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Quantitative structure-property relationships (QSPR) of valency based topological indices with Covid-19 drugs and application
⁎Corresponding author. attari_ab092@yahoo.com (Abdul Rauf), abdul.rauf@aumc.edu.pk (Abdul Rauf),
-
Received: ,
Accepted: ,
This article was originally published by Elsevier and was migrated to Scientific Scholar after the change of Publisher.
Abstract
The purpose of this analysis is to establish a quantitative structure–property relationship (QSPR) between eV and ve-degree based topological descriptors and measured physicochemical parameters of phytochemicals screened against SARS-CoV-2 . A computer-based algorithm is developed to compute the eV and ve-degree based topological indices for the considered graphs. Our study revealed that the eV-degree based Zagreb index and ve-degree based first beta Zagreb index are two important topological indices that can be useful in the prediction of molecular weight and the topological polar surface area of phytochemicals. Applications to certain anticancer drug (Camptothecin-Polymer Conjugate IT-101) are presented at the end.
Keywords
Ev-degree
Ve-degree
Topological indices
Quantitative Structure-Property Relationships (QSPR)
Camptothecin-Polymer Conjugate IT-101
05C09
05C92
92E10

1 Introduction
Chemical graph theory is a branch of science which deals with the graphical representation of the chemical structure. In chemistry, the chemical compounds that have the same molecular formula but different structure are called isomers. In chemical graph theory, the vertices represent the atoms and the edges represent the bonds. Chemical graph theory is used in the modeling of the molecular structure of chemical compounds and also to study their chemical and physical properties. Due to its wide-ranging applications in various fields of life such as electrical networks, biological networks, chemistry, computer science and drug designs, it attains much attention of researchers (Hosamani et al., 2017; Li et al., 2021; Shao et al., 2018). Recently, a mixture field of information science, chemistry and mathematics have been developed, the so-called chem-informatics.
Several viral diseases continue to emerge causing serious public health issue. Among these viral diseases severe acute respiratory coronavirus syndrome (SAR-CoV) were reported in 2002 and 2003 and H1N1 influenza in 2009. A fatal respiratory disease as a result of novel coronavirus strain was reported at the end of 2019 (Xu et al., 2020). Soon after that researcher, Chinese health authorities and Centers for Disease Control and Prevention (CDC) had taken swift action against the disease. WHO temporarily named this virus as a novel coronavirus (2019-nCoV) (Ji et al., 2020).
The first complete 2019-nCoV genome sequence was published on 10 January 2020. On 12 February 2020 the WHO classified the 2019-nCoV pathogen permanently as SARS-CoV-2 and coronavirus disease 2019 as COVID-19. This outbreak was officially declares as pandemic on March 11, 2020 by WHO. Typically, after transcription of the genome, beta-coronaviruses generate 800 k Da polypeptide. Proteolytic clamping for several proteins is achieved. Proteolytic treatment is mediated by papain-like protease ( ) and 3-chymotrypsin-like protease (3CLpro). Potential inhibitors have been identified for SARS-CoV and MERS-CoV based on the structure of activity tests and high throughput studies (Ghosh et al., 2005; Kumar et al., 2016; Pillaiyar et al., 2016). This research is therefore carried out to gain structural insights of SARS-CoV- and to detect powerful natural compounds to battle COVID-19.
The first emergency use (EUA) vaccine for COVID-19 was released by Food and Drug Administration (FDA) On December 11, 2020. WHO listed Pfizer/BioNtech Comirnaty vaccine in Emergency Use Listing (EUL) on December 31, 2020. On February 16, 2021 the SII/Covishield and AstraZeneca/AZD1222 vaccines, on March 12, 2021 the Janssen/Ad26.COV 2.S developed by Johnson & Johnson and on April 30, 2021 the Moderna COVID-19 vaccine (mRNA 1273) was listed in WHO Emergency Use Listing (EUL). On May 7, 2021 the Sinopharm COVID-19 vaccine was listed for EUL and was produced by the China National Biotec Group. Globally, 165,772,430 confirmed COVID-19 cases were registered to the WHO till May 22, 2021 including 3,437,545 deaths. Various clinicians and researchers are focusing on research and production of antivirals using various methods that combine experimental and in silico (Kumar et al., 2016 Jul 1; Mittal et al., 2019; Muralidharan et al., 2020; Nutho et al., 2020; Needle et al., 2015; Pant et al., 2020; Pushpakom et al., 2019; ul Qamar et al., 2020). The SARS-CoV-2 replication cycle can be broken down into three steps: viral RNA replication, viral entry and viral assembly and evacuation from the host cell, as shown in Fig. 1.SARS-COV-19 replication cycle.
