
B −11.57 01.662 01
C −14.88 04.102 02
D −15.60 02.126 02
E −14.25 03.624 03
F −20.06 04.353 02
G −19.41 02.246 01
H −16.42 03.443 01
I −18.57 02.824 03
J −15.60 02.126 02

Only one interaction is established by derivative K. A total of seven amino acids are situated in the binding pocket of the receptor. The residue Thr 417 is located at the C-terminal and establishes a hydrogen bonding with the hydroxyl moiety of the ligand. The docking score and RMSD value were noted to be −16.02 kcal/mol and 1.857 Å, respectively.

A maximum of three interactions are shown by derivative L. A total of eight amino acids are situated in the binding pocket of the receptor. The residue Ser 24 is located in TM1, and the two residues (Arg 292 and Lys 286) are situated in TM5. A hydrogen bonding is observed between the residue Ser 24 and the oxygen of the SO2Cl moiety. A second hydrogen bonding is found between the residue Arg 292 and the oxygen of the carboxylic moiety. The third hydrogen bonding is formed between the residue Lys 286 and the oxygen of another carboxylic moiety. The docking score and RMSD value were noted to be −15.57 kcal/mol and 3.331 Å, respectively.

A maximum of three interactions are shown by derivative M. A total of 11 amino acids are found in the binding pocket of the receptor. The residues Lys 291 and Phe 359 are located in TM5 and TM6, respectively. The residue Lys 291 forms a hydrogen bond with the hydroxyl group of the ligand. The residue Phe 359 forms two hydrogen bonds with the oxygen of the carboxylic moiety and the hydrogen of the hydroxyl moiety. The docking score and RMSD value were noted to be −16.69 kcal/mol and 3.763 Å, respectively.

A maximum of three interactions are shown by derivative N. A total of nine amino acids are situated in the binding pocket of the receptor. The residues Lys 111, Ser 112, and Asn 89 are all found in TM3. The residues Lys 111 and Ser 112 both make hydrogen bonds with hydrogen of the same hydroxyl moiety on the ligand molecule. On the other hand, the residue Asn 89 also forms a hydrogen bond with the hydrogen of a different hydroxyl moiety on the ligand molecule. The docking score and RMSD value were noted to be −25.27 kcal/mol and 3.639 Å, respectively.

A maximum of four interactions are shown by derivative O. A total of five amino acids are present in the binding pocket of the receptor. The residues Arg 174 and Arg 403 are located in TM4 and TM7, respectively. The residue Arg 174 forms two arene–cationic interactions with two different aromatic rings. On the other hand, the residue Arg 403 forms an arene–cationic interaction and a hydrogen-bonding interaction with an aromatic ring and the amino group of aniline moiety, respectively. The docking score and RMSD value were recorded to be −19.89 kcal/mol and 16.65 Å, respectively.

A maximum of three interactions are displayed by derivative P. A total of six amino acids are present in the binding pocket of the receptor. The residues Glu 31 is found in TM1, whereas the residues Arg 292 and Glu 285 are both situated in TM5. The residue Arg 292 forms an arene–cationic interaction with the aromatic moiety of the ligand molecule. On the other hand, the residues Glu 31 and Glu 285 both establish hydrogen bonds with the hydrogen of an amino moiety and the hydrogen of a hydroxyl group, respectively. The docking score and RMSD value were observed to be −17.54 kcal/mol and 1.554 Å, respectively.

A maximum of four interactions are shown by derivative Q. A total of five amino acids are present in the binding pocket of the receptor. Three residues Glu 109, His 117, and Lys 113 all are located in TM3. A hydrogen bond between the residue Glu 109 and the hydrogen of the amino moiety is observed. The residue Lys 113 forms two hydrogen-bonding interactions with the nitrogen of an amino moiety and the doubly bonded oxygen atom of the carboxylic moiety. The fourth hydrogen-bonding interaction is displayed between the residue His 117 and the hydrogen of the amino group. The docking score and RMSD value were identified to be −16.92 kcal/mol and 3.385 Å, respectively.

