In Silico Assessment of Amino Acid–Protein Interactions in Coronary Artery Disease: Molecular Insights for Functional Biology

Year 2025, Volume: 8 Issue: 5, 1652 - 1658, 15.09.2025

Reşat Dikme , Adem Necip

https://doi.org/10.34248/bsengineering.1744802

Abstract

This study aimed to evaluate the molecular-level interactions between six Coronary artery disease (CAD)-associated amino acids (L-arginine, L-cystine, L-asparagine, L-isoleucine, L-leucine, and trans-4-hydroxyproline) and four cardiovascular target proteins (Angiotensin-converting enzyme (ACE)–1O86, Endothelial nitric oxide synthase (eNOS)–3NOS, β₁-adrenergic receptor (β₁-AR)–2VT4, and Transient Receptor Potential Vanilloid 2 (TRPV2)–8FFM). Ligands were prepared using Schrödinger LigPrep, and proteins were optimized with the Protein Preparation Wizard. Molecular docking simulations were conducted using the Glide SP and XP algorithms. Binding affinities were calculated using GlideScore. Hydrogen bonds, ionic interactions, metal coordination, and π–alkyl contacts were analyzed via Maestro visualization software. L-cystine exhibited high binding affinity with all target proteins, showing particularly strong interactions with ACE (−10.663 kcal/mol) and eNOS (−6.735 kcal/mol). Trans-4-hydroxyproline also displayed favorable binding, supported by extensive hydrogen bonding and zinc coordination. In contrast, hydrophobic amino acids such as L-isoleucine and L-leucine showed weaker interactions. ACE presented the most favorable binding environment for the selected ligands. The strong binding affinities of L-cystine and trans-4-hydroxyproline, particularly to ACE and eNOS, suggest their potential as candidate inhibitors. These effects may be attributed to disulfide bridge formation and hydrogen bond capacity, respectively, which contribute to enhanced binding stability. L-cystine and trans-4-hydroxyproline emerge as promising inhibitor candidates for key cardiovascular proteins implicated in CAD. These findings underscore the potential of amino acid–based therapeutic modulation and provide valuable insight for rational drug design and biomarker development in cardiovascular disease.

Keywords

Amino acid–protein interaction , Molecular docking , Cardiovascular molecular targets , In silico analysis

Ethical Statement

Ethics committee approval was not obtained as no studies on animals or humans were conducted in this study.

