More than thirty years ago, the first annonaceous acetogenin was discovered and named uvaricin with a nanomolar range minimum inhibitory concentration. These molecules were the subject of research as promising anticancer agents against several cancer cell lines, and over 500 analogues were reported ever since; nevertheless, the mode of action was not clearly understood and remained vague (Juang et al. 2016). Despite in-vitro and in-vivo studies suggesting the involvement of mitochondrial complex II disruption, cell cycle arrest, apoptosis or superoxide anion production, further advancing to produce pharmaceutical agents from acetogenins was hindered by the lack of a distinct mechanism (Juang et al. 2016). Moreover, the neurotoxicity manifested by the annonaceous acetogenins discouraged the attempts to proceed towards clinical trials (Lannuzel et al. 2002)
Today, multidrug resistant tumor cells are rising dramatically. Wherever a new chemotherapeutic agent was discovered and used, cancer cells respond with new resistance mechanism to maintain its survival in a vicious cycle that long existed and now realized to be more complex than ever perceived. Accordingly, discovering drug combinations with unique chemical components has never been more in demand (Liu et al. 2016).
Among the most chemo-resistant enzyme targets, EGFR and its inhibitors conferred a stromal micro environment and genetic factors largely hindering further cellular susceptibility (Garvey et al. 2020). Similarly, BCL-2 and MCL-1 encounter deletions or mutations in their genetic sequences, and abnormal pathway changes, which sustain proliferation and growth (Xu and Ye. 2022)
Based on the previous, we embarked on testing 18 acetogenins compounds using in-silico molecular docking with the aim of finding suitable molecules that could serve in low amounts in cancer therapeutic combination regimens to reverse the protein drug resistance.
A selected chemical scaffold of 18 acetogenin compounds were screened for their activity in four vital enzymes, human NAD[P]H-Quinone Oxidoreductase (PDB ID: 1H69), epidermal growth factor receptor (EGFR) tyrosine kinase (PDB ID: 1M17), Bcl2-xL (PDB ID: 2W3L), and human Mcl-1. In the EGFR, previous work of chen et al indicated the non-adjacent bis-THF were more effective than the mono THF derivatives, and the latter in turn was more powerful than compounds devoid of THF. The adjacent bis-THF acetogenins were of less efficacy than the non-adjacent with few carbon bonds between the rings. and the mono THF was less effective. This was clearly seen in our results where Squamostanin-A showed better binding than annosquacin C. Annosquatin IV was of better binding than tucupentol; even within the mono THF compounds, the position of the hydroxyl groups dictates the better binding as in annomontacin which scored lower Glidescroe than monlicin A.
The range of ∆G free energy was between − 7.273 and − 6.175Kcal/mol. compared to the native ligand − 9.379 kcal/mol (AQ4). Squamostanin-A was the best fitting compound in the EGFR showing hydrogen bonds with residues Lys692, Asp776, and Asp831 and Pi-alkyl non covalent bonds with Cys773, Tyr777 and other non-polar amino acids. The AQ4 ligand simulated the same binding mode with Cys 773; moreover, it interacted with the mutation site Met 769. The lack of binding with this residue Met769 in squamostanin A is advantageous as it supported our hypothesis that acetogenins could affect the drug resistance EGFR binding pockets (Table 3). The stability of these interactions was verified by molecular dynamic simulation of the EGFR squamostanin A complex.
Table 3
Binding free energy and docking interactions of selected acetogenins in the binding pocket of human NAD[P]H-quinone oxidoreductase.
