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Table 2 Analysis of molecular interactions for the bioactive compounds and the control medication

From: Evaluation of therapeutic potentials of some bioactive compounds in selected African plants targeting main protease (Mpro) in SARS-CoV-2: a molecular docking study

S/N

Plant source

Bioactive compounds

Binding energy (kcal/mol)

Number of hydrogen bond (s) formed

Residues involved in hydrogen bond formation (Ã…)

Residues involved in hydrophobic interaction (Ã…)

Residues involved in π-stacking (Å)

1

Adansonia digitata L

Catechin

− 7.1

6

Ser144(2.32,2.34)

His163(2.32)

Glu166(3.36,2.74)

Asp187(3.35

Met165(3.47)

Gln189(3.87)

 
  

Epicatechin

− 7.1

5

Thr26(3.34,1.93)

Tyr54(3.67,3.44)

Gly143(2.51)

Met165(3.39)

Gln189(3.68)

His41(4.81)

  

Vitexin

− 8.0

3

Asp187(2.15)

Gln189(2.78)

Thr190(2.68)

His41(3.88)

Glu166(3.61)

Gln189(3.86)

 
  

Quercetin

− 7.3

4

Phe140(2.71)

Thr190(3.22,2.04)Gln192(2.84

Met165(3.72)

Glu166(3.03)

Gln189(3.98)

 
  

Kaempferol

− 7.2

6

Thr26(2.22)

Gly143(2.19)

Ser144(3.11,2.28)

Cys145(2.37)

His163(3.13)

Glu166(3.86)

 
 

Aframomum melegueta K. Schum

n-Hexadecanoic acid

− 3.8

1

Gly275(2.03)

Phe223(3.73)

Glu270(3.37)

Leu271(3.63)

 
  

Corymbolone

− 5.6

3

Phe219(2.33)

Arg279(2.79,2.67)

Glu270(3.59,3.66)

 
  

Gamma-Sitosterol

− 6.8

–

 

Val104(3.88,3.45)

Ile106(3.82)

Ile249(3.68)

Phe294(3.62,3.41,3.50,3.94)

 
  

Myrtenyl acetate

− 5.1

–

 

Trp218(3.60)

Glu270(3.36)

Leu271(3.52)

Asn274(3.79)

 
  

Gamma-Muurolene

− 5.7

–

 

Thr199(3.80)

Tyr237(3.58)

Leu272(3.72)

Leu286(3.67)

Leu287(3.68,3.86)

 
  

Isonicotinic acid

− 4.3

2

Asn221(2.70)

Gly275(2.37)

Glu270(3.74)

 
 

Ageratum conyzoides (L.) L

Azulene

− 5.6

-

 

Trp218(3.69)

Asn221(3.68)

Phe223(3.79)

Glu270(3.70,3.69)

Leu271(3.45)

 
  

Norfenefrine

− 4.8

4

Gly15(1.89)

Gly71(2.63)

Asn95(2.92)

Gly120(2.53)

Trp31(3.92)

Lys97(4.64)

  

Kaur-16-ene

− 6.5

–

 

Trp218(3.60)

Arg222(3.77)

Glu270(3.73)

Asn274(3.74)

 
  

2-Acetylcyclopentanone

− 4.3

2

Arg279(2.90,2.39)

Glu270(3.69)

Asn274(3.78)

 
  

Alpha-Calacorene

− 5.8

–

 

Tyr239(3.50)

Leu286(3.67)

Leu287(3.80,3.73)

 
  

Longipinocarveol, trans-

− 6.2

2

Lys102(2.83)

Ser158(2.16)

Asp153(3.75)

Phe294(3.72,3.85,3.68)

 
 

Boswellia dalzielii Hutch

Lavandulol

− 4.4

3

Phe219(1.84)

Asn221(3.56)

Leu271(3.57)

Asn221(3.66)

Phe223(3.61)

Glu270(3.72)

Asn274(3.69)

 
  

Cyperene

− 6.1

  

Trp218(3.75)

Asn221(3.71)

Phe223(3.60)

Glu270(3.89,3.60)

Leu271(3.58)

Asn274(3.86)

 
  

Aromadendrene

− 6.1

  

Phe8(3.81)

Val104(3.61)

Ile106(3.68)

Gln110(3.79)

Asp153(3.93)

Phe294(3.52,3.52)

 
  

Viridiflorol

− 6.0

1

Gln110(2.06)

Val104(3.86)

Ile106(3.68)

Gln110(3.39)

Asn151(3.64)

Phe294(3.95,3.65,3.76,3.89)

 
  

Cis-Chrysanthemol

− 4.4

–

–

Phe3(3.31)

Lys5(3.68)

Leu282(3.84)

Glu288(3.56)

Phe291(3.90,3.96)

 
  

Beta-Phellandrene

− 4.5

–

 

Phe3(3.56)

Leu282(3.38)

Glu288(3.75)

Phe291(3.57)

 
  

Remdesivir

− 6.3

8

Arg131(3.02,2.69)

Lys137(2.60)

Thr199(1.92)

Tyr237(3.41)

Tyr239(2.93)

Leu287(1.99)

Asp289(1.93)

Tyr237(3.60)

Leu272(3.70)

Leu286(3.71,3.81)

Leu287(3.47)

 
  1. Compounds in bold letters are the best-hit ligands