References

• Ahmad A, Dempsey SK, Daneva Z, Azam M, Li N, Li PL, Ritter JK. 2018. Role of Nitric Oxide in the Cardiovascular and Renal Systems. Int J Mol Sci, 19(9): 2605.
• Ahn HJ, Lee H, Park HE, Han D, Chang HJ, Chun EJ, Han HW, Sung J, Jung HO, Choi SY. 2022. Changes in metabolic syndrome burden and risk of coronary artery calcification progression in statin-naïve young adults. Atherosclerosis, 360: 27-33.
• Alhayek S, Preuss CV. 2025. Beta 1 Receptors. In: StatPearls. Treasure Island (FL): StatPearls Publishing.
• Barton AK, Tzolos E, Bing R, Singh T, Weber W, Schwaiger M, Varasteh Z, Slart RHJA, Newby DE, Dweck MR. 2023. Emerging molecular imaging targets and tools for myocardial fibrosis detection. Eur Heart J Cardiovasc Imaging, 24(3): 261-275.
• Borghi C, Levy BI. 2022. Synergistic actions between angiotensin-converting enzyme inhibitors and statins in atherosclerosis. Nutr Metab Cardiovasc Dis, 32(4): 815-826.
• da Silva DVT, Baião DDS, Almeida CC, Paschoalin VMF. 2023. A Critical Review on Vasoactive Nutrients for the Management of Endothelial Dysfunction and Arterial Stiffness in Individuals under Cardiovascular Risk. Nutrients, 15(11): 2618.
• Demirbağ B, Yildirim M, Cimentepe M, Necip A, Unver H, Tiftik EN. 2025. Novel vanillin-derived Schiff Bases: Synthesis, characterization, antibacterial activity, enzyme inhibition, antioxidant activity, anti-inflammatory activity on LPS-induced RAW264.7 macrophage cell line, and In Silico studies. J Mol Struct, 1338: 142320.
• Dikme TG, Necip A, Dikme R, Güneş S. 2024. Effect of Phytosterols in Apricot Kernel on Cholesterol: Molecular Docking. MEHES J, 2(3): 28-38.
• Fan Y, Li Y, Chen Y, Zhao YJ, Liu LW, Li J, Wang SL, Alolga RN, Yin Y, Wang XM, Zhao DS, Shen JH, Meng FQ, Zhou X, Xu H, He GP, Lai MD, Li P, Zhu W, Qi LW. 2016. Comprehensive Metabolomic Characterization of Coronary Artery Diseases. J Am Coll Cardiol, 68(12): 1281-1293.
• Gammoh O, Aljabali AAA, Tambuwala MM. 2024. Plasma amino acids in major depressive disorder: between pathology to pharmacology. EXCLI J, 23: 62-78.
• Halgren TA, Murphy RB, Friesner RA, Beard HS, Frye LL, Pollard WT, Banks JL. 2004. Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. J Med Chem, 47(7): 1750-1759.
• Jauhiainen R, Vangipurapu J, Laakso A, Kuulasmaa T, Kuusisto J, Laakso M. 2021. The Association of 9 Amino Acids With Cardiovascular Events in Finnish Men in a 12-Year Follow-up Study. J Clin Endocrinol Metab, 106(12): 3448-3454.
• Jeong WJ, Lee J, Eom H, Song WJ. 2023. A Specific Guide for Metalloenzyme Designers: Introduction and Evolution of Metal-Coordination Spheres Embedded in Protein Environments. Acc Chem Res, 56(18): 2416-2425.
• Kaya B, Acar Çevik U, Necip A, Duran HE, Çiftçi B, Işık M, Soyer P, Bostancı HE, Kaplancıklı ZA, Beydemir Ş. 2025. Design, Synthesis, Biological Evaluation, and Molecular Docking Studies of Novel 1,3,4-Thiadiazole Derivatives Targeting Both Aldose Reductase and α-Glucosidase for Diabetes Mellitus. ACS Omega, 10(18): 18812-18828.
• Kurhaluk N, Tkaczenko H. 2025. L-Arginine and Nitric Oxide in Vascular Regulation-Experimental Findings in the Context of Blood Donation. Nutrients, 17(4): 665.
• Li M, Wu Y, Ye L. 2022. The Role of Amino Acids in Endothelial Biology and Function. Cells, 11(8): 1372.
• Libby P, Buring JE, Badimon L, Hansson GK, Deanfield J, Bittencourt MS, Tokgözoğlu L, Lewis EF. 2019. Atherosclerosis. Nat Rev Dis Primers, 5(1): 56.