| Human NAD[P]H-quinone oxidoreductase | |
No. | Compound | Glide score (Kcal/mol) | Interactions |
1 | Squamostanin-A | -11.098 | 3 Hydrogen bonds: His11, Tyr126, Trp105 7 Hydrophobic interactions: Phe106, Tyr128, His161, Pro102, His161, Met154, Ile50 |
2 | Squamocin-P | -10.66 | 6 Hydrogen bonds: Phe17, Asn18, Gly149, Gly150, Leu103, Trp105 9 Hydrophobic interactions: Phe106, Tyr128, His194, Pro68, Pro102, His11, His161, Met154, Ile192 |
3 | Muricin D | -10.5 | 7 Hydrogen bonds: His11, Gly149, Trp105, Tyr67, Tyr155, Leu103, Phe106 5 Hydrophobic interactions: Ile50, Pro68, Tyr128, Met154, Tyr42 2 Pi-Sigma bonds: His11, Trp105 |
4 | Annopurpuricin D | -10.461 | 5 Hydrogen bonds: Phe17, Gly149, Trp105, Tyr155, Gly150 10 Hydrophobic interactions: Ile50, Tyr67, Tyr126, Pro68, Pro102, Phe106, His161, Tyr128, Phe232, His194 |
5 | Calamistrin F | -10.241 | 5 Hydrogen bonds: Phe17, Asn18, Trp105, Tyr155, Gly150 9 Hydrophobic interactions: Ile50, Tyr67, Tyr126, Pro68, Pro102, Phe106, Tyr128, Phe232, His11 |
6 | Squamostanin-B | -10.157 | 5 Hydrogen bonds: Thr147, Gly150, Trp105, Phe106, Trp105 7 Hydrophobic interactions: Pro102, Pro68, Tyr126, His194, Ile192, Ala69, Phe232 |
7 | Squamotin A | -10.071 | 4 Hydrogen bonds: Gly150, Tyr155, His11, Arg200 7 Hydrophobic interactions: Ile192, Met154, Phe106, Trp105, Leu103, Pro102, Pro68 |
8 | Annopurpuricin C | -9.98 | 5 Hydrogen bonds: Phe17, Asn18, Gly150, Tyr151, His161 7 Hydrophobic interactions: Phe106, Tyr126, Tyr128, Phe232, His194, Pro68, Pro102 |
9 | Tucupentol | -9.79 | 3 Hydrogen bonds: Leu103, Trp105, Phe17 5 Hydrophobic interactions: Met154, His161, Phe178, Pro68, Pro102 1 Sigma-bond: Tyr128 |
10 | Cohibin D | -9.789 | 3 Hydrogen bonds: Tyr67, Tyr155, Gly150 10 Hydrophobic interactions: Ile50, Tyr126, Pro68, Trp105, Phe178, Tyr126, Pro102, Tyr128, Phe232, His11 1 Pi-Sigma bond: His161 |
11 | Annosquacin B | -9.745 | 5 Hydrogen bonds: His11, Phe17, Asn18, Gly150, Tyr155 4 Hydrophobic interactions: Pro68, Val72, Phe106, Tyr126 1 Pi-Sigma bond: Tyr128 |
12 | Montalicin E | -9.698 | 5 Hydrogen bonds: Thr147, Gln104, Tyr126, Phe120, Trp105 8 Hydrophobic interactions: Pro102, Tyr67, Pro68, Tyr128, His194, His11, His161, Ile50 |
13 | Muricin G | -9.489 | 3 Hydrogen bonds: Gly150, Glu117, Trp105 8 Hydrophobic interactions: Tyr67, Ile50, Ile192, His61, Tyr128, Tyr126, Phe232, Phe106 1 Pi-Sigma bond: His194 |
14 | calamistrin D | -9.464 | 4 Hydrogen bonds: Gly150, Tyr155, Gln104, Tyr126 8 Hydrophobic interactions: Phe17, Tyr67, Pro68, Pro102, Leu103, Trp105, Phe106, Met154 |
15 | Annosquacin D | -9.443 | 5 Hydrogen bonds: His11, Phe17, Asn18, Gly150, Tyr155 6 Hydrophobic interactions: Phe106, Tyr126, Pro68, Tyr128, Ala69, Phe232 |
16 | Montalicin H | -9.438 | 3 Hydrogen bonds: Thr147, His161, Trp105 5 Hydrophobic interactions: Ala69, Val72, Ile192, Pro68, Tyr128, |
17 | Annopurpuricin B | -9.426 | 7 Hydrogen bonds: His11, Phe17, Asn18, Leu103, Gly149, Gly150, Ser151 7 Hydrophobic interactions: Pro68, Val72, Phe106, Tyr128, Met154, His161, His194 |
18 | Annosquatin-II | -9.419 | 2 Hydrogen bonds: Gln104, Tyr128, 10 Hydrophobic interactions: Pro102, Pro68, Ile50, Tyr67, Ile121, Phe106, Trp105, Phe178, Val72, Met154 |
In the NQO1, the compounds chosen scored between − 11.098 and-9.261 kcal/mol. Squamostanin-A was the best fitting compound in the NQO1 where it showed three hydrogen bonds to His11, Trp105, and Tyr12 and pi-alkyl interactions with six amino acids Ile50, Pro102, Phe106, His161, Phe178 and Met154 while occupying the chemical specified space of the pocket. This explained the better glide score of squamostanin A compared to the native ligand Arh − 3.184kcal/mol, which revealed one hydrogen bond to His161 and another interaction with His 194 at distance 2.14 and 4.71, respectively. The interactions were verified to be stable through the molecular dynamics’ simulations. (Table 4)
Table 4
Binding free energy and docking interactions of selected acetogenins in the binding pocket of Epidermal growth factor receptor tyrosine kinase.