The genome sequence of SARS-CoV-2 was found to be very similar to that of SARS-CoV in recent studies. SARS-CoV-
-screened phytochemicals as given in Figs. 2–7 are recently published in (ul Qamar et al., 2020) and several researchers are working to find better and productive instruments and medicines to combat diseases.
Topological indices are often characterized by using vertex and edge degree-based concepts and play an important role in theoretical chemistry. The first topological descriptor was put forward by Wiener (1947) and is related with the critical point, boiling points, and density of paraffin. The Randic index was proposed by Randic in 1975 (Randic, 1975) and generalized by Bollobás and Erdös (1998). The first and second Zagreb index was introduced by Gutman and Trinajstic (1972) about forty years ago. The atom-bond connectivity (ABC) index was initiated by Estrada et al. (1998) and geometric-arithmetic index was introduced by Vukičević and Furtula (2009). The ve-degree and eV-degree definitions were introduced by Chellali et al. (2017). The work of Chellali et al. was investigated by Horoldagva (2019) and mathematical concepts were developed. The degree-based ideology transformed into ve-degree, eV-degree, degree-based M-polynomial and NM-polynomials and degree-based entropy. Various researchers calculated the different topological indices for COVID drugs-related structures, for the help of the production of antivirals (Rauf et al., 2021; Al-Ahmadi et al., 2021; Saleh et al., 2021). Liu et al. (2021) studied the structural properties by using bond additive and distance based topological descriptors of antiviral medications for the treatment of COVID 19 such as hydroxychloroquine, chloroquine, lopinavir, theaflavin, ritonavir, remdesivir, nafamostat, umifenovir, bevacizumab, and camostat. Topological indices of chloroquine, theaflavin, remdesivir and hydroxychloroquine are computed in (Mondal et al., 2020). Nandini, G. Kirithiga, et al. have computed topological indices of pandemic trees, corona product of Christmas trees and paths (Nandini et al., 2020). Mondal, Sourav, et al. calculated the multiplicative degree-based indices for some anti-COVID-19 chemicals such as hydroxychloroquine, theaflavin and remdesivir (GS-5734) (Mondal et al., 2020). Wei, Jianxin, et al. calculated the reverse indices for remdesivir (GS-5734) (Wei et al., 2021). Kirmani, Syed Ajaz K., Parvez Ali, and Faizul Azam investigated several antiviral drugs and QSPR was established between topological indices and various physical/chemical properties of antiviral drugs (Kirmani et al., 2021).
In the QSPR study, the bioactivity of chemical compounds can be predicted by using topological indices. Shirakol et al. (2019) study the QSPR analysis of degree-distance and distance based topological indices for their predicting power. Similarly, Luccic et al. (2001) study the QSPR for novel distance-related indices. Using modified Xu and atom-type-based AI topological indices a QSPR was performed for the prediction of enthalpies of 134 acyclic alkanes by Safa and Yekta (2017). H. Sunilkumar et al. studied the QSPR analysis of degree-based topological indices to characterize the useful topological indices based on their predicting power (Hosamani et al., 2017). For more details on QSPR study of topological indices see (Mondal et al., 2021; Sahoo et al., 2011). The main objective of this paper is to establish a relation between topological descriptors and physical/chemical parameters of phytochemicals that are used for screening against SARS-CoV- in a quantitative structure–property. In this paper, we have considered five ve and eV-degree based topological indices see (Şahin1 and Ediz, 2018).
Let G be a connected graph with vertex set and edge set denoted by and respectively. For any , let represent the degree of the vertex and is the number of edges linked to v. The open neighborhood of the vertex v is the set of all vertices that are adjacent to v. The closed neighborhood of v, denoted by is defined as the union of v vertex with open neighborhood of v. The eV-degree of any edge , denoted by is the total number of the vertices of closed neighborhoods of the end vertices of an edge e. The ve-degree of any vertex , denoted by is the total number of edges which are adjacent to v and the first neighbor of v, i.e., the sum of degrees of all closed neighbourhood vertices of v.