A maximum of two interactions are shown by derivative R. A total of five amino acids are found in the binding pocket of the receptor. The residues Glu 21 and Lys 256 are present in TM1 and TM5, respectively. A hydrogen bond is observed between the residue Glu 21 and the hydrogen of the carboxylic moiety. An arene–cationic interaction is formed between the residue Lys 256 and an aromatic ring of the ligand molecule. The docking score and RMSD value were identified to be −26.38 kcal/mol and 2.185 Å, respectively.

Only one interaction is shown by derivative S. A total of three amino acids are found in the binding pocket of the receptor. The residue Phe 313 is found in TM6, which forms an arene–arene interaction with an aromatic ring of the ligand molecule. The docking score and RMSD value were recognized to be −16.09 kcal/mol and 1.287 Å, respectively.

The overall docking results of CRH with CP376395 derivatives (K–S) are provided in Figure 9 and Table 4.

Figure 9 2D and 3D interaction images of CRH with CP376395 derivatives (K–S).
Figure 9 2D and 3D interaction images of CRH with CP376395 derivatives (K–S).
Figure 9 2D and 3D interaction images of CRH with CP376395 derivatives (K–S).
Figure 9

2D and 3D interaction images of CRH with CP376395 derivatives (K–S).

Table 4

Docking results of CP376395 derivatives (K–S)

CP376395 analogs Docking score (kcal/Mol) RMSD (Å) Number of interactions
K −16.02 01.857 01
L −15.57 03.331 03
M −16.69 03.763 03
N −25.27 03.639 03
O −19.89 16.65 04
P −17.51 01.554 03
Q −16.92 03.385 04
R −26.38 02.185 01
S −16.09 01.287 01

3 Conclusion

The key goal of this study is to design a 3D structure of CRH through computational work and to find the active sites for drug designing to affect their biological and biochemical activities. The 3D structure of CRHRs was architected by MOE and the I-TASSER package. The justification and assessment of the final model of CRHRs were made with RAMPAGE and ERRATE online servers. Molecular docking studies revealed that CRH exhibited robust interactions with the drug CP376395 and its analogs. It was noted that CP376395 derivatives O and Q showed a maximum of four interactions with CRH with a decent docking score. In contrast, the analogs E, I, L, M, N, and P each displayed a maximum of three interactions with CRH, accompanied by decent docking scores. The results showed good docking scores for most of the CP376395 derivatives after their molecular docking with the CRH. These investigations will support us to know the 3D structure of CRHRs and their function. Furthermore, the current study will propose a hypothetical path for chemists to design new drug candidates for the treatment of stress-related diseases.

Acknowledgment

The authors extend their appreciation to the researchers supporting Project Number RSP2024R45 King Saud University, Riyadh, Saudi Arabia.

  1. Funding information: This study was supported by researchers supporting Project Number (RSP2024R45), King Saud University, Riyadh, Saudi Arabia.

  2. Author contributions: N.A.: conceptualization, validation, software, and writing the original draft; K.K.: project administration, conceptualization, and visualization; S.W.K.: visualization, investigation, and software; H.ur.R.: software, validation, writing, review and editing; I.: formal analysis and investigation; M.Z.: data validation, visualization, and editing; R.U. and E.A.: funding acquisition and technical assistance. All authors read and approved the final manuscript.

  3. Conflict of interest: All the authors declare hereby that they have no conflict of interest.

  4. Ethical approval: The conducted research is not related to either human or animal use.

  5. Data availability statement: All the data are presented in this manuscript. There are no associated data in any repository.

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Received: 2024-02-22
Revised: 2024-05-30
Accepted: 2024-06-30
Published Online: 2024-07-25

© 2024 the author(s), published by De Gruyter

This work is licensed under the Creative Commons Attribution 4.0 International License.