| Epidermal growth factor receptor tyrosine kinase | |
No. | Compound | Glide score (Kcal/mol) | Interactions |
1 | Squamostanin-A | -7.273 | 3 Hydrogen bonds: Lys692, Asp776, Asp831 8 Hydrophobic interactions: Tyr777, Leu694, Leu768, Ala719, Leu820, Lys721, Val702, Cys773 |
2 | Montalicins G | -7.213 | 3 Hydrogen bonds: Lys721, Asn818, Asp831 7 Hydrophobic interactions: Val702, Met742, Leu764, Lys721, Leu820, Ala719, Leu794 |
3 | Squadiolin B | -7.029 | 2 Hydrogen bonds: Asn818, Asp831 9 Hydrophobic interactions: Ala731, Ile735, Leu820, Leu768, Met769, Pro770, Phe771, Cys773, Tyr777 |
4 | Annomontacin | -6.835 | 6 Hydrogen bonds: Arg817, Asp813, Cys773, Leu694, Pro770, Gly833 5 Hydrophobic interactions: Val702, Leu820, Leu802, Leu768, Ala719 |
5 | Anmontanin B | -6.698 | 3 Hydrogen bonds: Pro770, Gln704, Tyr728, 7 Hydrophobic interactions: Val702, Met742, Leu764, Lys721, Leu820, Ala719, Leu794 |
6 | Muricin E | -6.668 | 2 Hydrogen bonds: Lys693, Pro770 5 Hydrophobic interactions: Leu768, Met769, Phe771, Cys773, Tyr777 |
7 | Monlicin A | -6.65 | 3 Hydrogen bonds: Lys721 Asp831, Pro770 7 Hydrophobic interactions: Val702, Leu820, Leu694, Ala719, Phe699, Ile635, Cys773 |
8 | Montalicin B | -6.473 | 4 Hydrogen bonds: Thr766, Pro770, Lys692, Asp831 8 Hydrophobic interactions: Val702, Leu820, Cys773, Leu768, Leu694, Lys721, Ala719, Met769 |
9 | Annosquacin-I | -6.46 | 4 Hydrogen bonds: Thr830, Pro770, Leu694, Glu780 8 Hydrophobic interactions: Val702, Leu820, Cys773, Leu764, Leu768, Lys721, Ala719, Phe699 |
10 | Annosquacin C | -6.436 | 3 Hydrogen bonds: Glu780, Pro770, Lys692 5 Hydrophobic interactions: Leu820, Cys773, Leu768, Ala719, Leu694 |
11 | Annocherimolin | -6.436 | 4 Hydrogen bonds: Lys721, Asn818, Arg817, Asp831 7 Hydrophobic interactions: Val702, Leu820, Cys773, Leu694, Ile735, Leu794, Phe771 |
12 | Muricenin | -6.431 | 3 Hydrogen bonds: Met769, Asp831, Pro770 6 Hydrophobic interactions: Val702, Leu820, Leu694, Ala719, Phe699, Ile635 |
13 | Squamostanin-B | -6.424 | 4 Hydrogen bonds: Cys773, Asn818, Asp776, Asp831 6 Hydrophobic interactions: Tyr777, Leu775, Phe771, Pro770, Met769, Leu768 |
14 | Annosquatin IV | -6.373 | 3 Hydrogen bonds: Glu780, Met769, Phe771 4 Hydrophobic interactions: Tyr777, Pro770, Leu768, Leu820 |
15 | Annonamuricin A | -6.367 | 4 Hydrogen bonds: Lys792, Pro770, Asp831, Thr830 5 Hydrophobic interactions: Val702, Leu820, Leu694, Ala719, Lys721 |