Ev-degree based indices
The indices based on eV-degree, such as the Zagreb index ( ) and the Randic index ( ) for any edge are defined as
Ve-degree based index
For any vertex , the first Zagreb alpha index ( ) based on ve-degree is defined as
Ve-degree of end vertices of each edge
The first and second Zagreb beta index denoted by
and
respectively of each edge
based on ve-degree of end vertices are defined as
The distribution of the sections has the following details, see the procedure detail in Fig. 8. Section 2 describe the schematic computer-based algorithm to calculate the degree vector, ve-degree vector, and eV-degree matrix and the respective topological indices for a given graph through Maple software. The Section 4 describes the quantitative-structure–property analysis (QSPR) of phytochemicals screened against SARS-CoV-
with the help of eV and ve degree-based topological descriptors. Applications to certain anticancer drug (Camptothecin-Polymer Conjugate IT-101) is presented in Section 5. Section 6 is the numerical results and discussion and Section 7 is conclusion. Section 3 describes an illustrative example to demonstrate the algorithm described in Section 2.Working flowchart.
2 Algorithm
1: Start
2: Input: M is adjacency matrix of a Graph.
3: Output: Calculation of Ve-Degree, Ev-degree, Ve-degrees of end vertices of each edge, and the Ev and Ve degree based topological indices.
4: Initialization: E ←No. of edges, V ←No. of vertex, con[E] ←connection matrix, deg[V] ←degree of each vertex, VE←VE-Degree of vertices, deg [VE] ←No. of edges incident to the closed neighborhood vertices, EV←EV-Degree of adjacent vertices, deg[EV] ←the sum of the degree of two adjacent vertices, ver[V] ←Vertex list, count ←1, adj[count] ←adjacent element, Mq[count] ←VE-Degree matrices elements, Mp[count] ←EV-Degree matrices elements.
5: loop a = 1 to V
6: For each vertex from the array ver[V].
7: loop b = 1 to E
8:
count corresponding vertex from the matrix con[E].
9:
b++
10: end loop
11: deg[V] = count.
12: loop c = 1 to count
13:
adj[count] = store corresponding vertex.
14:
c++
15: end loop
16: loop d = 1 to deg[V]count
17:
Multiply Matrix M and adj[count]
18:
Store the result of the above as VE
19:
d++
20: end loop
21: loop e = 1 to V
22:
loop f = 1 to V
23:
Summation of deg[V][e] with deg[V][f] and multiply by (i,j) th element of Adjacency Matrix.
24:
Store the result of the above as EV
25:
f++
26:
end loop
27: e++
28: end loop
29: end loop
30: loop g = 1 to VE
31: For each vertex from the array VE
32: loop h = 1 to VE
33:
count vertex from the matrix for VE
34: end loop
35: deg[VE]=count
36: loop k = 1 to count
37:
Mq[count]= store vertices for VE.
38:
k++
39: end loop
40: end loop
41: loop l = 1 to EV
42: For each adjacent vertex from the array EV
43: loop m = 1 to EV
44:
count corresponding vertices from the array EV
45:
m++
46: end loop
47: deg[EV]=count
48: loop n = 1 to count
49:
Mp[count]=store EV
50:
n++
51: end loop
52: end loop
53: loop o = 1 to count
54: Calculate the VE-Degree based first Zagreb Alpha index.
55: end loop
56: loop p = 1 to count
57: Calculate the EV-Degree based Zagreb Index and Randic Index.
58: end loop
59: loop q = 1 to E
60: Calculate the End Vertices Ve degree for each Edge, the first and second Zagreb beta index based on the ve-degree of end vertices of each edge, the first Zagreb alpha index based on ve-degree, the Zagreb and Randic index based on eV-degree.
61: end loop
62: end
a, b, c, d, e, f, g, h, k, l, m, n, o, p and q all are variables whose data type is an integer. We are using these variables for iterating through the matrix using indices in a loop.
3 Illustrative example on Algorithm
We calculated the degree vector, ve-degree vector, and eV-degree matrix and the respective topological indices for a given graph through the Maple algorithm given above. For this we consider the example of starphene graph (S) for
and
, see Fig. 9. First, we write the adjacency matrix (A) of the graph S in MAPLE. We get the adjacency matrix A by newGraph software (procedure mentioned in (Hayat and Khan, 2021)). As there are 18 vertices in the graph, the order of the A will be 18–18 and from figure it is clear that the graph S has 21 edges.