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https://doi.org/10.1515/chem-2024-0069
Keywords for this article
homology modeling; molecular docking; corticotrophin; adenylate cyclase; nucleotides
Creative Commons
BY 4.0

Articles in the same Issue

  1. Regular Articles
  2. Porous silicon nanostructures: Synthesis, characterization, and their antifungal activity
  3. Biochar from de-oiled Chlorella vulgaris and its adsorption on antibiotics
  4. Phytochemicals profiling, in vitro and in vivo antidiabetic activity, and in silico studies on Ajuga iva (L.) Schreb.: A comprehensive approach
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  13. Evaluation of influence of Butea monosperma floral extract on inflammatory biomarkers
  14. Cannabis sativa L. essential oil: Chemical composition, anti-oxidant, anti-microbial properties, and acute toxicity: In vitro, in vivo, and in silico study
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  16. Hollow mushroom nanomaterials for potentiometric sensing of Pb2+ ions in water via the intercalation of iodide ions into the polypyrrole matrix
  17. Determination of essential oil and chemical composition of St. John’s Wort
  18. Computational design and in vitro assay of lantadene-based novel inhibitors of NS3 protease of dengue virus
  19. Anti-parasitic activity and computational studies on a novel labdane diterpene from the roots of Vachellia nilotica
  20. Microbial dynamics and dehydrogenase activity in tomato (Lycopersicon esculentum Mill.) rhizospheres: Impacts on growth and soil health across different soil types
  21. Correlation between in vitro anti-urease activity and in silico molecular modeling approach of novel imidazopyridine–oxadiazole hybrids derivatives
  22. Spatial mapping of indoor air quality in a light metro system using the geographic information system method
  23. Iron indices and hemogram in renal anemia and the improvement with Tribulus terrestris green-formulated silver nanoparticles applied on rat model
  24. Integrated track of nano-informatics coupling with the enrichment concept in developing a novel nanoparticle targeting ERK protein in Naegleria fowleri
  25. Cytotoxic and phytochemical screening of Solanum lycopersicum–Daucus carota hydro-ethanolic extract and in silico evaluation of its lycopene content as anticancer agent
  26. Protective activities of silver nanoparticles containing Panax japonicus on apoptotic, inflammatory, and oxidative alterations in isoproterenol-induced cardiotoxicity
  27. pH-based colorimetric detection of monofunctional aldehydes in liquid and gas phases
  28. Investigating the effect of resveratrol on apoptosis and regulation of gene expression of Caco-2 cells: Unravelling potential implications for colorectal cancer treatment
  29. Metformin inhibits knee osteoarthritis induced by type 2 diabetes mellitus in rats: S100A8/9 and S100A12 as players and therapeutic targets
  30. Effect of silver nanoparticles formulated by Silybum marianum on menopausal urinary incontinence in ovariectomized rats
  31. Synthesis of new analogs of N-substituted(benzoylamino)-1,2,3,6-tetrahydropyridines
  32. Response of yield and quality of Japonica rice to different gradients of moisture deficit at grain-filling stage in cold regions
  33. Preparation of an inclusion complex of nickel-based β-cyclodextrin: Characterization and accelerating the osteoarthritis articular cartilage repair
  34. Empagliflozin-loaded nanomicelles responsive to reactive oxygen species for renal ischemia/reperfusion injury protection
  35. Preparation and pharmacodynamic evaluation of sodium aescinate solid lipid nanoparticles
  36. Assessment of potentially toxic elements and health risks of agricultural soil in Southwest Riyadh, Saudi Arabia
  37. Theoretical investigation of hydrogen-rich fuel production through ammonia decomposition
  38. Biosynthesis and screening of cobalt nanoparticles using citrus species for antimicrobial activity