16 | Tucupentol | -6.3 | 2 Hydrogen bonds: Asp776, Asp831 8 Hydrophobic interactions: Phe699, Leu820, Leu768, Met769, Pro770, Phe771, Cys773, Tyr777 |
17 | Asitrilobin C | -6.215 | 3 Hydrogen bonds: Lys692 Asp831, Leu694 5 Hydrophobic interactions: Val702, Leu820, Val693, Ala719, Phe699 |
18 | Annonacin | -6.209 | 4 Hydrogen bonds: Asn818, Arg817, Leu694, Pro770 7 Hydrophobic interactions: Val702, Leu820, Cys773, Leu794, Ala719, Leu764, Leu834 |
In the BCl-2, the chosen acetogenin compounds scored between − 6.334 and − 5.283 kcal/mol. Annopupuricin revealed binding to Arg88, Glu95, and Asn102 through hydrogen bonds and to Phe63, Arg66, Tyr67, Met74, Val92, Arg105, Val107, and Ala108 through Pi alkyl bonds. The native ligand dro scored − 8.192kcal/mol with π-π stacking interaction to Phe63 (5.22) and Phe71(4.99) as well as salt bridge to Asp70 with a distance of 4.12Aº and two hydrogen bonds through water bridging. Phe 63 and Val92 were the vital amino acids in the BCl-2 binding pocket (Xu et al. 2019) and its interactions were verified to be stable in the MD simulations.(Table 5)
Table 5
Binding free energy and docking interactions of selected acetogenins in the binding pocket of Bcl2-xL
| Bcl2-xL | |
No. | Compound | Glide score (Kcal/mol) | Interactions |
1 | Annopurpuricin A | -6.334 | 3 Hydrogen bonds: Arg88, Glu95, Asn102 9 Hydrophobic interactions: Val92, Met74, Ala108, Arg105, Tyr67, Arg66, Val107, Phe63, Tyr161 |
2 | Muricin G | -6.14 | 4 Hydrogen bonds: Arg105, Glu95, Glu73, Leu96 7 Hydrophobic interactions: Val92, Met74, Ala108, Tyr67, Phe109, Phe112, Phe71 |
3 | Squamocin III | -6.046 | 4 Hydrogen bonds: Arg105, Glu95, Glu73, Asn102 8 Hydrophobic interactions: Val92, Met74, Ala108, Tyr67, Phe109, Phe112, Phe71, Leu96 |
4 | Annosquatin IV | -5.932 | 2 Hydrogen bonds: Glu95, Glu73 9 Hydrophobic interactions: Val92, Met74, Ala108, Tyr67, Phe71, Leu96, Val107, Ala59, Phe63 |
5 | Squadiolin A | -5.827 | 3 Hydrogen bonds: Glu95, Arg88, Arg105 9 Hydrophobic interactions: Val92, Met74, Ala108, Tyr67, Phe71, Leu96, Phe112, Leu78, Phe109 |
6 | Annosquatin B | -5.717 | 3 Hydrogen bonds: Glu95, Arg69, Asp70 6 Hydrophobic interactions: Val92, Met74, Tyr67, Phe71, Leu96, Phe63 |
7 | Muricin F | -5.707 | 3 Hydrogen bonds: Glu95, Arg105, Asp99 8 Hydrophobic interactions: Val92, Met74, Tyr67, Phe71, Leu96, Phe71, Phe97, Ala108 |