Now, with the help of the adjacency matrix we can calculate the degree of vertices, Ve-degree and Ev-degree. The degree of a vertex can be obtained by adding the entries of the corresponding row and we get the degree sequence of starphene graph S in the form of row matrix B.
Note that the degree sequence is according to the vertices labeled in Fig. 9. For Ve-degree of vertices, we multiplied the adjacency matrix A and B. The column matrix AB represent the Ve-degree of vertices.
Let
denote the entry in the i-th row and j-th column of adjacency matrix A and
denoted the i-th entry of row matrix B. We multiply the entry
of adjacency matrix A with the entry
to obtain a entry
of matrix L. The nonzero entries in the upper/lower triangular form of this matrix L give the Ev-degree list of the given graph.
We use separate formula commands against each index. The calculated values of the topological indices for the given graph are
Molecular structure of starphene for
and
.
4 Quality testing analysis
In this section, we study the QSPR of phytochemicals that are used for screening against SARS- CoV-
using eV and ve degree-based topological descriptors. The productivity of the topological indices listed above was checked using the phytochemical data set contained in (Balaban, 1982) and https://pubchem.ncbi.nlm.nih.gov/. The data contains the information of the following variables: binding affinity, molecular weight, docking score and topological polar surface. IDs of phytochemicals are mentioned in Table 1 and their properties in Table 2. We could not found topological polar surface and molecular weight of NPACT00105. Therefore, we do not include NPACT00105 for QSPR. Ve-degree and eV-degree based topological indices are presented in Table 3. Table 4 shows the results of correlation coefficients between each pair of variables. We note that all the results are highly significant at 1% level of significance. This shows that there exists a strong positive linear bivariate relationship in the group of variables. The same extent of correlation is depicted in the Figs. (10) and (11). The table suggests that molecular weight (MW) and topological polar surface (TPS) depend on other indices such as
and
. Keeping in mind the above relationships, we consider the following linear regression model for prediction analyses. (see Fig. 12)
Where P consists of either MW or TPS and TI denotes a predictor in the list (
).
1610052
Myricitrin
5281673
6479915
NPACT00105
10930068
5273567
5318606
Licoleafol
1111196
Amaranthin
6123095
Nelfinavir
64143
Prulifloxacin
65947
Colistin
5311054
1610052
−16.35
−29.57
354.40
107
5281673
−15.64
−22.13
464.40
207
6479915
−15.44
−20.62
374.30
134
NPACT00105
−14.42
−19.10
0.00
00
10930068
−14.41
−19.47
602.50
253
5273567
−14.36
−19.87
478.40
186
5318606
−13.70
−18.42
480.40
227
1111196
−13.63
−19.64
372.40
127
6123095
−12.67
−18.14
726.60
346
64143
−12.20
−17.31
567.80
127
65947
−11.32
−15.40
461.50
125
5311054
−13.73
−18.57
1155.40
491
PubChem IDs
11610052
1306
29.5225
1532
590
1954
5281673
1664
50.0469
2005
766
2699
6479915
1270
20.7257
1505
578
1855
NPACT00105
1532
22.9972
1857
700
2359
10930068
2190
32.5014
2110
1226
4862
5273567
1802
27.2264
2152
816
2784
5318606
1736
24.5579
1902
726
2404
11111496
1450
18.4823
1748
591
2197
6123095
2909
41.731
3483
1284
4822
64143
3000
37.4362
3602
1139
4801
605947
1804
24.0714
2133
804
2943
5311054
6116
76.8146
7152
2638
9107
MW
TPS
MW
1.000
0.934
0.974
0.873
0.961
0.987
0.970
TPS
1.000
0.846
0.816
0.826
0.886
0.847
1.000
0.880
0.996
0.986
0.975
1.000
0.880
0.883
0.861
1.000
0.969
0.955
1.000
0.989
1.000
Graphical representation of linear regression model between topological indices and molecular weight.
Graphical representation of linear regression model between topological indices and topological polar surface.
Molecular Structure of IT-101. The components of the parentpolymer are polyethylene glycol and
-cyclodextrin. Camptothecin is attached to the polymer via a single glycine amino acid linker, where n and m represent the number of repeating units of ethylene glycol and cyclodextrin-based polymer-camptothecin in the polymer-camptothecin conjugate respectively.