  39. Investigating the interplay of genetic variations, MCP-1 polymorphism, and docking with phytochemical inhibitors for combatting dengue virus pathogenicity through in silico analysis
  40. Ultrasound induced biosynthesis of silver nanoparticles embedded into chitosan polymers: Investigation of its anti-cutaneous squamous cell carcinoma effects
  41. Copper oxide nanoparticles-mediated Heliotropium bacciferum leaf extract: Antifungal activity and molecular docking assays against strawberry pathogens
  42. Sprouted wheat flour for improving physical, chemical, rheological, microbial load, and quality properties of fino bread
  43. Comparative toxicity assessment of fisetin-aided artificial intelligence-assisted drug design targeting epibulbar dermoid through phytochemicals
  44. Acute toxicity and anti-inflammatory activity of bis-thiourea derivatives
  45. Anti-diabetic activity-guided isolation of α-amylase and α-glucosidase inhibitory terpenes from Capsella bursa-pastoris Linn.
  46. GC–MS analysis of Lactobacillus plantarum YW11 metabolites and its computational analysis on familial pulmonary fibrosis hub genes
  47. Green formulation of copper nanoparticles by Pistacia khinjuk leaf aqueous extract: Introducing a novel chemotherapeutic drug for the treatment of prostate cancer
  48. Improved photocatalytic properties of WO3 nanoparticles for Malachite green dye degradation under visible light irradiation: An effect of La doping
  49. One-pot synthesis of a network of Mn2O3–MnO2–poly(m-methylaniline) composite nanorods on a polypyrrole film presents a promising and efficient optoelectronic and solar cell device
  50. Groundwater quality and health risk assessment of nitrate and fluoride in Al Qaseem area, Saudi Arabia
  51. A comparative study of the antifungal efficacy and phytochemical composition of date palm leaflet extracts
  52. Processing of alcohol pomelo beverage (Citrus grandis (L.) Osbeck) using saccharomyces yeast: Optimization, physicochemical quality, and sensory characteristics
  53. Specialized compounds of four Cameroonian spices: Isolation, characterization, and in silico evaluation as prospective SARS-CoV-2 inhibitors
  54. Identification of a novel drug target in Porphyromonas gingivalis by a computational genome analysis approach
  55. Physico-chemical properties and durability of a fly-ash-based geopolymer
  56. FMS-like tyrosine kinase 3 inhibitory potentials of some phytochemicals from anti-leukemic plants using computational chemical methodologies
  57. Wild Thymus zygis L. ssp. gracilis and Eucalyptus camaldulensis Dehnh.: Chemical composition, antioxidant and antibacterial activities of essential oils
  58. 3D-QSAR, molecular docking, ADMET, simulation dynamic, and retrosynthesis studies on new styrylquinolines derivatives against breast cancer
  59. Deciphering the influenza neuraminidase inhibitory potential of naturally occurring biflavonoids: An in silico approach
  60. Determination of heavy elements in agricultural regions, Saudi Arabia
  61. Synthesis and characterization of antioxidant-enriched Moringa oil-based edible oleogel
  62. Ameliorative effects of thistle and thyme honeys on cyclophosphamide-induced toxicity in mice
  63. Study of phytochemical compound and antipyretic activity of Chenopodium ambrosioides L. fractions
  64. Investigating the adsorption mechanism of zinc chloride-modified porous carbon for sulfadiazine removal from water
  65. Performance repair of building materials using alumina and silica composite nanomaterials with electrodynamic properties
  66. Effects of nanoparticles on the activity and resistance genes of anaerobic digestion enzymes in livestock and poultry manure containing the antibiotic tetracycline
  67. Effect of copper nanoparticles green-synthesized using Ocimum basilicum against Pseudomonas aeruginosa in mice lung infection model
  68. Cardioprotective effects of nanoparticles green formulated by Spinacia oleracea extract on isoproterenol-induced myocardial infarction in mice by the determination of PPAR-γ/NF-κB pathway