8 | cis-montacin | -5.698 | 3 Hydrogen bonds: Glu95, Arg105, Asp99 8 Hydrophobic interactions: Val92, Met74, Tyr67, Phe71, Leu96, Phe71, Phe97, Ala108 |
9 | Annosquatin-I | -5.693 | 4 Hydrogen bonds: Gly77, Glu95, Arg105, Asn102 7 Hydrophobic interactions: Val92, Met74, Tyr67, Phe71, Leu96, Leu78, Ala108 |
10 | Annosquacin C | -5.669 | 4 Hydrogen bonds: Arg88, Glu95, Arg105, Glu73 9 Hydrophobic interactions: Val92, Tyr67, Phe71, Phe109, Leu78, Ala108, Phe112, Met74 |
11 | Asitrilobin C | -5.631 | 4 Hydrogen bonds: Arg88, Glu95, Arg105, Leu96 5 Hydrophobic interactions: Val92, Tyr67, Phe71, Ala108, Met74 |
12 | Annosquatin A | -5.62 | 3 Hydrogen bonds: Arg88, Glu95, Arg105 9 Hydrophobic interactions: Val92, Tyr67, Phe71, Ala108, Met74, Phe109, Phe112, Leu96, Leu78 |
13 | Squamostanin-A | -5.613 | 4 Hydrogen bonds: Asp70, Asp99, Arg105, Leu96 9 Hydrophobic interactions: Val92, Tyr67, Phe71, Ala108, Met74, Phe109, Phe112, Phe63, Leu96 |
14 | Squamocin-P | -5.504 | 4 Hydrogen bonds: Arg88, Asp99, Arg105, Glu95 7 Hydrophobic interactions: Val92, Tyr67, Phe71, Ala108, Met74, Leu78, Leu96 |
15 | Squamostanin-B | -5.477 | 3 Hydrogen bonds: Arg88, Gly77, Glu95 8 Hydrophobic interactions: Val92, Tyr67, Phe71, Ala108, Met74, Leu78, Leu96, Phe112 |
16 | (2,4)-cis- asitrocinone | -5.467 | 3 Hydrogen bonds: Glu73, Gly77, Arg105 8 Hydrophobic interactions: Val92, Tyr67, Phe71, Ala108, Met74, Leu78, Phe112, Phe109 |
17 | Muricin H | -5.467 | 3 Hydrogen bonds: Arg88, Glu95, Arg105 8 Hydrophobic interactions: Val92, Tyr67, Phe71, Ala108, Met74, Leu96, Phe112, Phe109 |
18 | Annocherimolin | -5.303 | 3 Hydrogen bonds: Glu73, Asp70, Arg66 6 Hydrophobic interactions: Val92, Tyr67, Phe71, Met74, Leu96, Phe63 |
Squamocin IV recorded the lowest binding energy − 7.01 kcal/mol and the best stability in the MCL-1. The selected compounds scored between − 7.01 and − 6.217 kcal/mol compared to the native ligand whose score was − 16.595 kcal/mol. While squamocin IV formed four hydrogen bonds with Lys234, His252, Arg263, and Thr266, and nine alkyl interactions with hydrophobic residues, the Q51 native ligand formed ten H bonds with three amino acids: Thr266, Arg263, Ala227 with distances from 1.80 Aº to 2.17 Aº; additionally, a pi-stacking bond was detected with Phe270 in a distance of 4.68 Aº. (Table 6) Binding to Thr266 and Arg263 featured a core interaction in the MCL1 chemical space (Osman et al. 2021) and its stability was confirmed further by the MD simulations.