Based on the data in Table 3 with 12 observations in each variable, we have the following estimated regression equations which can be used to predict molecular weight for a given value of any index and .
Table 5 gives the results for correlation coefficient (r), coefficient of determination (
), F-statistic (F) and standard error of the estimates (s) for simple linear regression models between MW and various predictors. The results exhibit that the estimated model of MW on
consists of highest coefficient of determination and F-value (
= 0.9742, F = 375.812) and least standard error (s = 37.0609). This means that the model is highly significant. The only index
has a high influence on MW and the observed values fall closer to the fitted line. Thus,
is the best predictor of molecular weight. Similarly,
predicts molecular weight better than others after
. A priority list of indices according to their performance is given in Table 7.
X
r
F
s
0.9737
0.9481
182.3956
52.4815
0.8729
0.762
31.996
112.3313
0.9606
0.9228
119.339
64.0086
0.987
0.9742
375.812
37.0609
0.9705
0.9419
161.769
55.5432
Following are the estimated models for predicting topological polar surface for a given value of any index and . The estimation results are based on the data in Table 3 with 12 observations in each variable.
Table 6 gives the results of various statistics for bivariate regression equations of TPS on either of
and
. We observe that the estimated regression of TPS on
possesses highest values of coefficient of determination and F-statistic (
= 0.7850, F = 36.529) and least value of standard error of regression (s = 54.4280). The results reveal that the regression model (TPS on
) is highly significant. TPS is highly determined by only
and the estimated line fits the observations closer than other lines. Hence,
seems to the best predictor of topological polar surface as well. The hierarchical order of the indices according to their performance is shown in Table 7.
X
r
F
s
0.8458
0.7154
25.140
62.6308
0.8160
0.6659
19.925
67.8686
0.8259
0.6821
21.457
66.1960
0.8860
0.7850
36.529
54.4280
0.8467
0.7169
25.324
62.4670
Index
Priority-wise Position
1
2
3
4
5
Based on correlation and regression analyses, we may conclude that both molecular weight and the topological polar surface can be predicted well by the indices in the order mentioned in Table 7. However, these indices cannot determine the other variables well such as docking scores (DS) and binding affinity (BA). Table 8 shows the results of the bivariate correlation coefficient which are all insignificant. This means that DS and BA are not linearly correlated with all the indices
,
and
. Thus, linear regression cannot model their relationship.
DS
BA
DS
1.000
0.840
0.311
0.015
0.322
0.257
0.325
BA
1.000
0.306
0.039
0.304
0.285
0.329
5 Camptothecin-Polymer Conjugate IT-101
Camptothecin (CA) is an alkaloid with a unique anticancer function, operates with a vital and unique mechanism of the action to target the topoisomerase (I) nuclear enzyme. The development of a large range of tumors is inhibited by CA. IT-101 is a conjugate of camptothecin with a cyclodextrin-based polymer (Schluep et al., 2006). Topoisomerase I is affected by a drug known as Camptothecin, derived from the Chinese tree, that allows the DNA cleavage, but it inhibits the subsequent ligation and breaks the DNA chain. The systemic application of the camptothecin has some limitations due to severe toxicity. Camptothecin shows potent in vitro anti-glioma activity, making it another common polymer delivery candidate. In the 9L gliosarcoma rat model, sodium salt of camptothecin loaded into 50 percent polymers was checked and resulted in a substantial survival increase (Thomas et al., 2004). The median survival with camptothecin polymers was nineteen days in the model of control rats and up to 120 days. Compared with controls, when we used direct intratumoral injection of our drug camptothecin without polymer then it showed no betterment in the survival (Liu et al., 2000). Studies integrating camptothecin into 50% polymers for the treatment of 9L gliosarcoma in the rats. It gives protection and efficacy with the survival of 69 days in animals that were treated with the drug camptothecin. Under similar conditions, polymer administration of intracranial camptothecin showed a substantial betterment in survival as compared with the alone camptothecin (Schultz, 1973). In our work, we compute five ve-degree and eV-degree based topological indices (Chen et al., 2021) of Camptothecin-Polymer Conjugate IT-101. The vertex set of Camptothecin-Polymer Conjugate IT-101 can be partitioned in four set based on the degree of vertices. There are vertices of degree vertices of degree vertices of degree 3 and vertices of degree 4. Similarly, the Edge partition of IT-101 based on the degree of end vertices i and j of an edge is as follows; with edges, with edges, with edges, with edges, with edges, with edges, with edges and with edges.