  69. Anti-OTC antibody-conjugated fluorescent magnetic/silica and fluorescent hybrid silica nanoparticles for oxytetracycline detection
  70. Curcumin conjugated zinc nanoparticles for the treatment of myocardial infarction
  71. Identification and in silico screening of natural phloroglucinols as potential PI3Kα inhibitors: A computational approach for drug discovery
  72. Exploring the phytochemical profile and antioxidant evaluation: Molecular docking and ADMET analysis of main compounds from three Solanum species in Saudi Arabia
  73. Unveiling the molecular composition and biological properties of essential oil derived from the leaves of wild Mentha aquatica L.: A comprehensive in vitro and in silico exploration
  74. Analysis of bioactive compounds present in Boerhavia elegans seeds by GC-MS
  75. Homology modeling and molecular docking study of corticotrophin-releasing hormone: An approach to treat stress-related diseases
  76. LncRNA MIR17HG alleviates heart failure via targeting MIR17HG/miR-153-3p/SIRT1 axis in in vitro model
  77. Development and validation of a stability indicating UPLC-DAD method coupled with MS-TQD for ramipril and thymoquinone in bioactive SNEDDS with in silico toxicity analysis of ramipril degradation products
  78. Biosynthesis of Ag/Cu nanocomposite mediated by Curcuma longa: Evaluation of its antibacterial properties against oral pathogens
  79. Development of AMBER-compliant transferable force field parameters for polytetrafluoroethylene
  80. Treatment of gestational diabetes by Acroptilon repens leaf aqueous extract green-formulated iron nanoparticles in rats
  81. Development and characterization of new ecological adsorbents based on cardoon wastes: Application to brilliant green adsorption
  82. A fast, sensitive, greener, and stability-indicating HPLC method for the standardization and quantitative determination of chlorhexidine acetate in commercial products
  83. Assessment of Se, As, Cd, Cr, Hg, and Pb content status in Ankang tea plantations of China
  84. Effect of transition metal chloride (ZnCl2) on low-temperature pyrolysis of high ash bituminous coal
  85. Evaluating polyphenol and ascorbic acid contents, tannin removal ability, and physical properties during hydrolysis and convective hot-air drying of cashew apple powder
  86. Development and characterization of functional low-fat frozen dairy dessert enhanced with dried lemongrass powder
  87. Scrutinizing the effect of additive and synergistic antibiotics against carbapenem-resistant Pseudomonas aeruginosa
  88. Preparation, characterization, and determination of the therapeutic effects of copper nanoparticles green-formulated by Pistacia atlantica in diabetes-induced cardiac dysfunction in rat
  89. Antioxidant and antidiabetic potentials of methoxy-substituted Schiff bases using in vitro, in vivo, and molecular simulation approaches
  90. Anti-melanoma cancer activity and chemical profile of the essential oil of Seseli yunnanense Franch
  91. Molecular docking analysis of subtilisin-like alkaline serine protease (SLASP) and laccase with natural biopolymers
  92. Overcoming methicillin resistance by methicillin-resistant Staphylococcus aureus: Computational evaluation of napthyridine and oxadiazoles compounds for potential dual inhibition of PBP-2a and FemA proteins
  93. Exploring novel antitubercular agents: Innovative design of 2,3-diaryl-quinoxalines targeting DprE1 for effective tuberculosis treatment
  94. Drimia maritima flowers as a source of biologically potent components: Optimization of bioactive compound extractions, isolation, UPLC–ESI–MS/MS, and pharmacological properties
  95. Estimating molecular properties, drug-likeness, cardiotoxic risk, liability profile, and molecular docking study to characterize binding process of key phyto-compounds against serotonin 5-HT2A receptor
  96. Fabrication of β-cyclodextrin-based microgels for enhancing solubility of Terbinafine: An in-vitro and in-vivo toxicological evaluation
  97. Phyto-mediated synthesis of ZnO nanoparticles and their sunlight-driven photocatalytic degradation of cationic and anionic dyes
