Computational prediction of analog compounds of the membrane protein MCHR1 antagonists ALB-127158 and KRX-104130

Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215(3):403–410

Article  CAS  PubMed  Google Scholar 

Bell CG, Meyre D, Samson C, Boyle C, Lecoeur C, Tauber M et al (2005) Association of melanin-concentrating hormone receptor 1 5′ polymorphism with early-onset extreme obesity. Diabetes 54(10):3049–3055

Article  CAS  PubMed  Google Scholar 

Bertoline LM, Lima AN, Krieger JE, Teixeira SK (2023) Before and after AlphaFold2: an overview of protein structure prediction. Front Bioinf 3:1120370

Article  Google Scholar 

Case D, Walker R, Cheatham T, Simmerling C, Roitberg A, Merz K et al (2018) Amber 18, Univ. California, San Fr.(2018)

Chung S, Parks GS, Lee C, Civelli O (2011) Recent updates on the melanin-concentrating hormone (MCH) and its receptor system: lessons from MCH1R antagonists. J Mol Neurosci 43:115–121

Article  CAS  PubMed  Google Scholar 

Dickson CJ, Walker RC, Gould IR (2022) Lipid21: complex lipid membrane simulations with AMBER. J Chem Theory Comput 18(3):1726–1736

Article  CAS  PubMed  PubMed Central  Google Scholar 

Eberhardt J, Santos-Martins D, Tillack AF, Forli S (2021) AutoDock Vina 1.2. 0: new docking methods, expanded force field, and python bindings. J Chem Inf Model 61(8):3891–3898

Article  CAS  PubMed  Google Scholar 

Ferrulli A, Terruzzi I, Senesi P, Succi M, Cannavaro D, Luzi L (2022) Turning the clock forward: New pharmacological and not pharmacological targets for the treatment of obesity. Nutrition, Metabolism and Cardiovascular Diseases

Genheden S, Ryde U (2015) The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities. Expert Opin Drug Discov 10(5):449–461

Article  CAS  PubMed  PubMed Central  Google Scholar 

Glykofrydi S, Kokkinos A, Barber TM, Mastorakos G, Valsamakis G (2020) Existing and Emerging Molecular Targets for the Pharmacotherapy of Obesity. Endotext [Internet]

Gomez YK, Natale AM, Lincoff J, Wolgemuth CW, Rosenberg JM, Grabe M (2022) Taking the Monte-Carlo gamble: how not to buckle under the pressure! J Comput Chem 43(6):431–434

Article  CAS  PubMed  Google Scholar 

He X, Man VH, Yang W, Lee T-S, Wang J (2020) A fast and high-quality charge model for the next generation general AMBER force field. J Chem Phys 153(11):114502

Article  CAS  PubMed  PubMed Central  Google Scholar 

Helal MA, Chittiboyina AG, Avery MA (2023) Structure-based design of novel melanin-concentrating hormone receptor-1 ligands based on saturated nitrogen-containing heterocycles. Bioorg Med Chem Lett 84:129194

Article  CAS  PubMed  Google Scholar 

Igawa H, Takahashi M, Ikoma M, Kaku H, Kakegawa K, Kina A et al (2016) Amine-free melanin-concentrating hormone receptor 1 antagonists: novel non-basic 1-(2H-indazole-5-yl) pyridin-2 (1H)-one derivatives and mitigation of mutagenicity in Ames test. Bioorg Med Chem 24(11):2504–2518

Article  CAS  PubMed  Google Scholar 

Jakalian A, Jack DB, Bayly CI (2002) Fast, efficient generation of high-quality atomic charges. AM1‐BCC model: II. Parameterization and validation. J Comput Chem 23(16):1623–1641

Article  CAS  PubMed  Google Scholar 

Jo S, Kim T, Iyer VG, Im W (2008) CHARMM-GUI: a web‐based graphical user interface for CHARMM. J Comput Chem 29(11):1859–1865

Article  CAS  PubMed  Google Scholar 

Jumper J, Evans R, Pritzel A, Green T, Figurnov M, Ronneberger O et al (2021) Highly accurate protein structure prediction with AlphaFold. Nature 596(7873):583–589

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kamata M, Yamashita T, Imaeda T, Tanaka T, Terauchi J, Miyamoto M et al (2011) Discovery, synthesis, and structure–activity relationship of 6-aminomethyl-7, 8-dihydronaphthalenes as human melanin-concentrating hormone receptor 1 antagonists. Bioorg Med Chem 19(18):5539–5552

Article  CAS  PubMed  Google Scholar 

Kasai S, Kamaura M, Kamata M, Aso K, Ogino H, Nakano Y et al (2011) Melanin-concentrating hormone receptor 1 antagonists: synthesis, structure–activity relationship, docking studies, and biological evaluation of 2, 3, 4, 5-tetrahydro-1H-3-benzazepine derivatives. Bioorg Med Chem 19(21):6261–6273

Article  CAS  PubMed  Google Scholar 

Kowalski TJ, Sasikumar T (2007) Melanin-concentrating hormone receptor-1 antagonists as antiobesity therapeutics: current status. BioDrugs 21:311–321