Let H be a molecular graph of Camptothecin-Polymer Conjugate IT-101 structure, then eV-degrees based Zagreb index and eV-degree based Randic index are given by,
(a) .
(b) . .
By using the definition, we have calculated the eV-degree of the each edge partition as shown in Table 1.
Frequency | ||
---|---|---|
3 | ||
4 | ||
5 | ||
5 | ||
6 | ||
6 | ||
7 | ||
8 |
Frequency | ||
---|---|---|
1 | 2 | |
1 | 3 | |
1 | 4 | |
2 | 5 | |
2 | 6 | |
2 | 7 | |
2 | 8 | |
3 | 7 | |
3 | 8 | |
3 | 9 | |
3 | 10 | |
4 | 6 | 2 |
4 | 7 | |
4 | 8 | |
4 | 9 | |
4 | 10 | |
4 | 11 | |
4 | 12 |
(a) The Zagreb index
(b) The Randic index
Let H be a molecular graph of Camptothecin-Polymer Conjugate IT-101 structure, then vertex ve-degree based first Zagreb -index is
By using the definition, the ve-degrees of the vertices are computed. This computation is presented Table 2.
By using the above table, we have a first ve-degree based Zagreb -index.
Let H be a molecular graph of Camptothecin-Polymer Conjugate IT-101 structure, then ve-degree based indices of end vertices of each edges are given by,
(a) .
(b) .
According to definition of ve-degree of end vertices of each edge, we divides the edges into 46 partitions i.e., respectively, as shown in Table 3.
By using the table we can compute indices based on ve-degree of end vertices of each edge as (a) The first Zagreb -index
(b) The second Zagreb -index
6 Numerical results
In this section, we will discuss the numerical results related to the eV-degree and ve-degree based topological descriptors for the Camptothecin-Polymer Conjugate IT-101 molecular structures. We have used different values of m and n and computed numerical values for the eV-degree and ve-degree based indices such as
and
for the Camptothecin-Polymer Conjugate IT-101 structures. (see Table 11).
Edge
Frequency
(2, 5)
(3, 7)
(3, 8)
(3, 9)
(4, 6)
6
(4, 7)
(4, 8)
(4, 9)
(4, 10)
(4, 11)
(6, 8)
(7, 7)
(5, 8)
(5, 11)
(7, 7)
(7, 12)
(8, 8)
(8, 9)
(8, 11)
(7, 7)
(7, 8)
(7, 9)
(7, 10)
(8, 8)
(8, 9)
(8, 10)
(9, 10)
(10, 10)
(7, 8)
(7, 12)
(8, 8)
(8, 9)
m
(10, 8)
(8, 11)
(9, 6)
(9, 11)
m
(10, 7)
(10, 12)
(7, 10)
(8, 8)
mn
(8, 9)
(8, 11)
(10, 12)
(11, 11)
(9, 11)
(9, 9)
1
We can see in Table 12 and Figs. 13–15 that value topological descriptors increases when we increase the value of m and n. The Zagreb types indices were found to occur for the computation of the total
-electron energy of molecules; thus, for higher values of m and n, the total
-electron energy is increasing. The Randić index is used in the study of the chemical similarity of molecular compounds and in computing the Kovats constants and boiling point of molecules. The results shows that the value of Randic index increases and with the increase in value of m and n.
10512
133.0960589
12288
4626
16722
21160
267.3542194
24830
9307
33650
32208
406.7136921
37884
14148
51090
43656
551.1744769
51450
19149
69042
55504
700.7365737
65528
24310
87506
67752
855.3999827
80118
29631
106482
80400
1015.164704
95220
35112
125970
93448
1180.030738
110834
40753
145970
106896
1349.998082
126960
46554
166482
120744
1525.066740
143598
52515
187506
The eV-degrees based indices, (a) The Zagreb index, (b) The Randic index.
The first Zagreb
-index.
(a) The first Zagreb
-index, (b) The second
-Zagreb index.