  98. Monosodium glutamate induces hypothalamic–pituitary–adrenal axis hyperactivation, glucocorticoid receptors down-regulation, and systemic inflammatory response in young male rats: Impact on miR-155 and miR-218
  99. Quality control analyses of selected honey samples from Serbia based on their mineral and flavonoid profiles, and the invertase activity
  100. Eco-friendly synthesis of silver nanoparticles using Phyllanthus niruri leaf extract: Assessment of antimicrobial activity, effectiveness on tropical neglected mosquito vector control, and biocompatibility using a fibroblast cell line model
  101. Green synthesis of silver nanoparticles containing Cichorium intybus to treat the sepsis-induced DNA damage in the liver of Wistar albino rats
  102. Quality changes of durian pulp (Durio ziberhinus Murr.) in cold storage
  103. Study on recrystallization process of nitroguanidine by directly adding cold water to control temperature
  104. Determination of heavy metals and health risk assessment in drinking water in Bukayriyah City, Saudi Arabia
  105. Larvicidal properties of essential oils of three Artemisia species against the chemically insecticide-resistant Nile fever vector Culex pipiens (L.) (Diptera: Culicidae): In vitro and in silico studies
  106. Design, synthesis, characterization, and theoretical calculations, along with in silico and in vitro antimicrobial proprieties of new isoxazole-amide conjugates
  107. The impact of drying and extraction methods on total lipid, fatty acid profile, and cytotoxicity of Tenebrio molitor larvae
  108. A zinc oxide–tin oxide–nerolidol hybrid nanomaterial: Efficacy against esophageal squamous cell carcinoma
  109. Research on technological process for production of muskmelon juice (Cucumis melo L.)
  110. Physicochemical components, antioxidant activity, and predictive models for quality of soursop tea (Annona muricata L.) during heat pump drying
  111. Characterization and application of Fe1−xCoxFe2O4 nanoparticles in Direct Red 79 adsorption
  112. Torilis arvensis ethanolic extract: Phytochemical analysis, antifungal efficacy, and cytotoxicity properties
  113. Magnetite–poly-1H pyrrole dendritic nanocomposite seeded on poly-1H pyrrole: A promising photocathode for green hydrogen generation from sanitation water without using external sacrificing agent
  114. HPLC and GC–MS analyses of phytochemical compounds in Haloxylon salicornicum extract: Antibacterial and antifungal activity assessment of phytopathogens
  115. Efficient and stable to coking catalysts of ethanol steam reforming comprised of Ni + Ru loaded on MgAl2O4 + LnFe0.7Ni0.3O3 (Ln = La, Pr) nanocomposites prepared via cost-effective procedure with Pluronic P123 copolymer
  116. Nitrogen and boron co-doped carbon dots probe for selectively detecting Hg2+ in water samples and the detection mechanism
  117. Heavy metals in road dust from typical old industrial areas of Wuhan: Seasonal distribution and bioaccessibility-based health risk assessment
  118. Phytochemical profiling and bioactivity evaluation of CBD- and THC-enriched Cannabis sativa extracts: In vitro and in silico investigation of antioxidant and anti-inflammatory effects
  119. Investigating dye adsorption: The role of surface-modified montmorillonite nanoclay in kinetics, isotherms, and thermodynamics
  120. Antimicrobial activity, induction of ROS generation in HepG2 liver cancer cells, and chemical composition of Pterospermum heterophyllum
  121. Study on the performance of nanoparticle-modified PVDF membrane in delaying membrane aging
  122. Impact of cholesterol in encapsulated vitamin E acetate within cocoliposomes
  123. Review Articles
  124. Structural aspects of Pt(η3-X1N1X2)(PL) (X1,2 = O, C, or Se) and Pt(η3-N1N2X1)(PL) (X1 = C, S, or Se) derivatives
  125. Biosurfactants in biocorrosion and corrosion mitigation of metals: An overview
  126. Stimulus-responsive MOF–hydrogel composites: Classification, preparation, characterization, and their advancement in medical treatments