Table 6
Binding free energy and docking interactions of selected acetogenins in the binding pocket of Human Mcl-1.
| Human Mcl-1 | |
No. | Compound | Glide score (Kcal/mol) | Interactions |
1 | Squamocin IV | -7.01 | 4 Hydrogen Bonds: His252, Lys234, Arg263, Thr266 9 Hydrophobic interactions: Val274, Met250, Val253, Leu246, Leu267, Phe270, Val258, Val249 |
2 | Muricenin | -6.766 | 1 Hydrogen Bonds: Arg263 8 Hydrophobic interactions: Phe270, Val274, Leu267, Val253, Phe254, Leu246, Met250, Val249 |
3 | Squamostanin-B | -6.72 | 3 Hydrogen Bonds: Lys234, His252, Asp256 9 Hydrophobic interactions: Met231, Phe270, Val253, Val258, Phe254, Val249, Leu246, Met250, Ala227 |
4 | Rollicosin | -6.569 | 1 Hydrogen Bonds: Thr266 9 Hydrophobic interactions: Ala227, Phe228, Met231, Phe270, Val253, Leu246, Met250, Leu267, Val249 |
5 | Squamostanin-A | -6.543 | 3 Hydrogen Bonds: Asn260, Arg263, Thr266 11 Hydrophobic interactions: Ala227, Phe228, Met231, Phe270, Val253, Val258, Phe254, Val249, Leu246, Met250, Ala227 |
6 | Muricin F | -6.512 | 1 Hydrogen Bonds: Arg263, Asn223 10 Hydrophobic interactions: Ala227, Phe228, Met231, Phe270, Val253, Leu267, Phe254, Met250, Val249, Val220 |
7 | Annocatacin B | -6.505 | 1 Hydrogen Bonds: Asp256 10 Hydrophobic interactions: Ala227, Phe228, Met231, Phe270, Val253, Val258, His224, Arg263, Leu267, Met250 |
8 | Anmontanin B | -6.474 | 2 Hydrogen Bonds: Arg263, Asn260 5 Hydrophobic interactions: Ala227, Phe228, Met231, Phe270, Val253 |
9 | Annonamuricin C | -6.453 | 1 Hydrogen Bonds: Arg263 7 Hydrophobic interactions: Ala227, Phe228, Met231, Leu235, Phe270, Leu267, Val274 |
10 | Annocherimolin | -6.408 | 5 Hydrogen Bonds: His252, Arg263, Thr266, Val253, Asp256 5 Hydrophobic interactions: Val249, His224, Ala227, Met250, Phe270 |
11 | Squamocin-P | -6.38 | 1 Hydrogen Bonds: Arg263 10 Hydrophobic interactions: Ala227, Phe228, Met231, Val253, Phe254, Val249, Met250, Leu246, Val258, Leu235 |
12 | Annonamuricin B | -6.352 | 1 Hydrogen Bonds: Asp256 5 Hydrophobic interactions: Val249, Val249, Ala227, Leu246, Arg263 |
13 | Annonamuricin A | -6.325 | 2 Hydrogen Bonds: Asn260, Thr266 10 Hydrophobic interactions: Ala227, Phe228, Met231, Phe270, Val253, Phe254, Val274, Arg263, Leu246, Met250 |
14 | Annonamuricin D | -6.319 | 10 Hydrophobic interactions: Ala227, Phe228, Met231, Phe270, Val253, Phe254, Val249, Met250, Leu246, Leu267 |
15 | Calamistrin E | -6.305 | 1 Hydrogen Bonds: Arg263 9 Hydrophobic interactions: Ala227, Phe228, Met231, Val253, Leu246, Val249, Val258, Leu235, Met250 |
16 | Dotistenin | -6.26 | 2 Hydrogen Bonds: Asn260, Thr266 11 Hydrophobic interactions: Ala227, Phe228, Met231, Val253, Leu246, Val249, Val258, Met250, Leu267, Phe270, Phe254 |
17 | Annosquatin B | -6.242 | 2 Hydrogen Bonds: Asp256, Thr259 10 Hydrophobic interactions: Ala227, Phe228, Met231, Phe270, Val253, Phe254, Val274, Leu246, Val249, Val258 |
18 | Squafosacin B | -6.217 | 2 Hydrogen Bonds: Arg233, Thr266 6 Hydrophobic interactions: Ala227, Phe228, Met231, Phe270, Leu267, Val265 |
Chen et al pointed out structural activity relationships for acetogenins bioactivity as anticancer agents to be due to the THF rings, a-b-unsaturated lactone ring, the number of carbons separating the THF units where non-adjacent bis-THF with few carbons’ separation recorded the highest activity followed by adjacent bis-THF units then mono THF derivatives with the weakest effect before the non-THF acetogenins; moreover, the long alkyl flexible chain was essential for potency
(Chen et al. 2015) (Lima et al. 2022). It is worth mentioning that synthetic derivatives of acetogenins were not as effective as the natural ones and acetogenins flexiblity rendered their structural prediction of activity challenging, which supported the use of computational studies to provide accurate molecular interaction data about compounds in a time and cost-effective way (Liao et al. 2016)