7 Conclusion
We proposed topological indices based on eV-degree and ve-degree concepts. It has been shown that these indices can be used as predictive means in QSPR researches. The predictive power of these indices has been tested by using some physiochemical properties of COVID drug-related compounds. Acquired results show that all the results are highly significant and there exists a strong positive linear bivariate relationship in the molecular weight, topological polar surface, and the used topological indices. But the indices cannot determine docking scores and binding affinity, and the results are insignificant for these chemical properties. The index is the best predictor of topological polar surface and molecular weight. has a high influence on topological polar surface and molecular weight. The observed values fall closer to the fitted line. Moreover, the ve-degree and eV-degree based topological indices of anti-tumor drug Camptothecin-Polymer Conjugate IT-101 have been calculated at the end.
Declaration of Competing Interest
None.
References
- Downhill Zagreb Topological Indices and M dn-Polynomial of Some Chemical Structures Applied for the Treatment of COVID-19 Patients. Open Journal of Applied Sciences. 2021;10(04):395.
- [Google Scholar]
- Highly discriminating distance-based topological index. Chemical physics letters. 1982;89(5):399-404.
- [Google Scholar]
- On ve-degree-and ev-degree-based topological properties of crystallographic structure of cuprite Cu2O. Open Chemistry. 2021;19(1):576-585.
- [Google Scholar]
- Indian J. Chem.. 1998;37A:849-855.
- Design and synthesis of peptidomimetic severe acute respiratory syndrome chymotrypsin-like protease inhibitors. Journal of medicinal chemistry. 2005;48(22):6767-6771.
- [Google Scholar]
- Chem. Phys. Lett.. 1972;17:535-538.
- Quality testing of spectrum-based valency descriptors for polycyclic aromatic hydrocarbons with applications. J. Mol. Struct.. 2021;1228:129789.
- [Google Scholar]
- Kinkar Ch Das, and Tsend-Ayush Selenge. On ve-degree and evdegree of graphs. Discrete Optimization. 2019;31:1-7.
- [Google Scholar]
- QSPR analysis of certain graph theocratical matrices and their corresponding energy. Applied Mathematics and Nonlinear Sciences. 2017;2(1):131-150.
- [Google Scholar]
- QSPR analysis of certain degree based topological indices. J. Stat. Appl. Pro. 2017;6(2):361-371.
- [Google Scholar]
- Cross-species transmission of the newly identified coronavirus 2019-nCoV. Journal of medical virology. 2020;92(4):433-440.
- [Google Scholar]
- Kirmani, Syed Ajaz K., Parvez Ali, and Faizul Azam. Topological indices and QSPR/QSAR analysis of some antiviral drugs being investigated for the treatment of COVID-19 patients. International Journal of Quantum Chemistry 121, no. 9 (2021): e26594.
- Identification, synthesis and evaluation of SARS-CoV and MERS-CoV 3C-like protease inhibitors. Bioorganic and medicinal chemistry. 2016;24(13):3035-3042.
- [Google Scholar]
- Identification, synthesis and evaluation of SARS-CoV and MERS-CoV 3C-like protease inhibitors. Bioorganic & medicinal chemistry.. 2016 1;24(13):3035-3042.
- [Google Scholar]
- Yi-Xia Li, Abdul Rauf, Muhammad Naeem, Muhammad Ahsan Binyamin, Adnan Aslam, Valency-Based Topological Properties of Linear Hexagonal Chain and Hammer-Like Benzenoid, Complexity, vol. 2021, 2021.
- Liu, L.F., Desai, S.D., LI, T.K., Mao, Y., Sun, M.E.I. and SIM, S.P., 2000. Mechanism of action of camptothecin. Annals of the New York Academy of Sciences, 922(1), pp.1-10.
- Liu, Jia-Bao, Micheal Arockiaraj, M. Arulperumjothi, and Savari Prabhu. Distance based and bond additive topological indices of certain repurposed antiviral drug compounds tested for treating COVID-19. International Journal of Quantum Chemistry 121, no. 10 (2021): e26617.
- Distance-related indexes in the quantitative structure- property relationship modeling. Journal of chemical information and computer sciences. 2001;41(3):527-535.
- [Google Scholar]
- Conformational characterization of linker revealed the mechanism of cavity formation by 227G in BVDV RDRP. J. Phys. Chem. B. 2019;123(29):6150-6160.
- [Google Scholar]
- Topological indices of some chemical structures applied for the treatment of COVID-19 patients. Polycyclic Aromat. Compd. 2020:1-15.
- [Google Scholar]
- Mondal, Sourav, Nilanjan De, Anita Pal, and Wei Gao. Molecular descriptors of some chemicals that prevent COVID-19. Current organic synthesis (2020).