  127. Electrochemical dissolution of titanium under alternating current polarization to obtain its dioxide
  128. Special Issue on Recent Trends in Green Chemistry
  129. Phytochemical screening and antioxidant activity of Vitex agnus-castus L.
  130. Phytochemical study, antioxidant activity, and dermoprotective activity of Chenopodium ambrosioides (L.)
  131. Exploitation of mangliculous marine fungi, Amarenographium solium, for the green synthesis of silver nanoparticles and their activity against multiple drug-resistant bacteria
  132. Study of the phytotoxicity of margines on Pistia stratiotes L.
  133. Special Issue on Advanced Nanomaterials for Energy, Environmental and Biological Applications - Part III
  134. Impact of biogenic zinc oxide nanoparticles on growth, development, and antioxidant system of high protein content crop (Lablab purpureus L.) sweet
  135. Green synthesis, characterization, and application of iron and molybdenum nanoparticles and their composites for enhancing the growth of Solanum lycopersicum
  136. Green synthesis of silver nanoparticles from Olea europaea L. extracted polysaccharides, characterization, and its assessment as an antimicrobial agent against multiple pathogenic microbes
  137. Photocatalytic treatment of organic dyes using metal oxides and nanocomposites: A quantitative study
  138. Antifungal, antioxidant, and photocatalytic activities of greenly synthesized iron oxide nanoparticles
  139. Special Issue on Phytochemical and Pharmacological Scrutinization of Medicinal Plants
  140. Hepatoprotective effects of safranal on acetaminophen-induced hepatotoxicity in rats
  141. Chemical composition and biological properties of Thymus capitatus plants from Algerian high plains: A comparative and analytical study
  142. Chemical composition and bioactivities of the methanol root extracts of Saussurea costus
  143. In vivo protective effects of vitamin C against cyto-genotoxicity induced by Dysphania ambrosioides aqueous extract
  144. Insights about the deleterious impact of a carbamate pesticide on some metabolic immune and antioxidant functions and a focus on the protective ability of a Saharan shrub and its anti-edematous property
  145. A comprehensive review uncovering the anticancerous potential of genkwanin (plant-derived compound) in several human carcinomas
  146. A study to investigate the anticancer potential of carvacrol via targeting Notch signaling in breast cancer
  147. Assessment of anti-diabetic properties of Ziziphus oenopolia (L.) wild edible fruit extract: In vitro and in silico investigations through molecular docking analysis
  148. Optimization of polyphenol extraction, phenolic profile by LC-ESI-MS/MS, antioxidant, anti-enzymatic, and cytotoxic activities of Physalis acutifolia
  149. Phytochemical screening, antioxidant properties, and photo-protective activities of Salvia balansae de Noé ex Coss
  150. Antihyperglycemic, antiglycation, anti-hypercholesteremic, and toxicity evaluation with gas chromatography mass spectrometry profiling for Aloe armatissima leaves
  151. Phyto-fabrication and characterization of gold nanoparticles by using Timur (Zanthoxylum armatum DC) and their effect on wound healing
  152. Does Erodium trifolium (Cav.) Guitt exhibit medicinal properties? Response elements from phytochemical profiling, enzyme-inhibiting, and antioxidant and antimicrobial activities
  153. Integrative in silico evaluation of the antiviral potential of terpenoids and its metal complexes derived from Homalomena aromatica based on main protease of SARS-CoV-2
  154. 6-Methoxyflavone improves anxiety, depression, and memory by increasing monoamines in mice brain: HPLC analysis and in silico studies
  155. Simultaneous extraction and quantification of hydrophilic and lipophilic antioxidants in Solanum lycopersicum L. varieties marketed in Saudi Arabia
  156. Biological evaluation of CH3OH and C2H5OH of Berberis vulgaris for in vivo antileishmanial potential against Leishmania tropica in murine models
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