Article  CAS  PubMed  Google Scholar 

Lim G, You KY, Lee JH, Jeon MK, Lee BH, Ryu JY et al (2022) Identification and new indication of melanin-concentrating hormone receptor 1 (MCHR1) antagonist derived from machine learning and transcriptome-based drug repositioning approaches. Int J Mol Sci 23(7):3807

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lustig RH, Collier D, Kassotis C, Roepke TA, Kim MJ, Blanc E et al (2022) Obesity I: overview and molecular and biochemical mechanisms. Biochem Pharmacol, 115012

Maier JA, Martinez C, Kasavajhala K, Wickstrom L, Hauser KE, Simmerling C (2015) ff14SB: improving the accuracy of protein side chain and backbone parameters from ff99SB. J Chem Theory Comput 11(8):3696–3713

Article  CAS  PubMed  PubMed Central  Google Scholar 

Mihalic JT, Fan P, Chen X, Chen X, Fu Y, Motani A et al (2012) Discovery of a novel melanin concentrating hormone receptor 1 (MCHR1) antagonist with reduced hERG inhibition. Bioorg Med Chem Lett 22(11):3781–3785

Article  CAS  PubMed  Google Scholar 

Miller III BR, McGee Jr TD, Swails JM, Homeyer N, Gohlke H, Roitberg AE (2012) MMPBSA. Py: an efficient program for end-state free energy calculations. J Chem Theory Comput 8(9):3314–3321

Moradi S, Nowroozi A, Shahlaei M (2019) Shedding light on the structural properties of lipid bilayers using molecular dynamics simulation: a review study. RSC Adv 9(8):4644–4658

Article  CAS  PubMed  PubMed Central  Google Scholar 

Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS et al (2009) AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility. J Comput Chem 30(16):2785–2791

Article  CAS  PubMed  PubMed Central  Google Scholar 

Müller TD, Blüher M, Tschöp MH, DiMarchi RD (2022) Anti-obesity drug discovery: advances and challenges. Nat Rev Drug Discovery 21(3):201–223

Article  PubMed  Google Scholar 

O’Boyle NM, Banck M, James CA, Morley C, Vandermeersch T, Hutchison GR (2011) Open Babel: an open chemical toolbox. J Cheminform 3(1):1–14

Google Scholar 

Onufriev A, Bashford D, Case DA (2000) Modification of the generalized born model suitable for macromolecules. J Phys Chem B 104(15):3712–3720

Article  CAS  Google Scholar 

Presse F, Conductier G, Rovere C, Nahon J (2014) The melanin-concentrating hormone receptors: neuronal and non-neuronal functions. Int J Obes Supplements 4(1):S31–S36

Article  CAS  Google Scholar 

Prida E, Fernández-González S, Pena-León V, Pérez-Lois R, Fernø J, Seoane LM et al (2022) Crosstalk between melanin concentrating hormone and endocrine factors: implications for obesity. Int J Mol Sci 23(5):2436

Article  CAS  PubMed  PubMed Central  Google Scholar 

Puranen JS, Vainio MJ, Johnson MS (2010) Accurate conformation-dependent molecular electrostatic potentials for high‐throughput in silico drug discovery. J Comput Chem 31(8):1722–1732

Article  CAS  PubMed  Google Scholar 

PyMOL (2017) The PyMOL Molecular Graphics System, Version 2.0. Schrödinger. LLC

Saeedimasine M, Montanino A, Kleiven S, Villa A (2019) Role of lipid composition on the structural and mechanical features of axonal membranes: a molecular simulation study. Sci Rep 9(1):1–12

Article  CAS  Google Scholar 

Sasmal S, Balaji G, Reddy HRK, Balasubrahmanyam D, Srinivas G, Kyasa S et al (2012) Design and optimization of quinazoline derivatives as melanin concentrating hormone receptor 1 (MCHR1) antagonists. Bioorg Med Chem Lett 22(9):3157–3162

Article  CAS  PubMed  Google Scholar 

Varadi M, Anyango S, Deshpande M, Nair S, Natassia C, Yordanova G et al (2022) AlphaFold protein structure database: massively expanding the structural coverage of protein-sequence space with high-accuracy models. Nucleic Acids Res 50(D1):D439–D444

Article  CAS  PubMed  Google Scholar 

Vitale RM, Pedone C, De Benedetti PG, Fanelli F (2004) Structural features of the inactive and active states of the melanin-concentrating hormone receptors: insights from molecular simulations. Proteins Struct Funct Bioinform 56(3):430–448

Article  CAS  Google Scholar 

Wang J, Wang W, Kollman PA, Case DA (2006) Automatic atom type and bond type perception in molecular mechanical calculations. J Mol Graph Model 25(2):247–260

Article  PubMed  Google Scholar 

Wilson CJ, Choy W-Y, Karttunen M (2022) AlphaFold2: a role for disordered protein/region prediction? Int J Mol Sci 23(9):4591

Article  CAS  PubMed  PubMed Central  Google Scholar 

Yee SM, Gillams RJ, McLain SE, Lorenz CD (2021) Effects of lipid heterogeneity on model human brain lipid membranes. Soft Matter 17(1):126–135

Article  CAS  PubMed  Google Scholar 

Ylilauri M, Pentikäinen OT (2013) MMGBSA as a tool to understand the binding affinities of filamin–peptide interactions. J Chem Inf Model 53(10):2626–2633

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