• Lima A, Ferin R, Fontes A, Santos E, Martins D, Baptista J, Pavão ML. 2020. Cysteine is a better predictor of coronary artery disease than conventional homocysteine in high-risk subjects under preventive medication. Nutr Metab Cardiovasc Dis, 30(8): 1281-1288.
• Lu C, Wu C, Ghoreishi D, Chen W, Wang L, Damm W, Ross GA, Dahlgren MK, Russell E, Von Bargen CD, Abel R, Friesner RA, Harder ED. 2021. OPLS4: Improving Force Field Accuracy on Challenging Regimes of Chemical Space. J Chem Theory Comput, 17(7): 4291-4300.
• McGarrah RW. 2023. Branched-chain amino acids in cardiovascular disease. Nat Rev Cardiol, 20(2): 77-89.
• Melnychuk I, Sharayeva M, Kramarova V, Lyzogub V. 2023. Platelet amino acid spectrum and gut microbiota, their links in patients with coronary artery disease and atrial fibrillation. Gastroenterologia, 57(4): 227-233.
• Miller M, Koch SE, Veteto A, Domeier T, Rubinstein J. 2021. Role of Known Transient Receptor Potential Vanilloid Channels in Modulating Cardiac Mechanobiology. Front Physiol, 12: 734113.
• Necip A. 2024. Kardiyovasküler Hastaliklarda Doğal Ürünler: Kurkumin ve Quercetin Moleküler Docking. MEHES J, 2(1): 1-9.
• Raad M, AlBadri A, Wei J, Mehta PK, Maughan J, Gadh A, Thomson L, Jones DP, Quyyumi AA, Pepine CJ, Bairey Merz CN. 2020. Oxidative Stress Is Associated With Diastolic Dysfunction in Women With Ischemia With No Obstructive Coronary Artery Disease. J Am Heart Assoc, 9(10): e015602.
• Rappu P, Salo AM, Myllyharju J, Heino J. 2019. Role of prolyl hydroxylation in the molecular interactions of collagens. Essays Biochem, 63(3): 325-335.
• Stroik DR, Yuen SL, Janicek KA, Schaaf TM, Li J, Ceholski DK, Hajjar RJ, Cornea RL, Thomas DD. 2018. Targeting protein-protein interactions for therapeutic discovery via FRET-based high-throughput screening in living cells. Sci Rep, 8(1): 12560.
• Suzuki S, Shino M, Fujikawa T, Itoh Y, Ueda E, Hashimoto T, Kuji T, Kobayashi N, Ohnishi T, Hirawa N, Tamura K, Toya Y. 2018. Plasma Cystine Levels and Cardiovascular and All-Cause Mortality in Hemodialysis Patients. Ther Apher Dial, 22(5): 476-484.
• Teav T, Königstein K, Wagner J, Knaier R, Infanger D, Streese L, Hinrichs T, Hanssen H, Ivanisevic J, Schmidt-Trucksäss A. 2024. Circulating amino acid signature features urea cycle alterations associated with coronary artery disease. Sci Rep, 14(1): 25848.
• Wang K, Oudit G, Gheblawi M. 2020. Angiotensin Converting Enzyme 2: A Double-Edged Sword. Circulation, 142(5): 426-428.
• Wu CH, Mohammadmoradi S, Chen JZ, Sawada H, Daugherty A, Lu HS. 2018. Renin-Angiotensin System and Cardiovascular Functions. Arterioscler Thromb Vasc Biol, 38(7): e108-e116.
• Yang RY, Wang SM, Sun L, Liu JM, Li HX, Sui XF, Wang M, Xiu HL, Wang S, He Q, Dong J, Chen WX. 2015. Association of branched-chain amino acids with coronary artery disease: A matched-pair case-control study. Nutr Metab Cardiovasc Dis, 25(10): 937-942.
• Ye J, Zhang Y, Meng J. 2022. Protein–Ligand interactions for hydrophobic charge-induction chromatography: A QCM-D study. Appl Surf Sci, 572: 151420.
• Yildirim M, Cimentepe M, Dogan K, Necip A, Amangeldinova M. 2025. Next-generation antibacterial cryogels: Berberine-infused smart membranes with molecular docking-guided targeting of MRSA and MDR E. coli. Biophys Chem, 325: 107481.
• Yildirim M, Dogan K, Necip A, Cimentepe M. 2025. Naringenin-loaded pHEMA cryogel membrane: preparation, characterization, antibacterial activity and in silico studies. Chem Pap, 79(1): 211-220.
• Zhao G, Zhang J. 2024. Molecular dynamics studies of disulfide bonds for enhancing the stability of serine protease PB92. New J Chem, 48(4): 1614-1622.