- QSPR analysis of some novel neighbourhood degree-based topological descriptors. Complex & Intelligent Systems. 2021;7(2):977-996.
- [Google Scholar]
- Computational studies of drug repurposing and synergism of lopinavir, oseltamivir and ritonavir binding with SARS-CoV-2 protease against COVID-19. J. Biomol. Struct. Dyn. 2020:1-6.
- [Google Scholar]
- Topological and Thermodynamic Entropy Measures for COVID-19 Pandemic through Graph Theory. Symmetry. 2020;12(12):1992.
- [Google Scholar]
- Structures of the Middle East respiratory syndrome coronavirus 3C-like protease reveal insights into substrate specificity. Acta Crystallographica Section D: Biological Crystallography.. 2015;71(5):1102-1111.
- [Google Scholar]
- Why are lopinavir and ritonavir effective against the newly emerged Coronavirus 2019, Atomistic insights into the inhibitory mechanisms. Biochemistry. 2020;59(18):1769-1779.
- [Google Scholar]
- Peptide- like and small-molecule inhibitors against Covid-19. J. Biomol. Struct. Dyn. 2020:1-15.
- [Google Scholar]
- An overview of severe acute respiratory syndrome-coronavirus (SARS-CoV) 3CL protease inhibitors: peptidomimetics and small molecule chemotherapy. Journal of medicinal chemistry. 2016;59(14):6595-6628.
- [Google Scholar]
- Drug repurposing: Progress, challenges and recommendations. Nat. Rev. Drug Discovery. 2019;18(1):41-58.
- [Google Scholar]
- Topological study of hydroxychloroquine conjugated molecular structure used for novel coronavirus (COVID-19) treatment. Polycyclic Aromat. Compd. 2021:1-17.
- [Google Scholar]
- Quantitative structure-property relationship study of standard formation enthalpies of acyclic alkanes using atom-type-based AI topological indices. Arabian Journal of Chemistry. 2017;10(4):439-447.
- [Google Scholar]
- B. ŞAHIN1, AND S. EDIZ, On ev-Degree and ve-Degree Topological Indices, Iranian J. Math. Chem. 9 (4) December (2018) 263 - 277.
- Quantitative structure property relationship for Henry’s law constant of some alkane isomers. Thermochimica acta. 2011;512(1–2):273-277.
- [Google Scholar]
- The Reduced Neighborhood Topological Indices and RNM-Polynomial for the Treatment of COVID-19. Biointerface Research in Applied Chemistry 2021:11817-11832.
- [Google Scholar]
- Preclinical efficacy of the camptothecin-polymer conjugate IT-101 in multiple cancer models. Clin. Cancer Res.. 2006;12(5):1606-1614.
- [Google Scholar]
- On the maximum ABC index of graphs with prescribed size and without pendent vertices. IEEE Access. 2018;6:27604-27616.
- [Google Scholar]
- QSPR analysis of certain distance based topological indices. Applied Mathematics and Nonlinear Sciences. 2019;4(2):371-386.
- [Google Scholar]
- Camptothecin: current perspectives. Bioorganic and medicinal chemistry. 2004;12(7):1585-1604.
- [Google Scholar]
- ul Qamar, Muhammad Tahir, Safar M. Alqahtani, Mubarak A. Alamri, and Ling-Ling Chen. Structural basis of SARS-CoV-2 3CLpro and anti-COVID-19 drug discovery from medicinal plants. Journal of pharmaceutical analysis 10, no. 4 (2020): 313-319.
- J. Math. Chem.. 2009;46:1369-1376.
- Wei, Jianxin, Murat Cancan, Atiq Ur Rehman, Muhammad Kamran Siddiqui, Muhammad Nasir, Muhammad Tayyab Younas, and Muhammad Farhan Hanif. On Topological Indices of Remdesivir Compound Used in Treatment of Corona Virus (COVID 19). Polycyclic Aromatic Compounds (2021): 1–19.
- Structural determination of paraffin boiling points. Journal of the American chemical society. 1947;69(1):17-20.
- [Google Scholar]
- Evolution of the novel coronavirus from the ongoing Wuhan outbreak and modeling of its spike protein for risk of human transmission. Science China Life Sciences. 2020;63(3):457-460.
- [Google Scholar]