Table 3.
Molecular docking parameters of the interaction between Mpro and T. brownii and A. asak compounds (1–15).
| Compound |
ΔG, kcal/mol |
Receptor amino acids |
Unfavorable amino acids Interaction |
ΔG (SP), kcal/mol |
ΔG (XP), kcal/mol |
MM-GBSA, kcal/mol |
|---|---|---|---|---|---|---|
| 1 | −5.3 | Gln189, His172, Glu166, Met165, His163, Ser144, Gly143, Asn142, Leu141, Phe140 | Cys145 | −5.1 | −4.4 | −10.465 |
| 2 | −5.5 | Gln189, Glu166, Met165, His163, Cys145, Ser144, Gly143, Asn142, Leu141, Phe140 | – | −4.0 | −3.5 | −23.298 |
| 3 | −7.8 | Glu178, Val104, Phe103, Lys102, Tyr101, Lys90, Lys88, Asn84, Gln83, Ser81, Tyr37, Val35, Asp34, Asp33 | Asn180 | −4.1 | −4.6 | −27.357 |
| 4 | −9.3 | Gln192, Thr190, Gln189, Arg188, Asp187, Pro168, Glu166, Met165, His164, Cys145, Gly143, Asn142, Met49, Ser46, Thr45, His41, Leu27, Thr26, Thr25, Thr24 | – | −6.9 | −8.8 | −49.034 |
| 5 | −8.5 | Gln192, Thr190, Gln189, Arg188, Asp187, Pro168, Glu166, Met165, His164, Cys145, Gly143, Asn142, Met49, Ser46, Thr45, Cys44, His41, Leu27, Thr26, Thr25, Thr24 | – | −7.6 | −8.0 | −47.075 |
| 6 | −7.2 | Val186, Pro184, Gly183, Phe181, Asn180, Gly179, Phe134, Arg105, Cys85, Asn84, Arg40 | – | −3.2 | −3.9 | −22.253 |
| 7 | −7.1 | Gln189, Pro168, Glu166, His164, His163, Cys145, Ser144, Gly143, Asn142, Leu141, Phe140, Tyr118, Met49, Ser46, Leu27, Thr26, Thr25 | His41 | −4.3 | −4.7 | −26.741 |
| 8 | −7.7 | Arg188, Val186, Phe185, Pro184, Phe181, Asn180, Arg105, Cys85, Asn84, Tyr54, Arg40 | Gly183 | −0.3 | −1.3 | −27.919 |
| 9 | −7.7 | Glu178, Phe103, Lys102, Tyr101, Lys100, Lys90, Leu89, Lys88, Gln83, His80, Tyr37, Val36, Val35, Asp33 | Ser81 | −2.2 | −3.0 | −23.299 |
| 10 | −8.1 | Gln192, Thr190, Gln189, Arg188, Asp187, Pro168, Leu167, Glu166, Met165, His164, Cys145, Gly143, Asn142, Met49, His41, Leu27, Thr26, Thr25 | – | −5.5 | −7.0 | −38.182 |
| 11 | −7.3 | Gln192, Thr190, Gln189, Arg188, His172, Glu166, Met165, His164, Cys145, Ser144, Gly143, Asn142, Leu141, Phe140, Met49, His41 | His163 | −2.0 | −6.2 | −10.414 |
| 12 | −7.4 | Gln189, Arg188, Asp187, His172, Glu166, Met165, His164, His163, Cys145, Ser144, Leu141, Phe140, Tyr54, Met49, His41 | – | −5.0 | −5.6 | −20.124 |
| 13 | −7.4 | Gln192, Thr190, Gln189, Arg188, Glu166, Met165, His163, Cys145, Ser144, Gly143, Asn142, Leu141, Phe140 | – | −5.0 | −3.9 | −15.923 |
| 14 | −7.8 | Gln189, Arg188, Asp187, His172, Glu166, Met165, His164, Cys145, Gly143, Asn142, Leu141, Phe140, Tyr54, Pro52, Met49, His41 | – | −5.3 | −6.7 | −30.814 |
| 15 | −7.4 | Gln189, His172, Glu166, Met165, His163, Cys145, Ser144, Gly143, Asn142, Leu141, Phe140, Met49, Ser46, Thr45, Cys44, Thr25, Thr24 | Thr26 | −4.8 | −6.2 | −21.713 |
| Ritonavir (Control) |
−8.2 | Gln192, Ala191, Thr190, Gln189, Arg188, Asp187, His172, Pro168, Leu167, Glu166, Met165, His164, His163, Ser144, Gly143, Asn142, Leu141, Phe140, Tyr54, Met49, His41, Leu27, Thr26, Thr25 | – | – | – | – |
Arg: Arginine; Asn: Asparagine; Asp: Aspartic acid; Cys: Cysteine; Glu: Glutamic acid; Gln: Glutamine; Gly: Glycine; His: Histidine; Leu: Leucine; Lys: Lysine; Met: Methionine; Phe: Phenylalanine; Pro: Proline; Ser: Serine; Thr: Threonine; Tyr: Tyrosine; Val: Valine. ΔG (SP), and ΔG (XP): docking scores obtained under standard-precision, and extra-precision docking modes using Glide software (Schrodinger, LLC, NY, USA).