The most promising compounds were selected for further molecular dynamics study Squamostanin-A (Juang et al. 2016)
The molecular dynamic trajectories in the NADH (NQO1) enzyme complex with squamostanin A in a 100ns simulation showed stability of the Root Mean Square Deviation (RMSD) values with no major conformational changes (Fig. 4). The protein residues were analyzed through the root mean square fluctuation (RMSF) values, which measured the average deviation of a particle from a reference position, and were revealed to be devoid of major changes. The probability of protein unfolding was analyzed by measuring the Rg value, which designated the human NAD[P]H-quinone oxidoreductase -Squamostanin-A complex compactness and manifested the absence of unfolding during the simulation process.
Regarding the EGFR squamostanin A complex, a sudden flip was noted between 10 and 20ns as reflected in the RMSD values; meanwhile, the loop containing region of the protein complex demonstrated major conformational changes between 50 and 60 ns that reverted back to the normal range at the end of the 100ns. The stability of the Rg values confirmed the good binding of the squamostanin A inside the binding pocket with no induction of unfolding. Unfortunately, the molecular interactions with squamostanin A were not seen to be consistent and stable here.
Annopurpuricin-A complex with BCL2 enzyme was stable in the period 3-3.5A with a slight deviation at the end of the simulation. A tendency of unfolding was revealed at the end of the simulation time according to the measured RMSF values, and some unfolding was experienced during the time 80 to 95ns. Overall, the complex showed no flexibility and remained compact.
The Mcl-1 protein complex with squamocin IV showed no conformational changes, and the fluctuations were minimal except for the C-terminal. The molecular interactions between the ligand and MCl-1, namely the four hydrogen bonds with Lys234, His252, Arg263, and Thr266 were stable during the simulation. The native ligand showed analogous binding to Arg263 and Thr266, which are core residues in the MCl-1 enzyme.
The ADME (Absorption, Distribution, Metabolism, Excretion) and drug likeness descriptors were calculated using the QikProp wizard for all the selected scaffold molecules (Table1). The filtering strategy was employed before conducting the molecular docking procedures to exclude the carbon skeletons with unpromising pharmacokinetics and pharmacodynamics. Twenty-five properties were used in the QikProp tool to indicate the molecules that lie within the 95% range of known drugs, and the rest are omitted. This favorable range is reflected through a value of #stars index, which should be between 0 and 5. All the compounds reported a suitable #Stars value in this study and were included for further analysis. Lipinski’ rule of five expressed the weight of parameters like hydrogen bonds for donors and acceptors, with a value not exceeding 5 for the former and not exceeding 10 for the latter. The hydrophobicity ratio between octanol and water or the partition coefficient value must remain equal to or less than 5 together with a molecular weight not over 500Da. By assessing solubility prediction, permeability and liver first pass factors, compounds bioavailability was estimated using the Jorgensen’s rule of three. While Caco-2 cell rate permeability (BIPcaco-2) should be greater than 22, the aqueous solubility (LogSwat) must be more than 5.7, and the metabolites number should not be over 7. In the same way, skin permeability characteristics (LogKp)together with human oral absorption (1–3) were considered.
The QPlogBB term expressed a value from 3.0 to 1.2 and indicated the absorption coefficient of the blood brain barrier. A satisfactory drug likeness was inferred as the QPlogKhsa coefficient denoting the plasma protein binding showed more than 90% binding to all of the compounds with an adequate blood brain absorption.